WorldWideScience

Sample records for accurate mass metabolomics

  1. Accurate mass error correction in liquid chromatography time-of-flight mass spectrometry based metabolomics

    NARCIS (Netherlands)

    Mihaleva, V.V.; Vorst, O.F.J.; Maliepaard, C.A.; Verhoeven, H.A.; Vos, de C.H.; Hall, R.D.; Ham, van R.C.H.J.

    2008-01-01

    Compound identification and annotation in (untargeted) metabolomics experiments based on accurate mass require the highest possible accuracy of the mass determination. Experimental LC/TOF-MS platforms equipped with a time-to-digital converter (TDC) give the best mass estimate for those mass signals

  2. Isotopic Ratio Outlier Analysis of the S. cerevisiae Metabolome Using Accurate Mass Gas Chromatography/Time-of-Flight Mass Spectrometry: A New Method for Discovery.

    Science.gov (United States)

    Qiu, Yunping; Moir, Robyn; Willis, Ian; Beecher, Chris; Tsai, Yu-Hsuan; Garrett, Timothy J; Yost, Richard A; Kurland, Irwin J

    2016-03-01

    Isotopic ratio outlier analysis (IROA) is a (13)C metabolomics profiling method that eliminates sample to sample variance, discriminates against noise and artifacts, and improves identification of compounds, previously done with accurate mass liquid chromatography/mass spectrometry (LC/MS). This is the first report using IROA technology in combination with accurate mass gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS), here used to examine the S. cerevisiae metabolome. S. cerevisiae was grown in YNB media, containing randomized 95% (13)C, or 5%(13)C glucose as the single carbon source, in order that the isotopomer pattern of all metabolites would mirror the labeled glucose. When these IROA experiments are combined, the abundance of the heavy isotopologues in the 5%(13)C extracts, or light isotopologues in the 95%(13)C extracts, follows the binomial distribution, showing mirrored peak pairs for the molecular ion. The mass difference between the (12)C monoisotopic and the (13)C monoisotopic equals the number of carbons in the molecules. The IROA-GC/MS protocol developed, using both chemical and electron ionization, extends the information acquired from the isotopic peak patterns for formulas generation. The process that can be formulated as an algorithm, in which the number of carbons, as well as the number of methoximations and silylations are used as search constraints. In electron impact (EI/IROA) spectra, the artifactual peaks are identified and easily removed, which has the potential to generate "clean" EI libraries. The combination of chemical ionization (CI) IROA and EI/IROA affords a metabolite identification procedure that enables the identification of coeluting metabolites, and allowed us to characterize 126 metabolites in the current study. PMID:26820234

  3. Accurate, fully-automated NMR spectral profiling for metabolomics.

    Directory of Open Access Journals (Sweden)

    Siamak Ravanbakhsh

    Full Text Available Many diseases cause significant changes to the concentrations of small molecules (a.k.a. metabolites that appear in a person's biofluids, which means such diseases can often be readily detected from a person's "metabolic profile"-i.e., the list of concentrations of those metabolites. This information can be extracted from a biofluids Nuclear Magnetic Resonance (NMR spectrum. However, due to its complexity, NMR spectral profiling has remained manual, resulting in slow, expensive and error-prone procedures that have hindered clinical and industrial adoption of metabolomics via NMR. This paper presents a system, BAYESIL, which can quickly, accurately, and autonomously produce a person's metabolic profile. Given a 1D 1H NMR spectrum of a complex biofluid (specifically serum or cerebrospinal fluid, BAYESIL can automatically determine the metabolic profile. This requires first performing several spectral processing steps, then matching the resulting spectrum against a reference compound library, which contains the "signatures" of each relevant metabolite. BAYESIL views spectral matching as an inference problem within a probabilistic graphical model that rapidly approximates the most probable metabolic profile. Our extensive studies on a diverse set of complex mixtures including real biological samples (serum and CSF, defined mixtures and realistic computer generated spectra; involving > 50 compounds, show that BAYESIL can autonomously find the concentration of NMR-detectable metabolites accurately (~ 90% correct identification and ~ 10% quantification error, in less than 5 minutes on a single CPU. These results demonstrate that BAYESIL is the first fully-automatic publicly-accessible system that provides quantitative NMR spectral profiling effectively-with an accuracy on these biofluids that meets or exceeds the performance of trained experts. We anticipate this tool will usher in high-throughput metabolomics and enable a wealth of new applications of

  4. Fusion of mass spectrometry-based metabolomics data

    NARCIS (Netherlands)

    Smilde, A.K.; Werf, M.J. van der; Bijlsma, S.; Werff-van der Vat, B.J.C. van der; Jellema, R.H.

    2005-01-01

    A general method is presented for combining mass spectrometry-based metabolomics data. Such data are becoming more and more abundant, and proper tools for fusing these types of data sets are needed. Fusion of metabolomics data leads to a comprehensive view on the metabolome of an organism or biologi

  5. Gas chromatography mass spectrometry : key technology in metabolomics

    NARCIS (Netherlands)

    Koek, Maud Marijtje

    2009-01-01

    Metabolomics involves the unbiased quantitative and qualitative analysis of the complete set of metabolites present in cells, body fluids and tissues. Gas chromatography coupled to mass spectrometry (GC-MS) is very suitable for metabolomics analysis, as it combines high separation power with sensiti

  6. Mass spectrometry as a quantitative tool in plant metabolomics.

    Science.gov (United States)

    Jorge, Tiago F; Mata, Ana T; António, Carla

    2016-10-28

    Metabolomics is a research field used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include the analysis of a wide range of chemical species with very diverse physico-chemical properties, and therefore powerful analytical tools are required for the separation, characterization and quantification of this vast compound diversity present in plant matrices. In this review, challenges in the use of mass spectrometry (MS) as a quantitative tool in plant metabolomics experiments are discussed, and important criteria for the development and validation of MS-based analytical methods provided.This article is part of the themed issue 'Quantitative mass spectrometry'. PMID:27644967

  7. Mass spectrometry for high-throughput metabolomics analysis of urine

    OpenAIRE

    Abdelrazig, Salah M.A.

    2015-01-01

    Direct electrospray ionisation-mass spectrometry (direct ESI-MS), by omitting the chromatographic step, has great potential for application as a high-throughput approach for untargeted urine metabolomics analysis compared to liquid chromatography-mass spectrometry (LC-MS). The rapid development and technical innovations revealed in the field of ambient ionisation MS such as nanoelectrospray ionisation (nanoESI) chip-based infusion and liquid extraction surface analysis mass spectrometry (LESA...

  8. Mass spectrometry-based metabolomics: applications to biomarker and metabolic pathway research.

    Science.gov (United States)

    Zhang, Aihua; Sun, Hui; Yan, Guangli; Wang, Ping; Wang, Xijun

    2016-01-01

    Mass spectrometry-based metabolomics has become increasingly popular in molecular medicine. High-definition mass spectrometry (MS), coupled with pattern recognition methods, have been carried out to obtain comprehensive metabolite profiling and metabolic pathway of large biological datasets. This sets the scene for a new and powerful diagnostic approach. Analysis of the key metabolites in body fluids has become an important part of improving disease diagnosis. With technological advances in analytical techniques, the ability to measure low-molecular-weight metabolites in bio-samples provides a powerful platform for identifying metabolites that are uniquely correlated with a specific human disease. MS-based metabolomics can lead to enhanced understanding of disease mechanisms and to new diagnostic markers and has a strong potential to contribute to improving early diagnosis of diseases. This review will highlight the importance and benefit with certain characteristic examples of MS-metabolomics for identifying metabolic pathways and metabolites that accurately screen for potential diagnostic biomarkers of diseases. PMID:25739660

  9. High precision mass measurements for wine metabolomics

    Science.gov (United States)

    Roullier-Gall, Chloé; Witting, Michael; Gougeon, Régis; Schmitt-Kopplin, Philippe

    2014-11-01

    An overview of the critical steps for the non-targeted Ultra-High Performance Liquid Chromatography coupled with Quadrupole Time-of-Flight Mass Spectrometry (UPLC-Q-ToF-MS) analysis of wine chemistry is given, ranging from the study design, data preprocessing and statistical analyses, to markers identification. UPLC-Q-ToF-MS data was enhanced by the alignment of exact mass data from FTICR-MS, and marker peaks were identified using UPLC-Q-ToF-MS². In combination with multivariate statistical tools and the annotation of peaks with metabolites from relevant databases, this analytical process provides a fine description of the chemical complexity of wines, as exemplified in the case of red (Pinot noir) and white (Chardonnay) wines from various geographic origins in Burgundy.

  10. Metabolomics

    DEFF Research Database (Denmark)

    Pedersen, Hans

    how to properly handle complex metabolomics data, in order to achieve reliable and valid multivariate models. This has been illustrated by three case studies with examples of forecasting breast cancer and early detection of colorectal cancer based on data from nuclear magnetic resonance (NMR...... in metabolomics studies has been presented in the three case studies. In the first case study, plasma samples from healthy individuals have been analysed by NMR. Some have developed breast cancer later in life and these have been separated from healthy individuals by means of a properly validated PLS-DA model...... based on NMR data with RRV and known risk markers. The sensitivity and specificity values are 0.80 and 0.79, respectively, for a test set validated model. The second case study is based on plasma samples with verified colorectal cancer and three types of control samples analysed by fluorescence...

  11. Metabolomic imaging of prostate cancer with magnetic resonance spectroscopy and mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Spur, Eva-Margarete [Massachusetts General Hospital, Harvard Medical School, Department of Pathology, Boston, MA (United States); Massachusetts General Hospital, Harvard Medical School, Department of Radiology, Boston, MA (United States); Charite Universitaetsmedizin, Berlin (Germany); Decelle, Emily A.; Cheng, Leo L. [Massachusetts General Hospital, Harvard Medical School, Department of Pathology, Boston, MA (United States); Massachusetts General Hospital, Harvard Medical School, Department of Radiology, Boston, MA (United States)

    2013-07-15

    Metabolomic imaging of prostate cancer (PCa) aims to improve in vivo imaging capability so that PCa tumors can be localized noninvasively to guide biopsy and evaluated for aggressiveness prior to prostatectomy, as well as to assess and monitor PCa growth in patients with asymptomatic PCa newly diagnosed by biopsy. Metabolomics studies global variations of metabolites with which malignancy conditions can be evaluated by profiling the entire measurable metabolome, instead of focusing only on certain metabolites or isolated metabolic pathways. At present, PCa metabolomics is mainly studied by magnetic resonance spectroscopy (MRS) and mass spectrometry (MS). With MRS imaging, the anatomic image, obtained from magnetic resonance imaging, is mapped with values of disease condition-specific metabolomic profiles calculated from MRS of each location. For example, imaging of removed whole prostates has demonstrated the ability of metabolomic profiles to differentiate cancerous foci from histologically benign regions. Additionally, MS metabolomic imaging of prostate biopsies has uncovered metabolomic expression patterns that could discriminate between PCa and benign tissue. Metabolomic imaging offers the potential to identify cancer lesions to guide prostate biopsy and evaluate PCa aggressiveness noninvasively in vivo, or ex vivo to increase the power of pathology analysis. Potentially, this imaging ability could be applied not only to PCa, but also to different tissues and organs to evaluate other human malignancies and metabolic diseases. (orig.)

  12. Vinegar Metabolomics: An Explorative Study of Commercial Balsamic Vinegars Using Gas Chromatography-Mass Spectrometry

    Science.gov (United States)

    Pinu, Farhana R.; de Carvalho-Silva, Samuel; Trovatti Uetanabaro, Ana Paula; Villas-Boas, Silas G.

    2016-01-01

    Balsamic vinegar is a popular food condiment produced from cooked grape must by two successive fermentation (anaerobic and aerobic) processes. Although many studies have been performed to determine the composition of major metabolites, including sugars and aroma compounds, no study has been undertaken yet to characterize the comprehensive metabolite composition of balsamic vinegars. Here, we present the first metabolomics study of commercial balsamic vinegars by gas chromatography coupled to mass spectrometry (GC-MS). The combination of three GC-MS methods allowed us to detect >1500 features in vinegar samples, of which 123 metabolites were accurately identified, including 25 amino acids, 26 carboxylic acids, 13 sugars and sugar alcohols, four fatty acids, one vitamin, one tripeptide and over 47 aroma compounds. Moreover, we identified for the first time in vinegar five volatile metabolites: acetin, 2-methylpyrazine, 2-acetyl-1-pyroline, 4-anisidine and 1,3-diacetoxypropane. Therefore, we demonstrated the capability of metabolomics for detecting and identifying large number of metabolites and some of them could be used to distinguish vinegar samples based on their origin and potentially quality. PMID:27455339

  13. Metabolome analysis - mass spectrometry and microbial primary metabolites

    DEFF Research Database (Denmark)

    Højer-Pedersen, Jesper Juul

    2008-01-01

    . Statistical analysis of the footprinting data revealed discriminating ions, which could be assigned using the in silico metabolome. By this approach metabolic footprinting can advance from a classification method that is used to derive biological information based on guilt-by-association, to a tool...... of metabolites by one method. The results highlighted that there were discrepancies between different methods. To increase the throughput of cultivation, S. cerevisiae was grown in microtitier plates (MTPs), and the growth was found to be comparable with cultivations in shake flasks. The carbon source was either...... for databases that contain metabolite specific information, which will speed up the identification of profiled metabolites. To address the capabilities of electrospray ionization (ESI)-MS in detecting the metabolome of S. cerevisiae, the in silico metabolome of this organism was used as a template to present...

  14. Unified and isomer-specific NMR metabolomics database for the accurate analysis of (13)C-(1)H HSQC spectra.

    Science.gov (United States)

    Bingol, Kerem; Li, Da-Wei; Bruschweiler-Li, Lei; Cabrera, Oscar A; Megraw, Timothy; Zhang, Fengli; Brüschweiler, Rafael

    2015-02-20

    A new metabolomics database and query algorithm for the analysis of (13)C-(1)H HSQC spectra is introduced, which unifies NMR spectroscopic information on 555 metabolites from both the Biological Magnetic Resonance Data Bank (BMRB) and Human Metabolome Database (HMDB). The new database, termed Complex Mixture Analysis by NMR (COLMAR) (13)C-(1)H HSQC database, can be queried via an interactive, easy to use web interface at http://spin.ccic.ohio-state.edu/index.php/hsqc/index . Our new HSQC database separately treats slowly exchanging isomers that belong to the same metabolite, which permits improved query in cases where lowly populated isomers are below the HSQC detection limit. The performance of our new database and query web server compares favorably with the one of existing web servers, especially for spectra of samples of high complexity, including metabolite mixtures from the model organisms Drosophila melanogaster and Escherichia coli. For such samples, our web server has on average a 37% higher accuracy (true positive rate) and a 82% lower false positive rate, which makes it a useful tool for the rapid and accurate identification of metabolites from (13)C-(1)H HSQC spectra at natural abundance. This information can be combined and validated with NMR data from 2D TOCSY-type spectra that provide connectivity information not present in HSQC spectra. PMID:25333826

  15. Unified and Isomer-Specific NMR Metabolomics Database for the Accurate Analysis of 13C–1H HSQC Spectra

    Science.gov (United States)

    2015-01-01

    A new metabolomics database and query algorithm for the analysis of 13C–1H HSQC spectra is introduced, which unifies NMR spectroscopic information on 555 metabolites from both the Biological Magnetic Resonance Data Bank (BMRB) and Human Metabolome Database (HMDB). The new database, termed Complex Mixture Analysis by NMR (COLMAR) 13C–1H HSQC database, can be queried via an interactive, easy to use web interface at http://spin.ccic.ohio-state.edu/index.php/hsqc/index. Our new HSQC database separately treats slowly exchanging isomers that belong to the same metabolite, which permits improved query in cases where lowly populated isomers are below the HSQC detection limit. The performance of our new database and query web server compares favorably with the one of existing web servers, especially for spectra of samples of high complexity, including metabolite mixtures from the model organisms Drosophila melanogaster and Escherichia coli. For such samples, our web server has on average a 37% higher accuracy (true positive rate) and a 82% lower false positive rate, which makes it a useful tool for the rapid and accurate identification of metabolites from 13C–1H HSQC spectra at natural abundance. This information can be combined and validated with NMR data from 2D TOCSY-type spectra that provide connectivity information not present in HSQC spectra. PMID:25333826

  16. Mass spectrometry-based plant metabolomics: Metabolite responses to abiotic stress.

    Science.gov (United States)

    Jorge, Tiago F; Rodrigues, João A; Caldana, Camila; Schmidt, Romy; van Dongen, Joost T; Thomas-Oates, Jane; António, Carla

    2016-09-01

    Metabolomics is one omics approach that can be used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include analysis of a wide range of chemical species with diverse physical properties, from ionic inorganic compounds to biochemically derived hydrophilic carbohydrates, organic and amino acids, and a range of hydrophobic lipid-related compounds. This complexitiy brings huge challenges to the analytical technologies employed in current plant metabolomics programs, and powerful analytical tools are required for the separation and characterization of this extremely high compound diversity present in biological sample matrices. The use of mass spectrometry (MS)-based analytical platforms to profile stress-responsive metabolites that allow some plants to adapt to adverse environmental conditions is fundamental in current plant biotechnology research programs for the understanding and development of stress-tolerant plants. In this review, we describe recent applications of metabolomics and emphasize its increasing application to study plant responses to environmental (stress-) factors, including drought, salt, low oxygen caused by waterlogging or flooding of the soil, temperature, light and oxidative stress (or a combination of them). Advances in understanding the global changes occurring in plant metabolism under specific abiotic stress conditions are fundamental to enhance plant fitness and increase stress tolerance. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:620-649, 2016. PMID:25589422

  17. High-Performance Chemical Isotope Labeling Liquid Chromatography-Mass Spectrometry for Profiling the Metabolomic Reprogramming Elicited by Ammonium Limitation in Yeast.

    Science.gov (United States)

    Luo, Xian; Zhao, Shuang; Huan, Tao; Sun, Difei; Friis, R Magnus N; Schultz, Michael C; Li, Liang

    2016-05-01

    Information about how yeast metabolism is rewired in response to internal and external cues can inform the development of metabolic engineering strategies for food, fuel, and chemical production in this organism. We report a new metabolomics workflow for the characterization of such metabolic rewiring. The workflow combines efficient cell lysis without using chemicals that may interfere with downstream sample analysis and differential chemical isotope labeling liquid chromatography mass spectrometry (CIL LC-MS) for in-depth yeast metabolome profiling. Using (12)C- and (13)C-dansylation (Dns) labeling to analyze the amine/phenol submetabolome, we detected and quantified a total of 5719 peak pairs or metabolites. Among them, 120 metabolites were positively identified using a library of 275 Dns-metabolite standards, and 2980 metabolites were putatively identified based on accurate mass matches to metabolome databases. We also applied (12)C- and (13)C-dimethylaminophenacyl (DmPA) labeling to profile the carboxylic acid submetabolome and detected over 2286 peak pairs, from which 33 metabolites were positively identified using a library of 188 DmPA-metabolite standards, and 1595 metabolites were putatively identified. Using this workflow for metabolomic profiling of cells challenged by ammonium limitation revealed unexpected links between ammonium assimilation and pantothenate accumulation that might be amenable to engineering for better acetyl-CoA production in yeast. We anticipate that efforts to improve other schemes of metabolic engineering will benefit from application of this workflow to multiple cell types. PMID:26947805

  18. Accurate mass measurements on neutron-deficient krypton isotopes

    CERN Document Server

    Rodríguez, D; Äystö, J; Beck, D

    2006-01-01

    The masses of $^{72–78,80,82,86}$Kr were measured directly with the ISOLTRAP Penning trap mass spectrometer at ISOLDE/CERN. For all these nuclides, the measurements yielded mass uncertainties below 10 keV. The ISOLTRAP mass values for $^{72–75}$Kr being more precise than the previous results obtained by means of other techniques, and thus completely determine the new values in the Atomic-Mass Evaluation. Besides the interest of these masses for nuclear astrophysics, nuclear structure studies, and Standard Model tests, these results constitute a valuable and accurate input to improve mass models. In this paper, we present the mass measurements and discuss the mass evaluation for these Kr isotopes.

  19. A dried blood spot mass spectrometry metabolomic approach for rapid breast cancer detection

    Directory of Open Access Journals (Sweden)

    Wang Q

    2016-03-01

    Full Text Available Qingjun Wang,1,2,* Tao Sun,3,* Yunfeng Cao,1,2,4,5 Peng Gao,2,4,6 Jun Dong,2,4 Yanhua Fang,2 Zhongze Fang,2 Xiaoyu Sun,2 Zhitu Zhu1,2 1Oncology Department 2, The First Affiliated Hospital of Liaoning Medical University, 2Personalized Treatment and Diagnosis Research Center, The First Affiliated Hospital of Liaoning Medical University and Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Jinzhou, 3Department of Internal Medicine 1, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Insititute, Shenyang, 4CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 5Key Laboratory of Contraceptives and Devices Research (NPFPC, Shanghai Engineer and Technology Research Center of Reproductive Health Drug and Devices, Shanghai Institute of Planned Parenthood Research, Shanghai, 6Clinical Laboratory, Dalian Sixth People’s Hospital, Dalian, People’s Republic of China *These authors contributed equally to this work Objective: Breast cancer (BC is still a lethal threat to women worldwide. An accurate screening and diagnosis strategy performed in an easy-to-operate manner is highly warranted in clinical perspective. Besides the routinely focused protein markers, blood is full of small molecular metabolites with diverse structures and properties. This study aimed to screen metabolite markers with BC diagnosis potentials.Methods: A dried blood spot-based direct infusion mass spectrometry (MS metabolomic analysis was conducted for BC and non-BC differentiation. The targeted analytes included 23 amino acids and 26 acylcarnitines.Results: Multivariate analysis screened out 21 BC-related metabolites in the blood. Regression analysis generated a diagnosis model consisting of parameters Pip, Asn, Pro, C14:1/C16, Phe/Tyr, and Gly/Ala. Tested with another set of BC and non-BC samples, this model showed a sensitivity of 92.2% and a specificity

  20. Global mass spectrometry based metabolomics profiling of erythrocytes infected with Plasmodium falciparum.

    Directory of Open Access Journals (Sweden)

    Theodore R Sana

    Full Text Available Malaria is a global infectious disease that threatens the lives of millions of people. Transcriptomics, proteomics and functional genomics studies, as well as sequencing of the Plasmodium falciparum and Homo sapiens genomes, have shed new light on this host-parasite relationship. Recent advances in accurate mass measurement mass spectrometry, sophisticated data analysis software, and availability of biological pathway databases, have converged to facilitate our global, untargeted biochemical profiling study of in vitro P. falciparum-infected (IRBC and uninfected (NRBC erythrocytes. In order to expand the number of detectable metabolites, several key analytical steps in our workflows were optimized. Untargeted and targeted data mining resulted in detection of over one thousand features or chemical entities. Untargeted features were annotated via matching to the METLIN metabolite database. For targeted data mining, we queried the data using a compound database derived from a metabolic reconstruction of the P. falciparum genome. In total, over one hundred and fifty differential annotated metabolites were observed. To corroborate the representation of known biochemical pathways from our data, an inferential pathway analysis strategy was used to map annotated metabolites onto the BioCyc pathway collection. This hypothesis-generating approach resulted in over-representation of many metabolites onto several IRBC pathways, most prominently glycolysis. In addition, components of the "branched" TCA cycle, partial urea cycle, and nucleotide, amino acid, chorismate, sphingolipid and fatty acid metabolism were found to be altered in IRBCs. Interestingly, we detected and confirmed elevated levels for cyclic ADP ribose and phosphoribosyl AMP in IRBCs, a novel observation. These metabolites may play a role in regulating the release of intracellular Ca(2+ during P. falciparum infection. Our results support a strategy of global metabolite profiling by untargeted

  1. Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity

    Directory of Open Access Journals (Sweden)

    Fumio eMatsuda

    2011-08-01

    Full Text Available A novel framework for automated elucidation of metabolite structures in liquid chromatography-mass spectrometer (LC-MS metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method.

  2. Advances in high-resolution mass spectrometry based on metabolomics studies for food--a review.

    Science.gov (United States)

    Rubert, Josep; Zachariasova, Milena; Hajslova, Jana

    2015-01-01

    Food authenticity becomes a necessity for global food policies, since food placed in the market without fail has to be authentic. It has always been a challenge, since in the past minor components, called also markers, have been mainly monitored by chromatographic methods in order to authenticate the food. Nevertheless, nowadays, advanced analytical methods have allowed food fingerprints to be achieved. At the same time they have been also combined with chemometrics, which uses statistical methods in order to verify food and to provide maximum information by analysing chemical data. These sophisticated methods based on different separation techniques or stand alone have been recently coupled to high-resolution mass spectrometry (HRMS) in order to verify the authenticity of food. The new generation of HRMS detectors have experienced significant advances in resolving power, sensitivity, robustness, extended dynamic range, easier mass calibration and tandem mass capabilities, making HRMS more attractive and useful to the food metabolomics community, therefore becoming a reliable tool for food authenticity. The purpose of this review is to summarise and describe the most recent metabolomics approaches in the area of food metabolomics, and to discuss the strengths and drawbacks of the HRMS analytical platforms combined with chemometrics. PMID:26365870

  3. Advances in high-resolution mass spectrometry based on metabolomics studies for food--a review.

    Science.gov (United States)

    Rubert, Josep; Zachariasova, Milena; Hajslova, Jana

    2015-01-01

    Food authenticity becomes a necessity for global food policies, since food placed in the market without fail has to be authentic. It has always been a challenge, since in the past minor components, called also markers, have been mainly monitored by chromatographic methods in order to authenticate the food. Nevertheless, nowadays, advanced analytical methods have allowed food fingerprints to be achieved. At the same time they have been also combined with chemometrics, which uses statistical methods in order to verify food and to provide maximum information by analysing chemical data. These sophisticated methods based on different separation techniques or stand alone have been recently coupled to high-resolution mass spectrometry (HRMS) in order to verify the authenticity of food. The new generation of HRMS detectors have experienced significant advances in resolving power, sensitivity, robustness, extended dynamic range, easier mass calibration and tandem mass capabilities, making HRMS more attractive and useful to the food metabolomics community, therefore becoming a reliable tool for food authenticity. The purpose of this review is to summarise and describe the most recent metabolomics approaches in the area of food metabolomics, and to discuss the strengths and drawbacks of the HRMS analytical platforms combined with chemometrics.

  4. Quantitative metabolomics based on gas chromatography mass spectrometry: Status and perspectives

    NARCIS (Netherlands)

    Koek, M.M.; Jellema, R.H.; Greef, J. van der; Tas, A.C.; Hankemeier, T.

    2011-01-01

    Metabolomics involves the unbiased quantitative and qualitative analysis of the complete set of metabolites present in cells, body fluids and tissues (the metabolome). By analyzing differences between metabolomes using biostatistics (multivariate data analysis; pattern recognition), metabolites rele

  5. Mass appeal : metabolite identification in mass spectrometry-focused untargeted metabolomics

    NARCIS (Netherlands)

    Dunn, Warwick B.; Erban, Alexander; Weber, Ralf J.M.; Creek, Darren J.; Brown, Marie; Breitling, Rainer; Hankemeier, Thomas; Goodacre, Royston; Neumann, Steffen; Kopka, Joachim; Viant, Mark R.

    2013-01-01

    Metabolomics has advanced significantly in the past 10 years with important developments related to hardware, software and methodologies and an increasing complexity of applications. In discovery-based investigations, applying untargeted analytical methods, thousands of metabolites can be detected w

  6. Shotgun metabolomic approach based on mass spectrometry for hepatic mitochondria of mice under arsenic exposure.

    Science.gov (United States)

    García-Sevillano, M A; García-Barrera, T; Navarro, F; Montero-Lobato, Z; Gómez-Ariza, J L

    2015-04-01

    Mass spectrometry (MS)-based toxicometabolomics requires analytical approaches for obtaining unbiased metabolic profiles. The present work explores the general application of direct infusion MS using a high mass resolution analyzer (a hybrid systems triple quadrupole-time-of-flight) and a complementary gas chromatography-MS analysis to mitochondria extracts from mouse hepatic cells, emphasizing on mitochondria isolation from hepatic cells with a commercial kit, sample treatment after cell lysis, comprehensive metabolomic analysis and pattern recognition from metabolic profiles. Finally, the metabolomic platform was successfully checked on a case-study based on the exposure experiment of mice Mus musculus to inorganic arsenic during 12 days. Endogenous metabolites alterations were recognized by partial least squares-discriminant analysis. Subsequently, metabolites were identified by combining MS/MS analysis and metabolomics databases. This work reports for the first time the effects of As-exposure on hepatic mitochondria metabolic pathways based on MS, and reveals disturbances in Krebs cycle, β-oxidation pathway, amino acids degradation and perturbations in creatine levels. This non-target analysis provides extensive metabolic information from mitochondrial organelle, which could be applied to toxicology, pharmacology and clinical studies.

  7. Applications of Structural Mass Spectrometry to Metabolomics: Clarifying Bond Specific Spectral Signatures with Isotope Edited Spectroscopy

    Science.gov (United States)

    Gorlova, Olga; Wolke, Conrad T.; Fournier, Joseph; Colvin, Sean; Johnson, Mark; Miller, Scott

    2015-06-01

    Comprehensive FTIR, MS/MS and NMR of pharmaceuticals are generally readily available but characterization of their metabolites has been an obstacle. Atorvastatin is a statin drug responsible for the maintenance of cholesterol in the body. Diovan is an angiostensin receptor antagonist used to treat high blood pressure and congestive heart failure. The field of metabolomics, however, is struggling to obtain the identity of their structures. We implement mass spectrometry with cryogenic ion spectroscopy to study gaseous ions of the desired metabolites which, in combination, not only identify the mass of the metabolite but also elucidate their structures through isotope-specific infrared spectroscopy.

  8. Metabolomics, peptidomics and proteomics applications of capillary electrophoresis-mass spectrometry in Foodomics: A review

    Energy Technology Data Exchange (ETDEWEB)

    Ibáñez, Clara; Simó, Carolina; García-Cañas, Virginia; Cifuentes, Alejandro, E-mail: a.cifuentes@csic.es; Castro-Puyana, María

    2013-11-13

    Graphical abstract: -- Highlights: •Foodomics allows studying food and nutrition through the application of advanced omics approaches. •CE-MS plays a crucial role as analytical platform to carry out omics studies. •CE-MS applications for food metabolomics, proteomics and peptidomics are presented. -- Abstract: In the current post-genomic era, Foodomics has been defined as a discipline that studies food and nutrition through the application of advanced omics approaches. Foodomics involves the use of genomics, transcriptomics, epigenetics, proteomics, peptidomics, and/or metabolomics to investigate food quality, safety, traceability and bioactivity. In this context, capillary electrophoresis-mass spectrometry (CE-MS) has been applied mainly in food proteomics, peptidomics and metabolomics. The aim of this review work is to present an overview of the most recent developments and applications of CE-MS as analytical platform for Foodomics, covering the relevant works published from 2008 to 2012. The review provides also information about the integration of several omics approaches in the new Foodomics field.

  9. Metabolomics, peptidomics and proteomics applications of capillary electrophoresis-mass spectrometry in Foodomics: A review

    International Nuclear Information System (INIS)

    Graphical abstract: -- Highlights: •Foodomics allows studying food and nutrition through the application of advanced omics approaches. •CE-MS plays a crucial role as analytical platform to carry out omics studies. •CE-MS applications for food metabolomics, proteomics and peptidomics are presented. -- Abstract: In the current post-genomic era, Foodomics has been defined as a discipline that studies food and nutrition through the application of advanced omics approaches. Foodomics involves the use of genomics, transcriptomics, epigenetics, proteomics, peptidomics, and/or metabolomics to investigate food quality, safety, traceability and bioactivity. In this context, capillary electrophoresis-mass spectrometry (CE-MS) has been applied mainly in food proteomics, peptidomics and metabolomics. The aim of this review work is to present an overview of the most recent developments and applications of CE-MS as analytical platform for Foodomics, covering the relevant works published from 2008 to 2012. The review provides also information about the integration of several omics approaches in the new Foodomics field

  10. Data-Independent Microbial Metabolomics with Ambient Ionization Mass Spectrometry

    Science.gov (United States)

    Rath, Christopher M.; Yang, Jane Y.; Alexandrov, Theodore; Dorrestein, Pieter C.

    2013-08-01

    Atmospheric ionization methods are ideally suited for prolonged MS/MS analysis. Data-independent MS/MS is a complementary technique for analysis of biological samples as compared to data-dependent analysis. Here, we pair data-independent MS/MS with the ambient ionization method nanospray desorption electrospray ionization (nanoDESI) for untargeted analysis of bacterial metabolites. Proof-of-principle data and analysis are illustrated by sampling Bacillus subtilis and Pseudomonas aeruginosa directly from Petri dishes. We found that this technique enables facile comparisons between strains via MS and MS/MS plots which can be translated to chemically informative molecular maps through MS/MS networking. The development of novel techniques to characterize microbial metabolites allows rapid and efficient analysis of metabolic exchange factors. This is motivated by our desire to develop novel techniques to explore the role of interspecies interactions in the environment, health, and disease. This is a contribution to honor Professor Catherine C. Fenselau in receiving the prestigious ASMS Award for a Distinguished Contribution in Mass Spectrometry for her pioneering work on microbial mass spectrometry.

  11. Targeted Metabolomic Analysis of Head and Neck Cancer Cells Using High Performance Ion Chromatography Coupled with a Q Exactive HF Mass Spectrometer.

    Science.gov (United States)

    Hu, Shen; Wang, Junhua; Ji, Eoon Hye; Christison, Terri; Lopez, Linda; Huang, Yingying

    2015-06-16

    In this study, we have demonstrated a targeted metabolomics method for analysis of cancer cells, based on high-performance ion chromatography (IC) separation, Q Exactive HF MS for high-resolution and accurate-mass (HR/AM) measurement and the use of stable isotope-labeled internal standards for absolute quantitation. Our method offers great technical advantages for metabolite analysis, including exquisite sensitivity, high speed and reproducibility, and wide dynamic range. The high-performance IC provided fast separation of cellular metabolites within 20 min and excellent resolving power for polar molecules including many isobaric metabolites. The IC/Q Exactive HF MS achieved wide dynamic ranges of 5 orders of magnitude for six targeted metabolites, pyruvate, succinic acid, malic acid, citric acid, fumaric acid, and alpha-ketoglutaric acid, with R(2) ≈ 0.99. Using this platform, metabolites can be simultaneously quantified from low fmol/μL to nmol/μL levels in cellular samples. The high flow rate IC at 380 μL/min has shown excellent reproducibility for a large set of samples (150 injections), with minimal variations of retention time (SD < ± 0.03 min). In addition, the IC-MS-based approach acquires targeted and global metabolomic data in a same analytical run, and the use of stable isotope-labeled standards facilitates accurate quantitation of targeted metabolites in large-scale metabolomics analysis. This metabolomics approach has been successfully applied to analysis of targeted metabolites in head and neck cancer cells as well as cancer stem-like cells (CSCs), and the findings indicate that the metabolic phenotypes may be distinct between high and low invasive head and neck cancer cells and between CSCs and non-SCCs.

  12. Accurate mass measurements of very short-lived nuclei

    CERN Document Server

    Herfurth, F; Ames, F; Audi, G; Beck, D; Blaum, K; Bollen, G; Engels, O; Kluge, H J; Lunney, M D; Moores, R B; Oinonen, M; Sauvan, E; Bolle, C A; Scheidenberger, C; Schwarz, S; Sikler, G; Weber, C

    2002-01-01

    Mass measurements of /sup 34/Ar, /sup 73-78/Kr, and /sup 74,76/Rb were performed with the Penning-trap mass spectrometer ISOLTRAP. Very accurate Q/sub EC/-values are needed for the investigations of the F /sub t/-value of 0/sup +/ to 0/sup +/ nuclear beta -decays used to test the standard model predictions for weak interactions. The necessary accuracy on the Q/sub EC/-value requires the mass of mother and daughter nuclei to be measured with delta m/mmass has been measured with a relative accuracy of 1.1.10/sup -8/. The Q/sub EC/-value of the /sup 34/Ar 0 /sup +/ to 0/sup +/ decay can now he determined with an uncertainty of about 0.01%. Furthermore, /sup 74/Rb is the shortest-lived nuclide ever investigated in a Penning trap. (18 refs).

  13. Real-Time Digitization of Metabolomics Patterns from a Living System Using Mass Spectrometry

    Science.gov (United States)

    Heinemann, Joshua; Noon, Brigit; Mohigmi, Mohammad J.; Mazurie, Aurélien; Dickensheets, David L.; Bothner, Brian

    2014-10-01

    The real-time quantification of changes in intracellular metabolic activities has the potential to vastly improve upon traditional transcriptomics and metabolomics assays for the prediction of current and future cellular phenotypes. This is in part because intracellular processes reveal themselves as specific temporal patterns of variation in metabolite abundance that can be detected with existing signal processing algorithms. Although metabolite abundance levels can be quantified by mass spectrometry (MS), large-scale real-time monitoring of metabolite abundance has yet to be realized because of technological limitations for fast extraction of metabolites from cells and biological fluids. To address this issue, we have designed a microfluidic-based inline small molecule extraction system, which allows for continuous metabolomic analysis of living systems using MS. The system requires minimal supervision, and has been successful at real-time monitoring of bacteria and blood. Feature-based pattern analysis of Escherichia coli growth and stress revealed cyclic patterns and forecastable metabolic trajectories. Using these trajectories, future phenotypes could be inferred as they exhibit predictable transitions in both growth and stress related changes. Herein, we describe an interface for tracking metabolic changes directly from blood or cell suspension in real-time.

  14. Mass Spectrometry-Based Metabolomic and Proteomic Strategies in Organic Acidemias

    Science.gov (United States)

    Imperlini, Esther; Santorelli, Lucia; Orrù, Stefania; Scolamiero, Emanuela; Ruoppolo, Margherita

    2016-01-01

    Organic acidemias (OAs) are inherited metabolic disorders caused by deficiency of enzymatic activities in the catabolism of amino acids, carbohydrates, or lipids. These disorders result in the accumulation of mono-, di-, or tricarboxylic acids, generally referred to as organic acids. The OA outcomes can involve different organs and/or systems. Some OA disorders are easily managed if promptly diagnosed and treated, whereas, in others cases, such as propionate metabolism-related OAs (propionic acidemia, PA; methylmalonic acidemia, MMA), neither diet, vitamin therapy, nor liver transplantation appears to prevent multiorgan impairment. Here, we review the recent developments in dissecting molecular bases of OAs by using integration of mass spectrometry- (MS-) based metabolomic and proteomic strategies. MS-based techniques have facilitated the rapid and economical evaluation of a broad spectrum of metabolites in various body fluids, also collected in small samples, like dried blood spots. This approach has enabled the timely diagnosis of OAs, thereby facilitating early therapeutic intervention. Besides providing an overview of MS-based approaches most frequently used to study the molecular mechanisms underlying OA pathophysiology, we discuss the principal challenges of metabolomic and proteomic applications to OAs.

  15. Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics

    Science.gov (United States)

    Ghaste, Manoj; Mistrik, Robert; Shulaev, Vladimir

    2016-01-01

    Metabolomics, along with other “omics” approaches, is rapidly becoming one of the major approaches aimed at understanding the organization and dynamics of metabolic networks. Mass spectrometry is often a technique of choice for metabolomics studies due to its high sensitivity, reproducibility and wide dynamic range. High resolution mass spectrometry (HRMS) is a widely practiced technique in analytical and bioanalytical sciences. It offers exceptionally high resolution and the highest degree of structural confirmation. Many metabolomics studies have been conducted using HRMS over the past decade. In this review, we will explore the latest developments in Fourier transform mass spectrometry (FTMS) and Orbitrap based metabolomics technology, its advantages and drawbacks for using in metabolomics and lipidomics studies, and development of novel approaches for processing HRMS data. PMID:27231903

  16. Urinary exposure marker discovery for toxicants using ultra-high pressure liquid chromatography coupled with Orbitrap high resolution mass spectrometry and three untargeted metabolomics approaches.

    Science.gov (United States)

    Hsu, Jen-Yi; Hsu, Jing-Fang; Chen, Yet-Ran; Shih, Chia-Lang; Hsu, Yi-Sheng; Chen, Yi-Jen; Tsai, Shu-Han; Liao, Pao-Chi

    2016-10-01

    Human biomonitoring is the assessment of actual internal contamination of chemicals by measuring exposure markers, chemicals or their metabolites, in human urine, blood, serum, and other body fluids. However, the metabolism of chemicals within an organism is extremely complex. Therefore, the identification of metabolites is often difficult and laborious. Several untargeted metabolomics methods have been developed to perform objective searching/filtering of accurate-mass-based LC-MS data to facilitate metabolite identification. In this study, three metabolomics data processing approaches were used for chemical exposure marker discovery in urine with an LTQ-Orbitrap high-resolution mass spectrometry (HRMS) dataset; di-isononyl phthalate (DINP) was used as an example. The data processing techniques included the SMAIT, mass defect filtering (MDF), and XCMS Online. Sixteen, 83, and 139 probable DINP metabolite signals were obtained using the SMAIT, MDF, and XCMS procedures, respectively. Fourteen probable metabolite signals mined simultaneously by the three metabolomics approaches were confirmed as DINP metabolites by structural information provided by LC-MS/MS. Among them, 13 probable metabolite signals were validated as exposure-related markers in a rat model. Six (m/z 319.155, 361.127, 373.126, 389.157, 437.112 and 443.130) of the 13 exposure-related DINP metabolite signals have not previously been reported in the literature. Our data indicate that SMAIT provided an efficient method to discover effectively and systematically urinary exposure markers of toxicant. The DINP metabolism information can provide valuable information for further investigations of DINP toxicity, toxicokinetics, exposure assessment, and human health effects. PMID:27639145

  17. Applications of liquid chromatography coupled to mass spectrometry-based metabolomics in clinical chemistry and toxicology: A review.

    OpenAIRE

    Roux, Aurélie; Lison, Dominique; Junot, Christophe; Heillier, Jean-François

    2011-01-01

    International audience The metabolome is the set of small molecular mass organic compounds found in a given biological media. It includes all organic substances naturally occurring from the metabolism of the studied living organism, except biological polymers, but also xenobiotics and their biotransformation products. The metabolic fingerprints of biofluids obtained by mass spectrometry (MS) or nuclear magnetic resonance (NMR)-based methods contain a few hundreds to thousands of signals re...

  18. Direct infussion Electrospray Mass Spectrometry as a new non-invasive tool for serum metabolomics in induced-stress subjects

    Directory of Open Access Journals (Sweden)

    Mónica Lorenzo-Tejedor

    2015-12-01

    Full Text Available Background and Objectives: Nanotechnology is becoming a tool for the study of changes in the metabolome of patients in different states of disease. Analytical techniques such as Electrospray Mass Spectrometry, allow to find biomarkers by determination of metabolites. Nowadays, there is not an objective analytical approach for diagnosis of stress. Thus, the objectives of this pilot work are: Describing the development of a fast, direct and non-invasive analytical protocol, applied for the first time, to study the metabolomic profile of patient´s different states through a disease. Testing the protocol in a pilot sample with non-stressed and stress-induced subjects. Methods: High resolution direct infusion electrospray mass spectrometry has been used to analyse the metabolome of blood samples (0.3 ml from six subjects. Results: Data prove a clear discrimination between non-stressed and stressed states in the metabolome. Data showed different predominant metabolites in both states. Results allow objective characterization of the state of the patient. Conclusions: Although this is a pilot study, the method was successful in discriminating different metabolites in non-stressed and stress-induced subjects.

  19. Metabolic Profiling of Human Benign and Malignant Pulmonary Nodules Using Mass Spectrometry-Based Metabolomics

    Directory of Open Access Journals (Sweden)

    Choon Nam Ong

    2013-07-01

    Full Text Available Solitary pulmonary nodule (SPN or coin lesion is a mass in the lung and can be commonly found in chest X-rays or computerized tomography (CT scans. However, despite the advancement of imaging technologies, it is still difficult to distinguish malignant cancer from benign SPNs. Here we investigated the metabolic profiling of patients with benign and malignant pulmonary nodules. A combination of gas chromatography/mass spectrometry (GC/MS and liquid chromatography/mass spectrometry (LC/MS was used to profile the plasma metabolites in 17 patients with malignant SPNs, 15 patients with benign SPNs and 20 healthy controls. The metabolic profiles were assayed using OPLS-DA, and further analyzed to identify marker metabolites related to diseases. Both GC/MS- and LC/MS-derived models showed clear discriminations in metabolic profiles among three groups. It was found that 63 metabolites (12 from GC/MS, 51 from LC/MS contributed to the differences. Of these, 48 metabolites showed same change trend in both malignant and benign SPNs as compared with healthy controls, indicating some common pathways including inflammation and oxidative injury shared by two diseases. In contrast, 14 metabolites constituted distinct profiles that differentiated malignant from benign SPNs, which might be a unique biochemical feature associated with lung cancer. Overall, our data suggested that integration of two highly sensitive and complementary metabolomics platforms could enable a comprehensive metabolic profiling and assist in discrimination malignant from benign SPNs.

  20. Evaluation of dried blood spots as sample matrix for gas chromatography/mass spectrometry based metabolomic profiling.

    Science.gov (United States)

    Kong, Sing Teang; Lin, Hai-Shu; Ching, Jianhong; Ho, Paul C

    2011-06-01

    We propose using dried blood spots (DBS) as sample matrix for gas chromatography/mass spectrometry (GC/MS) based metabolomic profiling for the benefits of higher sample stability, more convenient sample acquisition with DBS, higher analyte separation power, and more readily biomarker identification with GC/MS. To establish this proposition, the metabolomic profiles generated from DBS were compared with that obtained from the conventional whole blood and plasma matrixes and also with dried plasma spots (DPS) as another covariate control. Our findings indicated that whole blood produced the most number of detectable markers (866), whereas DPS yielded the least number (614). DBS and plasma matrix, on the other hand, produced the most similar numbers of detectable (695 vs 749) and identifiable markers (137 vs 147, matching with Fiehn library). From the analysis of the DBS and plasma metabolomic profiles, it was concluded that when l-lysine 2, iminodiacetic acid 2, dl-threo-beta-hydroxyaspartic acid, citric acid, or adenosine-5-monophosphate 2 are not involved as markers, DBS could be a suitable substitute for plasma for metabolomic profiling.

  1. A Rough Guide to Metabolite Identification Using High Resolution Liquid Chromatography Mass Spectrometry in Metabolomic Profiling in Metazoans

    Directory of Open Access Journals (Sweden)

    David G Watson

    2013-01-01

    Full Text Available Compound identification in mass spectrometry based metabolomics can be a problem but sometimes the problem seems to be presented in an over complicated way. The current review focuses on metazoans where the range of metabolites is more restricted than for example in plants. The focus is on liquid chromatography with high resolution mass spectrometry where it is proposed that most of the problems in compound identification relate to structural isomers rather than to isobaric compounds. Thus many of the problems faced relate to separation of isomers, which is usually required even if fragmentation is used to support structural identification. Many papers report the use of MS/MS or MS2 as an adjunct to the identification of known metabolites but there a few examples in metabolomics studies of metazoans of complete structure elucidation of novel metabolites or metabolites where no authentic standards are available for comparison.

  2. Targeted metabolomics in cultured cells and tissues by mass spectrometry: method development and validation.

    Science.gov (United States)

    Abdel Rahman, Anas M; Pawling, Judy; Ryczko, Michael; Caudy, Amy A; Dennis, James W

    2014-10-01

    Metabolomics is the identification and quantitation of small bio-molecules (metabolites) in biological samples under various environmental and genetic conditions. Mass spectrometry provides the unique opportunity for targeted identification and quantification of known metabolites by selective reaction monitoring (SRM). However, reproducibility of this approach depends on careful consideration of sample preparation, chemical classes, and stability of metabolites to be evaluated. Herein, we introduce and validate a targeted metabolite profiling workflow for cultured cells and tissues by liquid chromatography-triple quadrupole tandem mass spectrometry. The method requires a one-step extraction of water-soluble metabolites and targeted analysis of central metabolites that include glycolysis, amino acids, nucleotides, citric acid cycle, and the hexosamine biosynthetic pathway. The sensitivity, reproducibility and molecular stability of each targeted metabolite were assessed under experimental conditions. Quantitation of metabolites by peak area ratio was linear with a dilution over a 4 fold dynamic range with minimal deviation R(2)=0.98. Inter- and intra-day precision with cells and tissues had an average coefficient of variation <15% for cultured cell lines, and somewhat higher for mouse liver tissues. The method applied in triplicate measurements readily distinguished immortalized cells from malignant cells, as well as mouse littermates based on their hepatic metabolic profiles.

  3. Maximum Mass of Strange Stars and Pulsars with the Most Accurately Measured Masses

    Science.gov (United States)

    Vartanyan, Yu. L.; Grigoryan, A. K.; Shahinyan, H. A.

    2015-06-01

    Strange quark matter (SQM) is studied using a bag model in which the transition to the SQM state takes place at energy densities of no more than twice the density in atomic nuclei. Thus, low mass neutron stars with a configuration consisting of SQM form a single family on a plot of the mass M of equilibrium superdense configurations as a function of central energy density ρ c (the M(ρ c ) curve). The bag model considered here depends on three constants: the vacuum pressure B, the quark-gluon interaction constant α c , and the strange quark mass m s . Sets of values of these constants are determined, which if used in the equation of state for SQM yield a maximal mass M max of the equilibrium quark configurations which exceeds the recently accurately determined mass of 2.01 M ⊙ for the binary radio pulsar PSR J0348+0432. The mass, radius, total baryon number, and red shift from the surface of the strange star are calculated for these configurations as a function of central energy density ρ c . The values of these integrated parameters are also calculated for each series with M max > 2.01 M ⊙ for superdense configurations with masses of 2.01, 1.97, and 1.44 solar masses, which have been determined with great accuracy from observations. It turns out that, according to the resulting equations of state, all of the three pulsars with the most accurately measured masses, may be possible candidate strange stars.

  4. Potential of monitoring isotopologues by quantitative gas chromatography with time-of-flight mass spectrometry for metabolomic assay.

    Science.gov (United States)

    Wang, Yi; Hu, Haiyan; Su, Yue; Zhang, Fang; Guo, Yinlong

    2016-03-01

    Because of the extreme complexity of metabolomic samples, the effectiveness of quantitative gas chromatography with time-of-flight mass spectrometry depends substantially on the expansion of the linear dynamic range. Facing the existence of numerous saturated detector signals, a data processing method based on monitoring isotopologues has been developed. The monoisotopic ion kept the high mass spectrometry sensitivity, and the less abundant isotopologue ions extended the linear dynamic range. This alternative method was proved to extend the linear dynamic range to five orders of magnitude successfully and overcome the quantitative problems induced by the ion detector saturation. Finally, to validate the applicability, the method was applied to a metabolomic assay of Alzheimer's disease. Comparing with the traditional monoisotopic method, the use of monitoring isotopologues helped us to discover an additional eight metabolites with significant difference and to conduct a more reliable principal component analysis as well. The results demonstrated that monitoring isotopologues in quantitative gas chromatography with time-of-flight mass spectrometry could improve the authenticity of metabolomic analysis. PMID:26763370

  5. Accurate Mass Determinations in Decay Chains with Missing Energy

    OpenAIRE

    Cheng, Hsin-Chia; Engelhardt, Dalit; Gunion, John F.; Han, Zhenyu; McElrath, Bob

    2008-01-01

    Many beyond the Standard Model theories include a stable dark matter candidate that yields missing / invisible energy in collider detectors. If observed at the Large Hadron Collider, we must determine if its mass and other properties (and those of its partners) predict the correct dark matter relic density. We give a new procedure for determining its mass with small error.

  6. Accurate, Empirical Radii and Masses of Planets with Gaia Parallaxes

    CERN Document Server

    Stassun, Keivan G; Gaudi, B Scott

    2016-01-01

    We present new, empirical measurements of the radii of 132 stars that host transiting planets. These stellar radii are determined using only direct observables---the bolometric flux at Earth, the stellar effective temperature, and the parallax newly provided by the Gaia first data release---and thus are virtually model independent, extinction being the only free parameter. We also determine each star's mass using our newly determined radius and the stellar density, itself a virtually model independent quantity from the previously published transit analysis. The newly determined stellar radii and masses are in turn used to re-determine the transiting planet radii and masses, once again using only direct observables. The uncertainties on the stellar radii and masses are typically 7% and 25%, respectively, and the resulting uncertainties on the planet radii and masses are 8% and 20%, respectively. These accuracies are generally larger than the previously published model-dependent precisions of 5% and 6% on the p...

  7. How accurate is ultrasound in evaluating palpable breast masses?

    Directory of Open Access Journals (Sweden)

    Mubuuke Aloysius Gonzaga

    2010-10-01

    Full Text Available INTRODUCTION: Breast masses have become common in women. Such masses pose a potential threat to women especially in the era of increased cases of breast cancer worldwide. Breast carcinoma ranks first among the malignant tumors affecting females in many parts of the world with the rate of breast cancer being 1 in 8 in USA. There are currently more than 600 000 cancer deaths annually in Africa. By 2020, 70% of the 15 million new annual cancer cases will be in developing countries. Ultrasound is a relatively inexpensive and readily accessible imaging modality that can be utilized in the evaluation of clinically palpable breast masses. The purpose of this study was to find out the accuracy of ultrasound in the diagnosis of palpable breast masses. METHODS: Eighty palpable breast masses were evaluated at ultrasound and information about the characteristic features of the masses was recorded. An impression about the diagnosis was made and results were correlated with histology findings. RESULTS: The overall sensitivity of ultrasound in detecting breast lumps was 92.5%. The sensitivity and specificity of ultrasound for detecting breast carcinoma was 57.1% and 62.8% respectively with a positive predictive value of 68.1%, a negative predictive value of 99.5%, a positive likelihood ratio of 39 and a negative likelihood ratio of 0.07. Ultrasound reliably differentiated cystic from solid breast masses. CONCLUSION: Ultrasound is significant in differentiating cystic from solid breast masses. Ultrasound is also important in detecting suspicious breast masses and should therefore be used in the evaluation of symptomatic breast masses

  8. Mass Spectrometry-Based Quantitative Metabolomics Revealed a Distinct Lipid Profile in Breast Cancer Patients

    Directory of Open Access Journals (Sweden)

    Yun Yen

    2013-04-01

    Full Text Available Breast cancer accounts for the largest number of newly diagnosed cases in female cancer patients. Although mammography is a powerful screening tool, about 20% of breast cancer cases cannot be detected by this method. New diagnostic biomarkers for breast cancer are necessary. Here, we used a mass spectrometry-based quantitative metabolomics method to analyze plasma samples from 55 breast cancer patients and 25 healthy controls. A number of 30 patients and 20 age-matched healthy controls were used as a training dataset to establish a diagnostic model and to identify potential biomarkers. The remaining samples were used as a validation dataset to evaluate the predictive accuracy for the established model. Distinct separation was obtained from an orthogonal partial least squares-discriminant analysis (OPLS-DA model with good prediction accuracy. Based on this analysis, 39 differentiating metabolites were identified, including significantly lower levels of lysophosphatidylcholines and higher levels of sphingomyelins in the plasma samples obtained from breast cancer patients compared with healthy controls. Using logical regression, a diagnostic equation based on three metabolites (lysoPC a C16:0, PC ae C42:5 and PC aa C34:2 successfully differentiated breast cancer patients from healthy controls, with a sensitivity of 98.1% and a specificity of 96.0%.

  9. Data preprocessing method for liquid chromatography-mass spectrometry based metabolomics.

    Science.gov (United States)

    Wei, Xiaoli; Shi, Xue; Kim, Seongho; Zhang, Li; Patrick, Jeffrey S; Binkley, Joe; McClain, Craig; Zhang, Xiang

    2012-09-18

    A set of data preprocessing algorithms for peak detection and peak list alignment are reported for analysis of liquid chromatography-mass spectrometry (LC-MS)-based metabolomics data. For spectrum deconvolution, peak picking is achieved at the selected ion chromatogram (XIC) level. To estimate and remove the noise in XICs, each XIC is first segmented into several peak groups based on the continuity of scan number, and the noise level is estimated by all the XIC signals, except the regions potentially with presence of metabolite ion peaks. After removing noise, the peaks of molecular ions are detected using both the first and the second derivatives, followed by an efficient exponentially modified Gaussian-based peak deconvolution method for peak fitting. A two-stage alignment algorithm is also developed, where the retention times of all peaks are first transferred into the z-score domain and the peaks are aligned based on the measure of their mixture scores after retention time correction using a partial linear regression. Analysis of a set of spike-in LC-MS data from three groups of samples containing 16 metabolite standards mixed with metabolite extract from mouse livers demonstrates that the developed data preprocessing method performs better than two of the existing popular data analysis packages, MZmine2.6 and XCMS(2), for peak picking, peak list alignment, and quantification.

  10. Mass spectrometric QUAL/QUAN approaches for drug metabolism and metabolomics.

    Science.gov (United States)

    Tonoli, David; Varesio, Emmanuel; Hopfgartner, Gérard

    2012-01-01

    A liquid chromatography-high-resolution mass spectrometry platform was used for simultaneous qualitative and quantitative (QUAL/QUAN) acquisition, enabling drug metabolism and metabolomics investi- gations. Plasma study samples were monitored for three different groups of patients at a single time-point (1 h after drug administration): one group received acetaminophen (APAP), one group received both APAP and ketorolac and one group was a control group. The quantification of APAP and two of its metabolites (APAP-glucuronide and APAP-cysteine) was performed on a fast acquisition quadrupole-Time-Of-Flight (50-100 ms duty cycle, resolving power of 30,000) compatible with UHPLC time constraints. High-resolution Selected Reaction Monitoring was used for quantification of APAP and its metabolites from 50-10,000 ng/mL using a 50 μL plasma aliquot. Average measured concentrations were for APAP 6,650 ng/mL vs 6,160 ng/mL, APAP-CYS concentrations were 154.2 ng/mL vs 140.6 ng/mL and APAP-GLU concentrations 8,750 ng/mL vs 8,430 ng/mL between the group that received only APAP (n = 11) and the group that received APAP in combination with ketorolac (n = 11). No major differences were observed between the two groups of patients, as it would be expected due to the differing metabolism pathway for both substances. For the qualitative aspect, a metabolomics data processing platform with biological QC samples was applied to the study samples to search for unanticipated metabolites and biomarkers related to APAP and ketorolac metabolism. Multivariate analysis (i.e. Principle Component Analysis), variables grouping tools (i.e. PCVG) and high-resolution MS(/MS) spectra from the MS(ALL) acquisition strategy enabled the profiling and characterization of circulating metabolites of APAP in plasma such as APAP-sulfate, APAP-mercapturate as well as ketorolac. PMID:22613154

  11. Analytical methods in untargeted metabolomics: state of the art in 2015

    Directory of Open Access Journals (Sweden)

    Arnald eAlonso

    2015-03-01

    Full Text Available Metabolomics comprises the methods and techniques that are used to measure the small molecule composition of biofluids and tissues, and is actually one of the most rapidly evolving research fields. The determination of the metabolomic profile –the metabolome- has multiple applications in many biological sciences, including the developing of new diagnostic tools in medicine. Recent technological advances in nuclear magnetic resonance (NMR and mass spectrometry (MS are significantly improving our capacity to obtain more data from each biological sample. Consequently, there is a need for fast and accurate statistical and bioinformatic tools that can deal with the complexity and volume of the data generated in metabolomic studies. In this review we provide an update of the most commonly used analytical methods in metabolomics, starting from raw data processing and ending with pathway analysis and biomarker identification. Finally, the integration of metabolomic profiles with molecular data from other high throughput biotechnologies is also reviewed.

  12. Metabolomic Profiles of Body Mass Index in the Framingham Heart Study Reveal Distinct Cardiometabolic Phenotypes.

    Directory of Open Access Journals (Sweden)

    Jennifer E Ho

    Full Text Available Although obesity and cardiometabolic traits commonly overlap, underlying pathways remain incompletely defined. The association of metabolite profiles across multiple cardiometabolic traits may lend insights into the interaction of obesity and metabolic health. We sought to investigate metabolic signatures of obesity and related cardiometabolic traits in the community using broad-based metabolomic profiling.We evaluated the association of 217 assayed metabolites and cross-sectional as well as longitudinal changes in cardiometabolic traits among 2,383 Framingham Offspring cohort participants. Body mass index (BMI was associated with 69 of 217 metabolites (P<0.00023 for all, including aromatic (tyrosine, phenylalanine and branched chain amino acids (valine, isoleucine, leucine. Additional metabolic pathways associated with BMI included the citric acid cycle (isocitrate, alpha-ketoglutarate, aconitate, the tryptophan pathway (kynurenine, kynurenic acid, and the urea cycle. There was considerable overlap in metabolite profiles between BMI, abdominal adiposity, insulin resistance [IR] and dyslipidemia, modest overlap of metabolite profiles between BMI and hyperglycemia, and little overlap with fasting glucose or elevated blood pressure. Metabolite profiles were associated with longitudinal changes in fasting glucose, but the involved metabolites (ornithine, 5-HIAA, aminoadipic acid, isoleucine, cotinine were distinct from those associated with baseline glucose or other traits. Obesity status appeared to "modify" the association of 9 metabolites with IR. For example, bile acid metabolites were strongly associated with IR among obese but not lean individuals, whereas isoleucine had a stronger association with IR in lean individuals.In this large-scale metabolite profiling study, body mass index was associated with a broad range of metabolic alterations. Metabolite profiling highlighted considerable overlap with abdominal adiposity, insulin resistance

  13. Reference Standardization for Mass Spectrometry and High-resolution Metabolomics Applications to Exposome Research.

    Science.gov (United States)

    Go, Young-Mi; Walker, Douglas I; Liang, Yongliang; Uppal, Karan; Soltow, Quinlyn A; Tran, ViLinh; Strobel, Frederick; Quyyumi, Arshed A; Ziegler, Thomas R; Pennell, Kurt D; Miller, Gary W; Jones, Dean P

    2015-12-01

    The exposome is the cumulative measure of environmental influences and associated biological responses throughout the lifespan, including exposures from the environment, diet, behavior, and endogenous processes. A major challenge for exposome research lies in the development of robust and affordable analytic procedures to measure the broad range of exposures and associated biologic impacts occurring over a lifetime. Biomonitoring is an established approach to evaluate internal body burden of environmental exposures, but use of biomonitoring for exposome research is often limited by the high costs associated with quantification of individual chemicals. High-resolution metabolomics (HRM) uses ultra-high resolution mass spectrometry with minimal sample preparation to support high-throughput relative quantification of thousands of environmental, dietary, and microbial chemicals. HRM also measures metabolites in most endogenous metabolic pathways, thereby providing simultaneous measurement of biologic responses to environmental exposures. The present research examined quantification strategies to enhance the usefulness of HRM data for cumulative exposome research. The results provide a simple reference standardization protocol in which individual chemical concentrations in unknown samples are estimated by comparison to a concurrently analyzed, pooled reference sample with known chemical concentrations. The approach was tested using blinded analyses of amino acids in human samples and was found to be comparable to independent laboratory results based on surrogate standardization or internal standardization. Quantification was reproducible over a 13-month period and extrapolated to thousands of chemicals. The results show that reference standardization protocol provides an effective strategy that will enhance data collection for cumulative exposome research. In principle, the approach can be extended to other types of mass spectrometry and other analytical methods. PMID

  14. On uplimit of accurate measurement of tau mass

    CERN Document Server

    Mo, X H

    2016-01-01

    Tau lepton as one of three elementary leptons in nature, the measurement of its mass has ever been performed since its discovery. The present relative accuracy is already at the level of better than 10 to minus 4 and more effects are still made in order to increase the accuracy further. However, the analysis of available techniques for and expectable luminosity from e+e- collider indicates that the precision uplimit of tau mass is almost reached, which means that brand new approaches should be looked for if the great improvement is yearned for.

  15. Quantitative proteomics using the high resolution accurate mass capabilities of the quadrupole-orbitrap mass spectrometer.

    Science.gov (United States)

    Gallien, Sebastien; Domon, Bruno

    2014-08-01

    High resolution/accurate mass hybrid mass spectrometers have considerably advanced shotgun proteomics and the recent introduction of fast sequencing capabilities has expanded its use for targeted approaches. More specifically, the quadrupole-orbitrap instrument has a unique configuration and its new features enable a wide range of experiments. An overview of the analytical capabilities of this instrument is presented, with a focus on its application to quantitative analyses. The high resolution, the trapping capability and the versatility of the instrument have allowed quantitative proteomic workflows to be redefined and new data acquisition schemes to be developed. The initial proteomic applications have shown an improvement of the analytical performance. However, as quantification relies on ion trapping, instead of ion beam, further refinement of the technique can be expected.

  16. Metabolomic Analysis of Gingival Crevicular Fluid Using Gas Chromatography/Mass Spectrometry

    Science.gov (United States)

    Ozeki, Miho; Nozaki, Takenori; Aoki, Jun; Bamba, Takeshi; Jensen, Kirk R.; Murakami, Shinya; Toyoda, Michisato

    2016-01-01

    Periodontitis is one of the most prevalent threats to oral health as the most common cause of tooth loss. In order to perform effective treatment, a clinical test that detect sites where disease activity is high and predicts periodontal tissue destruction is strongly desired, however, it is still difficult to prognose the periodontal tissue breakdown on the basis of conventional methods. The aim of this study is to examine the usefulness of gas chromatography/mass spectrometry (GC/MS), which could eventually be used for on-site analysis of metabolites in gingival crevicular fluid (GCF) in order to objectively diagnose periodontitis at a molecular level. GCF samples were collected from two diseased sites (one site with a moderate pocket and another site with a deep pocket) from each patient and from clinically healthy sites of volunteers. Nineteen metabolites were identified using GC/MS. Total ion current chromatograms showed broad differences in metabolite peak patterns between GCF samples obtained from healthy sites, moderate-pocket sites, and deep-pocket sites. The intensity difference of some metabolites was significant at sites with deep pockets compared to healthy sites. Additionally, metabolite intensities at moderate-pocket sites showed an intermediate profile between the severely diseased sites and healthy sites, which suggested that periodontitis progression could be observed with a changing metabolite profile. Principal component analysis confirmed these observations by clearly delineating healthy sites and sites with deep pockets. These results suggest that metabolomic analysis of GCF could be useful for prediction and diagnosis of periodontal disease in a single visit from a patient and provides the groundwork for establishing a new, on-site diagnostic method for periodontitis. PMID:27446770

  17. Metabolomic Analysis of Gingival Crevicular Fluid Using Gas Chromatography/Mass Spectrometry.

    Science.gov (United States)

    Ozeki, Miho; Nozaki, Takenori; Aoki, Jun; Bamba, Takeshi; Jensen, Kirk R; Murakami, Shinya; Toyoda, Michisato

    2016-01-01

    Periodontitis is one of the most prevalent threats to oral health as the most common cause of tooth loss. In order to perform effective treatment, a clinical test that detect sites where disease activity is high and predicts periodontal tissue destruction is strongly desired, however, it is still difficult to prognose the periodontal tissue breakdown on the basis of conventional methods. The aim of this study is to examine the usefulness of gas chromatography/mass spectrometry (GC/MS), which could eventually be used for on-site analysis of metabolites in gingival crevicular fluid (GCF) in order to objectively diagnose periodontitis at a molecular level. GCF samples were collected from two diseased sites (one site with a moderate pocket and another site with a deep pocket) from each patient and from clinically healthy sites of volunteers. Nineteen metabolites were identified using GC/MS. Total ion current chromatograms showed broad differences in metabolite peak patterns between GCF samples obtained from healthy sites, moderate-pocket sites, and deep-pocket sites. The intensity difference of some metabolites was significant at sites with deep pockets compared to healthy sites. Additionally, metabolite intensities at moderate-pocket sites showed an intermediate profile between the severely diseased sites and healthy sites, which suggested that periodontitis progression could be observed with a changing metabolite profile. Principal component analysis confirmed these observations by clearly delineating healthy sites and sites with deep pockets. These results suggest that metabolomic analysis of GCF could be useful for prediction and diagnosis of periodontal disease in a single visit from a patient and provides the groundwork for establishing a new, on-site diagnostic method for periodontitis. PMID:27446770

  18. Nutritional Metabolomics

    DEFF Research Database (Denmark)

    Gürdeniz, Gözde

    of the crucial steps is data preprocessing, which is particularly cumbersome for complex liquid chromatography mass spectrometry (LC-MS) data. Accordingly, in PAPER I, different LC-MS data preprocessing tools, MarkerLynx, MZmine, XCMS and a customised method (spectral binning and chromatographic collapsing) were...... and alignment algorithms, such that each has pros and cons. Thus, the use of more than one software tool and/or the use of several parameter settings during data preprocessing are likely to decrease the risk of failing to detect features (potential marker candidates) in untargeted metabolomics. On the other...... hand, customised methods lead to many false positives and negatives. Data preprocessing is followed by data analysis. In metabolomics, large amount of complex data characterise few samples, thus data analysis becomes a critical step as well. Principal component analysis (PCA) is useful for exploratory...

  19. Accurate, reliable control of process gases by mass flow controllers

    Energy Technology Data Exchange (ETDEWEB)

    Hardy, J.; McKnight, T.

    1997-02-01

    The thermal mass flow controller, or MFC, has become an instrument of choice for the monitoring and controlling of process gas flow throughout the materials processing industry. These MFCs are used on CVD processes, etching tools, and furnaces and, within the semiconductor industry, are used on 70% of the processing tools. Reliability and accuracy are major concerns for the users of the MFCs. Calibration and characterization technologies for the development and implementation of mass flow devices are described. A test facility is available to industry and universities to test and develop gas floe sensors and controllers and evaluate their performance related to environmental effects, reliability, reproducibility, and accuracy. Additional work has been conducted in the area of accuracy. A gravimetric calibrator was invented that allows flow sensors to be calibrated in corrosive, reactive gases to an accuracy of 0.3% of reading, at least an order of magnitude better than previously possible. Although MFCs are typically specified with accuracies of 1% of full scale, MFCs may often be implemented with unwarranted confidence due to the conventional use of surrogate gas factors. Surrogate gas factors are corrections applied to process flow indications when an MFC has been calibrated on a laboratory-safe surrogate gas, but is actually used on a toxic, or corrosive process gas. Previous studies have indicated that the use of these factors may cause process flow errors of typically 10%, but possibly as great as 40% of full scale. This paper will present possible sources of error in MFC process gas flow monitoring and control, and will present an overview of corrective measures which may be implemented with MFC use to significantly reduce these sources of error.

  20. The yeast metabolome addressed by electrospray ionization mass spectrometry: Initiation of a mass spectral library and its applications for metabolic footprinting by direct infusion mass spectrometry

    DEFF Research Database (Denmark)

    Højer-Pedersen, Jesper Juul; Smedsgaard, Jørn; Nielsen, Jens

    2008-01-01

    , which could be assigned using the in silico metabolome. By this approach metabolic footprinting can advance from a classification method that is used to derive biological information based on guilt-by-association, to a tool for extraction of metabolic differences, which can guide new targeted biological...... for ionization of microbial metabolites without any previous derivatization needed. To address the capabilities of ESI-MS in detecting the metabolome of Saccharomyces cerevisiae, the in silico metabolome of this organism was used as a template to present a theoretical metabolome. This showed that in combination...

  1. Multi-matrix, dual polarity, tandem mass spectrometry imaging strategy applied to a germinated maize seed: toward mass spectrometry imaging of an untargeted metabolome.

    Science.gov (United States)

    Feenstra, Adam D; Hansen, Rebecca L; Lee, Young Jin

    2015-11-01

    Mass spectrometry imaging (MSI) provides high spatial resolution information that is unprecedented in traditional metabolomics analyses; however, the molecular coverage is often limited to a handful of compounds and is insufficient to understand overall metabolomic changes of a biological system. Here, we propose an MSI methodology to increase the diversity of chemical compounds that can be imaged and identified, in order to eventually perform untargeted metabolomic analysis using MSI. In this approach, we use the desorption/ionization bias of various matrixes for different metabolite classes along with dual polarities and a tandem MSI strategy. The use of multiple matrixes and dual polarities allows us to visualize various classes of compounds, while data-dependent MS/MS spectra acquired in the same MSI scans allow us to identify the compounds directly on the tissue. In a proof of concept application to a germinated corn seed, a total of 166 unique ions were determined to have high-quality MS/MS spectra, without counting structural isomers, of which 52 were identified as unique compounds. According to an estimation based on precursor MSI datasets, we expect over five hundred metabolites could be potentially identified and visualized once all experimental conditions are optimized and an MS/MS library is available. Lastly, metabolites involved in the glycolysis pathway and tricarboxylic acid cycle were imaged to demonstrate the potential of this technology to better understand metabolic biology. PMID:26339687

  2. A signal filtering method for improved quantification and noise discrimination in fourier transform ion cyclotron resonance mass spectrometry-based metabolomics data.

    Science.gov (United States)

    Payne, Tristan G; Southam, Andrew D; Arvanitis, Theodoros N; Viant, Mark R

    2009-06-01

    Direct-infusion electrospray-ionization Fourier transform ion cyclotron resonance mass spectrometry (DI ESI FT-ICR MS) is increasingly being utilized in metabolomics, including the high sensitivity selected ion monitoring (SIM)-stitching approach. Accurate signal quantification and the discrimination of real signals from noise remain major challenges for this approach, with both adversely affected by factors including ion suppression during electrospray, ion-ion interactions in the detector cell, and thermally-induced white noise. This is particularly problematic for complex mixture analysis where hundreds of metabolites are present near the noise level. Here we address relative signal quantification and noise discrimination issues in SIM-stitched DI ESI FT-ICR MS-based metabolomics. Using liver tissue, we first optimized the number of scans (n) acquired per SIM window to address the balance between quantification accuracy versus acquisition time (and thus sample throughput); a minimum of n = 5 is recommended. Secondly, we characterized and computationally-corrected an effect whereby an ion's intensity is dependent upon its location within a SIM window, exhibiting a 3-fold higher intensity at the high m/z end. This resulted in significantly improved quantification accuracy. Finally, we thoroughly characterized a three-stage filter to discriminate noise from real signals, which comprised a signal-to-noise-ratio (SNR) hard threshold, then a "replicate" filter (retaining only peaks in r-out-of-3 replicate analyses), and then a "sample" filter (retaining only peaks in >s% of biological samples). We document the benefits of three-stage filtering versus one- and two-stage filters, and show the importance of selecting filter parameters that balance the confidence that a signal is real versus the total number of peaks detected.

  3. Systemic Metabolomic Changes in Blood Samples of Lung Cancer Patients Identified by Gas Chromatography Time-of-Flight Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Suzanne Miyamoto

    2015-04-01

    Full Text Available Lung cancer is a leading cause of cancer deaths worldwide. Metabolic alterations in tumor cells coupled with systemic indicators of the host response to tumor development have the potential to yield blood profiles with clinical utility for diagnosis and monitoring of treatment. We report results from two separate studies using gas chromatography time-of-flight mass spectrometry (GC-TOF MS to profile metabolites in human blood samples that significantly differ from non-small cell lung cancer (NSCLC adenocarcinoma and other lung cancer cases. Metabolomic analysis of blood samples from the two studies yielded a total of 437 metabolites, of which 148 were identified as known compounds and 289 identified as unknown compounds. Differential analysis identified 15 known metabolites in one study and 18 in a second study that were statistically different (p-values <0.05. Levels of maltose, palmitic acid, glycerol, ethanolamine, glutamic acid, and lactic acid were increased in cancer samples while amino acids tryptophan, lysine and histidine decreased. Many of the metabolites were found to be significantly different in both studies, suggesting that metabolomics appears to be robust enough to find systemic changes from lung cancer, thus showing the potential of this type of analysis for lung cancer detection.

  4. Vitroprocines, new antibiotics against Acinetobacter baumannii, discovered from marine Vibrio sp. QWI-06 using mass-spectrometry-based metabolomics approach

    Science.gov (United States)

    Liaw, Chih-Chuang; Chen, Pei-Chin; Shih, Chao-Jen; Tseng, Sung-Pin; Lai, Ying-Mi; Hsu, Chi-Hsin; Dorrestein, Pieter C.; Yang, Yu-Liang

    2015-08-01

    A robust and convenient research strategy integrating state-of-the-art analytical techniques is needed to efficiently discover novel compounds from marine microbial resources. In this study, we identified a series of amino-polyketide derivatives, vitroprocines A-J, from the marine bacterium Vibrio sp. QWI-06 by an integrated approach using imaging mass spectroscopy and molecular networking, as well as conventional bioactivity-guided fractionation and isolation. The structure-activity relationship of vitroprocines against Acinetobacter baumannii is proposed. In addition, feeding experiments with 13C-labeled precursors indicated that a pyridoxal 5‧-phosphate-dependent mechanism is involved in the biosynthesis of vitroprocines. Elucidation of amino-polyketide derivatives from a species of marine bacteria for the first time demonstrates the potential of this integrated metabolomics approach to uncover marine bacterial biodiversity.

  5. Pattern Recognition and Pathway Analysis with Genetic Algorithms in Mass Spectrometry Based Metabolomics

    Directory of Open Access Journals (Sweden)

    Wei Zou

    2009-04-01

    Full Text Available A robust and complete workflow for metabolic profiling and data mining was described in detail. Three independent and complementary analytical techniques for metabolic profiling were applied: hydrophilic interaction chromatography (HILIC–LC–ESI–MS, reversed-phase liquid chromatography (RP–LC–ESI–MS, and gas chromatography (GC–TOF–MS all coupled to mass spectrometry (MS. Unsupervised methods, such as principle component analysis (PCA and clustering, and supervised methods, such as classification and PCA-DA (discriminatory analysis were used for data mining. Genetic Algorithms (GA, a multivariate approach, was probed for selection of the smallest subsets of potentially discriminative predictors. From thousands of peaks found in total, small subsets selected by GA were considered as highly potential predictors allowing discrimination among groups. It was found that small groups of potential top predictors selected with PCA-DA and GA are different and unique. Annotated GC–TOF–MS data generated identified feature metabolites. Metabolites putatively detected with LC–ESI–MS profiling require further elemental composition assignment with accurate mass measurement by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS and structure elucidation by nuclear magnetic resonance spectroscopy (NMR. GA was also used to generate correlated networks for pathway analysis. Several case studies, comprising groups of plant samples bearing different genotypes and groups of samples of human origin, namely patients and healthy volunteers’ urine samples, demonstrated that such a workflow combining comprehensive metabolic profiling and advanced data mining techniques provides a powerful approach for pattern recognition and biomarker discovery

  6. Accurate on-line mass flow measurements in supercritical fluid chromatography.

    Science.gov (United States)

    Tarafder, Abhijit; Vajda, Péter; Guiochon, Georges

    2013-12-13

    This work demonstrates the possible advantages and the challenges of accurate on-line measurements of the CO2 mass flow rate during supercritical fluid chromatography (SFC) operations. Only the mass flow rate is constant along the column in SFC. The volume flow rate is not. The critical importance of accurate measurements of mass flow rates for the achievement of reproducible data and the serious difficulties encountered in supercritical fluid chromatography for its assessment were discussed earlier based on the physical properties of carbon dioxide. In this report, we experimentally demonstrate the problems encountered when performing mass flow rate measurements and the gain that can possibly be achieved by acquiring reproducible data using a Coriolis flow meter. The results obtained show how the use of a highly accurate mass flow meter permits, besides the determination of accurate values of the mass flow rate, a systematic, constant diagnosis of the correct operation of the instrument and the monitoring of the condition of the carbon dioxide pump. PMID:24210558

  7. BatMass: a Java Software Platform for LC-MS Data Visualization in Proteomics and Metabolomics.

    Science.gov (United States)

    Avtonomov, Dmitry M; Raskind, Alexander; Nesvizhskii, Alexey I

    2016-08-01

    Mass spectrometry (MS) coupled to liquid chromatography (LC) is a commonly used technique in metabolomic and proteomic research. As the size and complexity of LC-MS-based experiments grow, it becomes increasingly more difficult to perform quality control of both raw data and processing results. In a practical setting, quality control steps for raw LC-MS data are often overlooked, and assessment of an experiment's success is based on some derived metrics such as "the number of identified compounds". The human brain interprets visual data much better than plain text, hence the saying "a picture is worth a thousand words". Here, we present the BatMass software package, which allows for performing quick quality control of raw LC-MS data through its fast visualization capabilities. It also serves as a testbed for developers of LC-MS data processing algorithms by providing a data access library for open mass spectrometry file formats and a means of visually mapping processing results back to the original data. We illustrate the utility of BatMass with several use cases of quality control and data exploration. PMID:27306858

  8. Main-Sequence Effective Temperatures from a Revised Mass-Luminosity Relation Based on Accurate Properties

    CERN Document Server

    Eker, Z; Soydugan, E; Bilir, S; Gokce, E Yaz; Steer, I; Tuysuz, M; Senyuz, T; Demircan, O

    2015-01-01

    The mass-luminosity (M-L), mass-radius (M-R) and mass-effective temperature ($M-T_{eff}$) diagrams for a subset of galactic nearby main-sequence stars with masses and radii accurate to $\\leq 3\\%$ and luminosities accurate to $\\leq 30\\%$ (268 stars) has led to a putative discovery. Four distinct mass domains have been identified, which we have tentatively associated with low, intermediate, high, and very high mass main-sequence stars, but which nevertheless are clearly separated by three distinct break points at 1.05, 2.4, and 7$M_{\\odot}$ within the mass range studied of $0.38-32M_{\\odot}$. Further, a revised mass-luminosity relation (MLR) is found based on linear fits for each of the mass domains identified. The revised, mass-domain based MLRs, which are classical ($L \\propto M^{\\alpha}$), are shown to be preferable to a single linear, quadratic or cubic equation representing as an alternative MLR. Stellar radius evolution within the main-sequence for stars with $M>1M_{\\odot}$ is clearly evident on the M-R d...

  9. Normalization to specific gravity prior to analysis improves information recovery from high resolution mass spectrometry metabolomic profiles of human urine.

    Science.gov (United States)

    Edmands, William M B; Ferrari, Pietro; Scalbert, Augustin

    2014-11-01

    Extraction of meaningful biological information from urinary metabolomic profiles obtained by liquid-chromatography coupled to mass spectrometry (MS) necessitates the control of unwanted sources of variability associated with large differences in urine sample concentrations. Different methods of normalization either before analysis (preacquisition normalization) through dilution of urine samples to the lowest specific gravity measured by refractometry, or after analysis (postacquisition normalization) to urine volume, specific gravity and median fold change are compared for their capacity to recover lead metabolites for a potential future use as dietary biomarkers. Twenty-four urine samples of 19 subjects from the European Prospective Investigation into Cancer and nutrition (EPIC) cohort were selected based on their high and low/nonconsumption of six polyphenol-rich foods as assessed with a 24 h dietary recall. MS features selected on the basis of minimum discriminant selection criteria were related to each dietary item by means of orthogonal partial least-squares discriminant analysis models. Normalization methods ranked in the following decreasing order when comparing the number of total discriminant MS features recovered to that obtained in the absence of normalization: preacquisition normalization to specific gravity (4.2-fold), postacquisition normalization to specific gravity (2.3-fold), postacquisition median fold change normalization (1.8-fold increase), postacquisition normalization to urinary volume (0.79-fold). A preventative preacquisition normalization based on urine specific gravity was found to be superior to all curative postacquisition normalization methods tested for discovery of MS features discriminant of dietary intake in these urinary metabolomic datasets.

  10. Untargeted metabolomic analysis using liquid chromatography quadrupole time-of-flight mass spectrometry for non-volatile profiling of wines

    International Nuclear Information System (INIS)

    Highlights: • An untargeted metabolomic method for the non-volatile profile of the Graciano wine was developed. • 411 different metabolites in Graciano Vitis vinifera red wine were identified. • 15 compounds could serve to differentiate Graciano and Tempranillo wines. • An enological database (WinMet) with 2080 compounds was constructed. - Abstract: The current study presents a method for comprehensive untargeted metabolomic fingerprinting of the non-volatile profile of the Graciano Vitis vinifera wine variety, using liquid chromatography/electrospray ionization time of flight mass spectrometry (LC–ESI-QTOF). Pre-treatment of samples, chromatographic columns, mobile phases, elution gradients and ionization sources, were evaluated for the extraction of the maximum number of metabolites in red wine. Putative compounds were extracted from the raw data using the extraction algorithm, molecular feature extractor (MFE). For the metabolite identification the WinMet database was designed based on electronic databases and literature research and includes only the putative metabolites reported to be present in oenological matrices. The results from WinMet were compared with those in the METLIN database to evaluate how much the databases overlap for performing identifications. The reproducibility of the analysis was assessed using manual processing following replicate injections of Vitis vinifera cv. Graciano wine spiked with external standards. In the present work, 411 different metabolites in Graciano Vitis vinifera red wine were identified, including primary wine metabolites such as sugars (4%), amino acids (23%), biogenic amines (4%), fatty acids (2%), and organic acids (32%) and secondary metabolites such as phenols (27%) and esters (8%). Significant differences between varieties Tempranillo and Graciano were related to the presence of fifteen specific compounds

  11. Untargeted metabolomic analysis using liquid chromatography quadrupole time-of-flight mass spectrometry for non-volatile profiling of wines

    Energy Technology Data Exchange (ETDEWEB)

    Arbulu, M. [Department of Analytical Chemistry, Faculty of Pharmacy, University of the Basque Country, 01006 Vitoria-Gasteiz (Spain); Sampedro, M.C. [Central Service of Analysis, SGIker, University of the Basque Country, 01006 Vitoria-Gasteiz (Spain); Gómez-Caballero, A.; Goicolea, M.A. [Department of Analytical Chemistry, Faculty of Pharmacy, University of the Basque Country, 01006 Vitoria-Gasteiz (Spain); Barrio, R.J., E-mail: r.barrio@ehu.es [Department of Analytical Chemistry, Faculty of Pharmacy, University of the Basque Country, 01006 Vitoria-Gasteiz (Spain)

    2015-02-09

    Highlights: • An untargeted metabolomic method for the non-volatile profile of the Graciano wine was developed. • 411 different metabolites in Graciano Vitis vinifera red wine were identified. • 15 compounds could serve to differentiate Graciano and Tempranillo wines. • An enological database (WinMet) with 2080 compounds was constructed. - Abstract: The current study presents a method for comprehensive untargeted metabolomic fingerprinting of the non-volatile profile of the Graciano Vitis vinifera wine variety, using liquid chromatography/electrospray ionization time of flight mass spectrometry (LC–ESI-QTOF). Pre-treatment of samples, chromatographic columns, mobile phases, elution gradients and ionization sources, were evaluated for the extraction of the maximum number of metabolites in red wine. Putative compounds were extracted from the raw data using the extraction algorithm, molecular feature extractor (MFE). For the metabolite identification the WinMet database was designed based on electronic databases and literature research and includes only the putative metabolites reported to be present in oenological matrices. The results from WinMet were compared with those in the METLIN database to evaluate how much the databases overlap for performing identifications. The reproducibility of the analysis was assessed using manual processing following replicate injections of Vitis vinifera cv. Graciano wine spiked with external standards. In the present work, 411 different metabolites in Graciano Vitis vinifera red wine were identified, including primary wine metabolites such as sugars (4%), amino acids (23%), biogenic amines (4%), fatty acids (2%), and organic acids (32%) and secondary metabolites such as phenols (27%) and esters (8%). Significant differences between varieties Tempranillo and Graciano were related to the presence of fifteen specific compounds.

  12. Assessing temporal flux of plant hormones in stored processing potatoes using high definition accurate mass spectrometry

    OpenAIRE

    José Juan Ordaz-Ortiz; Sofia Foukaraki; Leon Alexander Terry

    2015-01-01

    Plant hormones are important molecules which at low concentration can regulate various physiological processes. Mass spectrometry has become a powerful technique for the quantification of multiple classes of plant hormones because of its high sensitivity and selectivity. We developed a new ultrahigh pressure liquid chromatography–full-scan high-definition accurate mass spectrometry method, for simultaneous determination of abscisic acid and four metabolites phaseic acid, dihydrophaseic acid, ...

  13. MetAlign: Interface-Driven, Versatile Metabolomics Tool for Hyphenated Full-Scan Mass Spectrometry Data Preprocessing

    NARCIS (Netherlands)

    Lommen, A.

    2009-01-01

    Hyphenated full-scan MS technology creates large amounts of data. A versatile easy to handle automation tool aiding in the data analysis is very important in handling such a data stream. MetAlign software-as described in this manuscript-handles a broad range of accurate mass and nominal mass GC/MS a

  14. Metabolomics Analysis of Health Functions of Physalis Pubescens L. using by Ultra-performance Liquid Chromatography/Electrospray Ionization Quadruple Time-of-Flight Mass Spectrometry

    Institute of Scientific and Technical Information of China (English)

    Hang Chu; Hui Sun; Guang-Li Yan; Ai-Hua Zhang; Chang Liu; Hui Dong; Xiang-Cai Meng; Xi-Jun Wang

    2015-01-01

    Herbal medicines may benefit from metabolomics studies, and applying metabolomics may provide answers about which herbal interventions may be effective for individuals, which metabolic processes are triggered, and the subsequent chemical pathways of activity. Physalis pubescens L (PPL) is an herbal fruit for one year living plant and has been developed into healthy function’s food. However, the mechanisms of health functions are still unclear. To comprehensively and holistically assess its anti-fatigue and antioxidant effects, a novel integrative metabolomics approach was applied. In this study, we present metabolomics analysis applying ultra performance liquid chromatography coupled to quadrupole with time-of-flight mass spectrometry (UPLC-Q/TOF-MS) to determine metabolite alterations after oral administration PPL to rats. Fifteen metabolites in urine were identified as potential biomarkers. Pattern analysis of the UPLC-Q/TOF-MS data disclosed that PPL could relieve fatigue rats by ameliorating the disturbance in amino acids metabolism and energy metabolism, alleviating the oxidative stress from reactive oxygen species and the inflammatory damage, and recovering the destructed regulation. Based on these results, we demonstrated that PPL is a promising source of natural anti-fatigue and antioxidants material for use in functional foods and medicines.

  15. Metabolomics Analysis of Health Functions of Physalis Pubescens L. using by Ultra-performance Liquid Chromatography/Electrospray Ionization Quadruple Time-of-Flight Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Hang Chu

    2015-07-01

    Full Text Available Herbal medicines may benefit from metabolomics studies, and applying metabolomics may provide answers about which herbal interventions may be effective for individuals, which metabolic processes are triggered, and the subsequent chemical pathways of activity. Physalis pubescens L (PPL is an herbal fruit for one year living plant and has been developed into healthy function's food. However, the mechanisms of health functions are still unclear. To comprehensively and holistically assess its anti-fatigue and antioxidant effects, a novel integrative metabolomics approach was applied. In this study, we present metabolomics analysis applying ultra performance liquid chromatography coupled to quadrupole with time-of-flight mass spectrometry (UPLC-Q/TOF-MS to determine metabolite alterations after oral administration PPL to rats. Fifteen metabolites in urine were identified as potential biomarkers. Pattern analysis of the UPLC-Q/TOF-MS data disclosed that PPL could relieve fatigue rats by ameliorating the disturbance in amino acids metabolism and energy metabolism, alleviating the oxidative stress from reactive oxygen species and the inflammatory damage, and recovering the destructed regulation. Based on these results, we demonstrated that PPL is a promising source of natural anti-fatigue and antioxidants material for use in functional foods and medicines.

  16. Multimode gradient high performance liquid chromatography mass spectrometry method applicable to metabolomics and environmental monitoring.

    Science.gov (United States)

    Ammann, Adrian A; Suter, Marc J-F

    2016-07-22

    Metabolomics or environmental investigations generate samples containing very large numbers of small molecular weight analytes. A single mode chromatographic separation excludes a substantial part of such complex analyte mixtures. For instance, a reversed-phase separation would not retain ionic species, resulting in a correspondingly huge front peak. To address this problem, we used two commercially available mixed-mode ion-exchange reversed-phase columns (WAX-1 and WCX-1) in sequence in a novel multimode separation method. After trapping hydrophobics on a C18-trap in loop position, hydrophilics passing the trap are separated by a simultaneous gradient for HILIC, anion and cation exchange chromatography. This gradient ends in a washout phase with a high percentage of water, the correct starting conditions for a reversed-phase gradient eluting hydrophobics from the trap in a second step of the run. Amino acids (9), organic acids (2), sugars (8), fatty acid derived compounds (11), antioxidants (4), miscellanea (6) and xenobiotics (4) were analyzed. Compounds were separated after a single sample injection during a 50min run. Lipids derived small fatty acids up to a chain length of 12 carbons were also accessible within this run time. PMID:27324626

  17. Application of metabolomics analysis to targeted and comprehensive detection of organic contaminants in food and environmental matrices using ultra-high resolution mass spectrometry

    OpenAIRE

    Cotton, Jérôme

    2015-01-01

    Pollution of agrifood and environmental water by pesticides and drugs is a real public health concern. There are many quantitative methods developed on triple quadrupole mass spectrometer for their detection, but drug residues and abiotic or biological degradation of pollutants are generally not considered and are limited to a predetermined and restricted list of molecules.In this context, we have developed an analytical method based on metabolomic analyses by high performance liquid chromato...

  18. Metabolomic profiling of human follicular fluid from patients with repeated failure of in vitro fertilization using gas chromatography/mass spectrometry

    OpenAIRE

    Xia, Lan; Zhao, Xiaoming; Sun, Yun; Hong, Yan; Gao, Yuping; Hu, Shuanggang

    2014-01-01

    Objective: To establish a gas chromatography/mass spectrometry (GC/MS)-based metabolomics method to compare the metabolites in the follicular fluid (FF) from patients with in vitro fertilization (IVF) and repeated IVF failure (RIF). Methods: A prospective study was employed in Center for Reprodutive Medcine, Renji Hospital, Shanghai, China, between January and October 2010. FF samples were collected from 13 patients with RIF and 15 patients who achieved pregnancy after the first IVF cycle. Re...

  19. The Use of Accurate Mass Tags for High-Throughput Microbial Proteomics

    International Nuclear Information System (INIS)

    We describe and demonstrate a global strategy that extends the sensitivity, dynamic range, comprehensiveness, and throughput of proteomic measurements based upon the use of peptide accurate mass tags (AMTs) produced by global protein enzymatic digestion. The two-stage strategy exploits Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry to validate peptide AMTs for a specific organism, tissue or cell type from potential mass tags identified using conventional tandem mass spectrometry (MS/MS) methods, providing greater confidence in identifications as well as the basis for subsequent measurements without the need for MS/MS, and thus with greater sensitivity and increased throughput. A single high resolution capillary liquid chromatography separation combined with high sensitivity, high resolution and ac-curate FT-ICR measurements has been shown capable of characterizing peptide mixtures of significantly more than 10 5 components with mass accuracies of -1 ppm, sufficient for broad protein identification using AMTs. Other attractions of the approach include the broad and relatively unbiased proteome coverage, the capability for exploiting stable isotope labeling methods to realize high precision for relative protein abundance measurements, and the projected potential for study of mammalian proteomes when combined with additional sample fractionation. Using this strategy, in our first application we have been able to identify AMTs for 60% of the potentially expressed proteins in the organism Deinococcus radiodurans

  20. Fast and accurate mock catalogue generation for low-mass galaxies

    Science.gov (United States)

    Koda, Jun; Blake, Chris; Beutler, Florian; Kazin, Eyal; Marin, Felipe

    2016-06-01

    We present an accurate and fast framework for generating mock catalogues including low-mass haloes, based on an implementation of the COmoving Lagrangian Acceleration (COLA) technique. Multiple realisations of mock catalogues are crucial for analyses of large-scale structure, but conventional N-body simulations are too computationally expensive for the production of thousands of realizations. We show that COLA simulations can produce accurate mock catalogues with a moderate computation resource for low- to intermediate-mass galaxies in 1012 M⊙ haloes, both in real and redshift space. COLA simulations have accurate peculiar velocities, without systematic errors in the velocity power spectra for k ≤ 0.15 h Mpc-1, and with only 3-per cent error for k ≤ 0.2 h Mpc-1. We use COLA with 10 time steps and a Halo Occupation Distribution to produce 600 mock galaxy catalogues of the WiggleZ Dark Energy Survey. Our parallelized code for efficient generation of accurate halo catalogues is publicly available at github.com/junkoda/cola_halo.

  1. Fast and accurate mock catalogue generation for low-mass galaxies

    CERN Document Server

    Koda, Jun; Beutler, Florian; Kazin, Eyal; Marin, Felipe

    2015-01-01

    We present an accurate and fast framework for generating mock catalogues including low-mass halos, based on an implementation of the COmoving Lagrangian Acceleration (COLA) technique. Multiple realisations of mock catalogues are crucial for analyses of large-scale structure, but conventional N-body simulations are too computationally expensive for the production of thousands of realisations. We show that COLA simulations can produce accurate mock catalogues with a moderate computation resource for low- to intermediate- mass galaxies in $10^{12} M_\\odot$ haloes, both in real and redshift space. COLA simulations have accurate peculiar velocities, without systematic errors in the velocity power spectra for k < 0.15 h/Mpc, and with only 3-per-cent error for k < 0.2 h/Mpc. We use COLA with 10 time steps and a Halo Occupation Distribution to produce 600 mock galaxy catalogues of the WiggleZ Dark Energy Survey. Our parallelized code for efficient generation of accurate halo catalogues is publicly available at ...

  2. Accurate Prediction of the Ammonia Probes of a Variable Proton-to-Electron Mass Ratio

    CERN Document Server

    Owens, Alec; Thiel, Walter; Špirko, Vladimir

    2015-01-01

    A comprehensive study of the mass sensitivity of the vibration-rotation-inversion transitions of $^{14}$NH$_3$, $^{15}$NH$_3$, $^{14}$ND$_3$, and $^{15}$ND$_3$ is carried out variationally using the TROVE approach. Variational calculations are robust and accurate, offering a new way to compute sensitivity coefficients. Particular attention is paid to the $\\Delta k=\\pm 3$ transitions between the accidentally coinciding rotation-inversion energy levels of the $\

  3. SPECT-OPT multimodal imaging enables accurate evaluation of radiotracers for β-cell mass assessments

    OpenAIRE

    Wael A. Eter; Saba Parween; Lieke Joosten; Cathelijne Frielink; Maria Eriksson; Maarten Brom; Ulf Ahlgren; Martin Gotthardt

    2016-01-01

    Single Photon Emission Computed Tomography (SPECT) has become a promising experimental approach to monitor changes in β-cell mass (BCM) during diabetes progression. SPECT imaging of pancreatic islets is most commonly cross-validated by stereological analysis of histological pancreatic sections after insulin staining. Typically, stereological methods do not accurately determine the total β-cell volume, which is inconvenient when correlating total pancreatic tracer uptake with BCM. Alternative ...

  4. SPECT-OPT multimodal imaging enables accurate evaluation of radiotracers for beta-cell mass assessments

    OpenAIRE

    Wael A. Eter; Parween, Saba; Joosten, Lieke; Frielink, Cathelijne; Eriksson, Maria; Brom, Maarten; Ahlgren, Ulf; Gotthardt, Martin

    2016-01-01

    Single Photon Emission Computed Tomography (SPECT) has become a promising experimental approach to monitor changes in beta-cell mass (BCM) during diabetes progression. SPECT imaging of pancreatic islets is most commonly cross-validated by stereological analysis of histological pancreatic sections after insulin staining. Typically, stereological methods do not accurately determine the total beta-cell volume, which is inconvenient when correlating total pancreatic tracer uptake with BCM. Altern...

  5. Novel Chemical Ligands to Ebola Virus and Marburg Virus Nucleoproteins Identified by Combining Affinity Mass Spectrometry and Metabolomics Approaches

    Science.gov (United States)

    Fu, Xu; Wang, Zhihua; Li, Lixin; Dong, Shishang; Li, Zhucui; Jiang, Zhenzuo; Wang, Yuefei; Shui, Wenqing

    2016-01-01

    The nucleoprotein (NP) of Ebola virus (EBOV) and Marburg virus (MARV) is an essential component of the viral ribonucleoprotein complex and significantly impacts replication and transcription of the viral RNA genome. Although NP is regarded as a promising antiviral druggable target, no chemical ligands have been reported to interact with EBOV NP or MARV NP. We identified two compounds from a traditional Chinese medicine Gancao (licorice root) that can bind both NPs by combining affinity mass spectrometry and metabolomics approaches. These two ligands, 18β-glycyrrhetinic acid and licochalcone A, were verified by defined compound mixture screens and further characterized with individual ligand binding assays. Accompanying biophysical analyses demonstrate that binding of 18β-glycyrrhetinic acid to EBOV NP significantly reduces protein thermal stability, induces formation of large NP oligomers, and disrupts the critical association of viral ssRNA with NP complexes whereas the compound showed no such activity on MARV NP. Our study has revealed the substantial potential of new analytical techniques in ligand discovery from natural herb resources. In addition, identification of a chemical ligand that influences the oligomeric state and RNA-binding function of EBOV NP sheds new light on antiviral drug development. PMID:27403722

  6. Novel Chemical Ligands to Ebola Virus and Marburg Virus Nucleoproteins Identified by Combining Affinity Mass Spectrometry and Metabolomics Approaches.

    Science.gov (United States)

    Fu, Xu; Wang, Zhihua; Li, Lixin; Dong, Shishang; Li, Zhucui; Jiang, Zhenzuo; Wang, Yuefei; Shui, Wenqing

    2016-01-01

    The nucleoprotein (NP) of Ebola virus (EBOV) and Marburg virus (MARV) is an essential component of the viral ribonucleoprotein complex and significantly impacts replication and transcription of the viral RNA genome. Although NP is regarded as a promising antiviral druggable target, no chemical ligands have been reported to interact with EBOV NP or MARV NP. We identified two compounds from a traditional Chinese medicine Gancao (licorice root) that can bind both NPs by combining affinity mass spectrometry and metabolomics approaches. These two ligands, 18β-glycyrrhetinic acid and licochalcone A, were verified by defined compound mixture screens and further characterized with individual ligand binding assays. Accompanying biophysical analyses demonstrate that binding of 18β-glycyrrhetinic acid to EBOV NP significantly reduces protein thermal stability, induces formation of large NP oligomers, and disrupts the critical association of viral ssRNA with NP complexes whereas the compound showed no such activity on MARV NP. Our study has revealed the substantial potential of new analytical techniques in ligand discovery from natural herb resources. In addition, identification of a chemical ligand that influences the oligomeric state and RNA-binding function of EBOV NP sheds new light on antiviral drug development. PMID:27403722

  7. Model-based peak alignment of metabolomic profiling from comprehensive two-dimensional gas chromatography mass spectrometry

    Directory of Open Access Journals (Sweden)

    Jeong Jaesik

    2012-02-01

    Full Text Available Abstract Background Comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GCxGC/TOF-MS has been used for metabolite profiling in metabolomics. However, there is still much experimental variation to be controlled including both within-experiment and between-experiment variation. For efficient analysis, an ideal peak alignment method to deal with such variations is in great need. Results Using experimental data of a mixture of metabolite standards, we demonstrated that our method has better performance than other existing method which is not model-based. We then applied our method to the data generated from the plasma of a rat, which also demonstrates good performance of our model. Conclusions We developed a model-based peak alignment method to process both homogeneous and heterogeneous experimental data. The unique feature of our method is the only model-based peak alignment method coupled with metabolite identification in an unified framework. Through the comparison with other existing method, we demonstrated that our method has better performance. Data are available at http://stage.louisville.edu/faculty/x0zhan17/software/software-development/mspa. The R source codes are available at http://www.biostat.iupui.edu/~ChangyuShen/CodesPeakAlignment.zip. Trial Registration 2136949528613691

  8. Accurate correction of magnetic field instabilities for high-resolution isochronous mass measurements in storage rings

    CERN Document Server

    Shuai, P; Zhang, Y H; Litvinov, Yu A; Wang, M; Tu, X L; Blaum, K; Zhou, X H; Yuan, Y J; Audi, G; Yan, X L; Chen, X C; Xu, X; Zhang, W; Sun, B H; Yamaguchi, T; Chen, R J; Fu, C Y; Ge, Z; Huang, W J; Liu, D W; Xing, Y M; Zeng, Q

    2014-01-01

    Isochronous mass spectrometry (IMS) in storage rings is a successful technique for accurate mass measurements of short-lived nuclides with relative precision of about $10^{-5}-10^{-7}$. Instabilities of the magnetic fields in storage rings are one of the major contributions limiting the achievable mass resolving power, which is directly related to the precision of the obtained mass values. A new data analysis method is proposed allowing one to minimise the effect of such instabilities. The masses of the previously measured at the CSRe $^{41}$Ti, $^{43}$V, $^{47}$Mn, $^{49}$Fe, $^{53}$Ni and $^{55}$Cu nuclides were re-determined with this method. An improvement of the mass precision by a factor of $\\sim 1.7$ has been achieved for $^{41}$Ti and $^{43}$V. The method can be applied to any isochronous mass experiment irrespective of the accelerator facility. Furthermore, the method can be used as an on-line tool for checking the isochronous conditions of the storage ring.

  9. Improving the quality of biomarker candidates in untargeted metabolomics via peak table-based alignment of comprehensive two-dimensional gas chromatography-mass spectrometry data.

    Science.gov (United States)

    Bean, Heather D; Hill, Jane E; Dimandja, Jean-Marie D

    2015-05-15

    The potential of high-resolution analytical technologies like GC×GC/TOF MS in untargeted metabolomics and biomarker discovery has been limited by the development of fully automated software that can efficiently align and extract information from multiple chromatographic data sets. In this work we report the first investigation on a peak-by-peak basis of the chromatographic factors that impact GC×GC data alignment. A representative set of 16 compounds of different chromatographic characteristics were followed through the alignment of 63 GC×GC chromatograms. We found that varying the mass spectral match parameter had a significant influence on the alignment for poorly-resolved peaks, especially those at the extremes of the detector linear range, and no influence on well-chromatographed peaks. Therefore, optimized chromatography is required for proper GC×GC data alignment. Based on these observations, a workflow is presented for the conservative selection of biomarker candidates from untargeted metabolomics analyses. PMID:25857541

  10. High-resolution accurate mass spectrometry as a technique for characterization of complex lysimeter leachate samples.

    Science.gov (United States)

    Hand, Laurence H; Marshall, Samantha J; Saeed, Mansoor; Earll, Mark; Hadfield, Stephen T; Richardson, Kevan; Rawlinson, Paul

    2016-06-01

    Lysimeter studies can be used to identify and quantify soil degradates of agrochemicals (metabolites) that have the potential to leach to groundwater. However, the apparent metabolic profile of such lysimeter leachate samples will often be significantly more complex than would be expected in true groundwater samples. This is particularly true for S-metolachlor, which has an extremely complex metabolic pathway. Consequently, it was not practically possible to apply a conventional analytical approach to identify all metabolites in an S-metolachlor lysimeter study, because there was insufficient mass to enable the use of techniques such as nuclear magnetic resonance. Recent advances in high-resolution accurate mass spectrometry, however, allow innovative screening approaches to characterize leachate samples to a greater extent than previously possible. Leachate from the S-metolachlor study was screened for accurate masses (±5 ppm of the nominal mass) corresponding to more than 400 hypothetical metabolite structures. A refined list of plausible metabolites was constructed from these data to provide a comprehensive description of the most likely metabolites present. The properties of these metabolites were then evaluated using a principal component analysis model, based on molecular descriptors, to visualize the entire chemical space and to cluster the metabolites into a number of subclasses. This characterization and principal component analysis evaluation enabled the selection of suitable representative metabolites that were subsequently used as exemplars to assess the toxicological relevance of the leachate as a whole. Environ Toxicol Chem 2016;35:1401-1412. © 2015 SETAC. PMID:26627902

  11. An accurate mass and radius measurement for an ultracool white dwarf

    CERN Document Server

    Parsons, S G; Marsh, T R; Bergeron, P; Copperwheat, C M; Dhillon, V S; Bento, J; Littlefair, S P; Schreiber, M R

    2012-01-01

    Studies of cool white dwarfs in the solar neighbourhood have placed a limit on the age of the Galactic disk of 8-9 billion years. However, determining their cooling ages requires the knowledge of their effective temperatures, masses, radii, and atmospheric composition. So far, these parameters could only be inferred for a small number of ultracool white dwarfs for which an accurate distance is known, by fitting their spectral energy distributions (SEDs) in conjunction with a theoretical mass-radius relation. However, the mass-radius relation remains largely untested, and the derived cooling ages are hence model-dependent. Here we report direct measurements of the mass and radius of an ultracool white dwarf in the double-lined eclipsing binary SDSS J013851.54-001621.6. We find M(WD)=0.529+/-0.010Msol and R(WD)=0.0131+/-0.0003Rsol. Our measurements are consistent with the mass-radius relation and we determine a robust cooling age of 9.5 billion years for the 3570K white dwarf. We find that the mass and radius o...

  12. Can NMR solve some significant challenges in metabolomics?

    Science.gov (United States)

    Nagana Gowda, G. A.; Raftery, Daniel

    2015-11-01

    The field of metabolomics continues to witness rapid growth driven by fundamental studies, methods development, and applications in a number of disciplines that include biomedical science, plant and nutrition sciences, drug development, energy and environmental sciences, toxicology, etc. NMR spectroscopy is one of the two most widely used analytical platforms in the metabolomics field, along with mass spectrometry (MS). NMR's excellent reproducibility and quantitative accuracy, its ability to identify structures of unknown metabolites, its capacity to generate metabolite profiles using intact bio-specimens with no need for separation, and its capabilities for tracing metabolic pathways using isotope labeled substrates offer unique strengths for metabolomics applications. However, NMR's limited sensitivity and resolution continue to pose a major challenge and have restricted both the number and the quantitative accuracy of metabolites analyzed by NMR. Further, the analysis of highly complex biological samples has increased the demand for new methods with improved detection, better unknown identification, and more accurate quantitation of larger numbers of metabolites. Recent efforts have contributed significant improvements in these areas, and have thereby enhanced the pool of routinely quantifiable metabolites. Additionally, efforts focused on combining NMR and MS promise opportunities to exploit the combined strength of the two analytical platforms for direct comparison of the metabolite data, unknown identification and reliable biomarker discovery that continue to challenge the metabolomics field. This article presents our perspectives on the emerging trends in NMR-based metabolomics and NMR's continuing role in the field with an emphasis on recent and ongoing research from our laboratory.

  13. Can NMR solve some significant challenges in metabolomics?

    Science.gov (United States)

    Nagana Gowda, G A; Raftery, Daniel

    2015-11-01

    The field of metabolomics continues to witness rapid growth driven by fundamental studies, methods development, and applications in a number of disciplines that include biomedical science, plant and nutrition sciences, drug development, energy and environmental sciences, toxicology, etc. NMR spectroscopy is one of the two most widely used analytical platforms in the metabolomics field, along with mass spectrometry (MS). NMR's excellent reproducibility and quantitative accuracy, its ability to identify structures of unknown metabolites, its capacity to generate metabolite profiles using intact bio-specimens with no need for separation, and its capabilities for tracing metabolic pathways using isotope labeled substrates offer unique strengths for metabolomics applications. However, NMR's limited sensitivity and resolution continue to pose a major challenge and have restricted both the number and the quantitative accuracy of metabolites analyzed by NMR. Further, the analysis of highly complex biological samples has increased the demand for new methods with improved detection, better unknown identification, and more accurate quantitation of larger numbers of metabolites. Recent efforts have contributed significant improvements in these areas, and have thereby enhanced the pool of routinely quantifiable metabolites. Additionally, efforts focused on combining NMR and MS promise opportunities to exploit the combined strength of the two analytical platforms for direct comparison of the metabolite data, unknown identification and reliable biomarker discovery that continue to challenge the metabolomics field. This article presents our perspectives on the emerging trends in NMR-based metabolomics and NMR's continuing role in the field with an emphasis on recent and ongoing research from our laboratory. PMID:26476597

  14. Mass spectrometry–based metabolomics, analysis of metabolite-protein interactions, and imaging

    Science.gov (United States)

    Lee, Do Yup; Bowen, Benjamin P.; Northen, Trent R.

    2010-01-01

    Our understanding of biology has been greatly improved through recent developments in mass spectrometry, which is providing detailed information on protein and metabolite composition as well as protein-metabolite interactions. The high sensitivity and resolution of mass spectrometry achieved with liquid or gas chromatography allows for detection and quantification of hundreds to thousands of molecules in a single measurement. Where homogenization-based sample preparation and extraction methods result in a loss of spatial information, mass spectrometry imaging technologies provide the in situ distribution profiles of metabolites and proteins within tissues. Mass spectrometry–based analysis of metabolite abundance, protein-metabolite interactions, and spatial distribution of compounds facilitates the high-throughput screening of biochemical reactions, the reconstruction of metabolic networks, biomarker discovery, determination of tissue compositions, and functional annotation of both proteins and metabolites. PMID:20701590

  15. Proteomics, lipidomics, metabolomics: a mass spectrometry tutorial from a computer scientist's point of view

    OpenAIRE

    Smith, Rob; Mathis, Andrew D.; Ventura, Dan; Prince, John T.

    2014-01-01

    Background For decades, mass spectrometry data has been analyzed to investigate a wide array of research interests, including disease diagnostics, biological and chemical theory, genomics, and drug development. Progress towards solving any of these disparate problems depends upon overcoming the common challenge of interpreting the large data sets generated. Despite interim successes, many data interpretation problems in mass spectrometry are still challenging. Further, though these challenges...

  16. Exo-metabolome of Pseudovibrio sp. FO-BEG1 analyzed by ultra-high resolution mass spectrometry and the effect of phosphate limitation.

    Directory of Open Access Journals (Sweden)

    Stefano Romano

    Full Text Available Oceanic dissolved organic matter (DOM is an assemblage of reduced carbon compounds, which results from biotic and abiotic processes. The biotic processes consist in either release or uptake of specific molecules by marine organisms. Heterotrophic bacteria have been mostly considered to influence the DOM composition by preferential uptake of certain compounds. However, they also secrete a variety of molecules depending on physiological state, environmental and growth conditions, but so far the full set of compounds secreted by these bacteria has never been investigated. In this study, we analyzed the exo-metabolome, metabolites secreted into the environment, of the heterotrophic marine bacterium Pseudovibrio sp. FO-BEG1 via ultra-high resolution mass spectrometry, comparing phosphate limited with phosphate surplus growth conditions. Bacteria belonging to the Pseudovibrio genus have been isolated worldwide, mainly from marine invertebrates and were described as metabolically versatile Alphaproteobacteria. We show that the exo-metabolome is unexpectedly large and diverse, consisting of hundreds of compounds that differ by their molecular formulae. It is characterized by a dynamic recycling of molecules, and it is drastically affected by the physiological state of the strain. Moreover, we show that phosphate limitation greatly influences both the amount and the composition of the secreted molecules. By assigning the detected masses to general chemical categories, we observed that under phosphate surplus conditions the secreted molecules were mainly peptides and highly unsaturated compounds. In contrast, under phosphate limitation the composition of the exo-metabolome changed during bacterial growth, showing an increase in highly unsaturated, phenolic, and polyphenolic compounds. Finally, we annotated the detected masses using multiple metabolite databases. These analyses suggested the presence of several masses analogue to masses of known bioactive

  17. Combined proteomic and metabolomic profiling of serum reveals association of the complement system with obesity and identifies novel markers of body fat mass changes.

    Science.gov (United States)

    Oberbach, Andreas; Blüher, Matthias; Wirth, Henry; Till, Holger; Kovacs, Peter; Kullnick, Yvonne; Schlichting, Nadine; Tomm, Janina M; Rolle-Kampczyk, Ulrike; Murugaiyan, Jayaseelan; Binder, Hans; Dietrich, Arne; von Bergen, Martin

    2011-10-01

    Obesity is associated with multiple adverse health effects and a high risk of developing metabolic and cardiovascular diseases. Therefore, there is a great need to identify circulating parameters that link changes in body fat mass with obesity. This study combines proteomic and metabolomic approaches to identify circulating molecules that discriminate healthy lean from healthy obese individuals in an exploratory study design. To correct for variations in physical activity, study participants performed a one hour exercise bout to exhaustion. Subsequently, circulating factors differing between lean and obese individuals, independent of physical activity, were identified. The DIGE approach yielded 126 differentially abundant spots representing 39 unique proteins. Differential abundance of proteins was confirmed by ELISA for antithrombin-III, clusterin, complement C3 and complement C3b, pigment epithelium-derived factor (PEDF), retinol binding protein 4 (RBP4), serum amyloid P (SAP), and vitamin-D binding protein (VDBP). Targeted serum metabolomics of 163 metabolites identified 12 metabolites significantly related to obesity. Among those, glycine (GLY), glutamine (GLN), and glycero-phosphatidylcholine 42:0 (PCaa 42:0) serum concentrations were higher, whereas PCaa 32:0, PCaa 32:1, and PCaa 40:5 were decreased in obese compared to lean individuals. The integrated bioinformatic evaluation of proteome and metabolome data yielded an improved group separation score of 2.65 in contrast to 2.02 and 2.16 for the single-type use of proteomic or metabolomics data, respectively. The identified circulating parameters were further investigated in an extended set of 30 volunteers and in the context of two intervention studies. Those included 14 obese patients who had undergone sleeve gastrectomy and 12 patients on a hypocaloric diet. For determining the long-term adaptation process the samples were taken six months after the treatment. In multivariate regression analyses, SAP, CLU

  18. Induced Dual-Nanospray: A Novel Internal Calibration Method for Convenient and Accurate Mass Measurement

    Science.gov (United States)

    Li, Yafeng; Zhang, Ning; Zhou, Yueming; Wang, Jianing; Zhang, Yiming; Wang, Jiyun; Xiong, Caiqiao; Chen, Suming; Nie, Zongxiu

    2013-09-01

    Accurate mass information is of great importance in the determination of unknown compounds. An effective and easy-to-control internal mass calibration method will dramatically benefit accurate mass measurement. Here we reported a simple induced dual-nanospray internal calibration device which has the following three advantages: (1) the two sprayers are in the same alternating current field; thus both reference ions and sample ions can be simultaneously generated and recorded. (2) It is very simple and can be easily assembled. Just two metal tubes, two nanosprayers, and an alternating current power supply are included. (3) With the low-flow-rate character and the versatility of nanoESI, this calibration method is capable of calibrating various samples, even untreated complex samples such as urine and other biological samples with small sample volumes. The calibration errors are around 1 ppm in positive ion mode and 3 ppm in negative ion mode with good repeatability. This new internal calibration method opens up new possibilities in the determination of unknown compounds, and it has great potential for the broad applications in biological and chemical analysis.

  19. A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics.

    Science.gov (United States)

    Stanley, Jeffrey R; Adkins, Joshua N; Slysz, Gordon W; Monroe, Matthew E; Purvine, Samuel O; Karpievitch, Yuliya V; Anderson, Gordon A; Smith, Richard D; Dabney, Alan R

    2011-08-15

    Current algorithms for quantifying peptide identification confidence in the accurate mass and time (AMT) tag approach assume that the AMT tags themselves have been correctly identified. However, there is uncertainty in the identification of AMT tags, because this is based on matching LC-MS/MS fragmentation spectra to peptide sequences. In this paper, we incorporate confidence measures for the AMT tag identifications into the calculation of probabilities for correct matches to an AMT tag database, resulting in a more accurate overall measure of identification confidence for the AMT tag approach. The method is referenced as Statistical Tools for AMT Tag Confidence (STAC). STAC additionally provides a uniqueness probability (UP) to help distinguish between multiple matches to an AMT tag and a method to calculate an overall false discovery rate (FDR). STAC is freely available for download, as both a command line and a Windows graphical application.

  20. Gas chromatography-mass spectrometry based metabolomic approach for optimization and toxicity evaluation of earthworm sub-lethal responses to carbofuran.

    Science.gov (United States)

    Mudiam, Mohana Krishna Reddy; Ch, Ratnasekhar; Saxena, Prem Narain

    2013-01-01

    Despite recent advances in understanding mechanism of toxicity, the development of biomarkers (biochemicals that vary significantly with exposure to chemicals) for pesticides and environmental contaminants exposure is still a challenging task. Carbofuran is one of the most commonly used pesticides in agriculture and said to be most toxic carbamate pesticide. It is necessary to identify the biochemicals that can vary significantly after carbofuran exposure on earthworms which will help to assess the soil ecotoxicity. Initially, we have optimized the extraction conditions which are suitable for high-throughput gas chromatography mass spectrometry (GC-MS) based metabolomics for the tissue of earthworm, Metaphire posthuma. Upon evaluation of five different extraction solvent systems, 80% methanol was found to have good extraction efficiency based on the yields of metabolites, multivariate analysis, total number of peaks and reproducibility of metabolites. Later the toxicity evaluation was performed to characterize the tissue specific metabolomic perturbation of earthworm, Metaphire posthuma after exposure to carbofuran at three different concentration levels (0.15, 0.3 and 0.6 mg/kg of soil). Seventeen metabolites, contributing to the best classification performance of highest dose dependent carbofuran exposed earthworms from healthy controls were identified. This study suggests that GC-MS based metabolomic approach was precise and sensitive to measure the earthworm responses to carbofuran exposure in soil, and can be used as a promising tool for environmental eco-toxicological studies.

  1. Gas chromatography-mass spectrometry based metabolomic approach for optimization and toxicity evaluation of earthworm sub-lethal responses to carbofuran.

    Directory of Open Access Journals (Sweden)

    Mohana Krishna Reddy Mudiam

    Full Text Available Despite recent advances in understanding mechanism of toxicity, the development of biomarkers (biochemicals that vary significantly with exposure to chemicals for pesticides and environmental contaminants exposure is still a challenging task. Carbofuran is one of the most commonly used pesticides in agriculture and said to be most toxic carbamate pesticide. It is necessary to identify the biochemicals that can vary significantly after carbofuran exposure on earthworms which will help to assess the soil ecotoxicity. Initially, we have optimized the extraction conditions which are suitable for high-throughput gas chromatography mass spectrometry (GC-MS based metabolomics for the tissue of earthworm, Metaphire posthuma. Upon evaluation of five different extraction solvent systems, 80% methanol was found to have good extraction efficiency based on the yields of metabolites, multivariate analysis, total number of peaks and reproducibility of metabolites. Later the toxicity evaluation was performed to characterize the tissue specific metabolomic perturbation of earthworm, Metaphire posthuma after exposure to carbofuran at three different concentration levels (0.15, 0.3 and 0.6 mg/kg of soil. Seventeen metabolites, contributing to the best classification performance of highest dose dependent carbofuran exposed earthworms from healthy controls were identified. This study suggests that GC-MS based metabolomic approach was precise and sensitive to measure the earthworm responses to carbofuran exposure in soil, and can be used as a promising tool for environmental eco-toxicological studies.

  2. SPARC: Mass Models for 175 Disk Galaxies with Spitzer Photometry and Accurate Rotation Curves

    CERN Document Server

    Lelli, Federico; Schombert, James M

    2016-01-01

    We introduce SPARC (Spitzer Photometry & Accurate Rotation Curves): a sample of 175 nearby galaxies with new surface photometry at 3.6 um and high-quality rotation curves from previous HI/Halpha studies. SPARC spans a broad range of morphologies (S0 to Irr), luminosities (~5 dex), and surface brightnesses (~4 dex). We derive [3.6] surface photometry and study structural relations of stellar and gas disks. We find that both the stellar mass-HI mass relation and the stellar radius-HI radius relation have significant intrinsic scatter, while the HI mass-radius relation is extremely tight. We build detailed mass models and quantify the ratio of baryonic-to-observed velocity (Vbar/Vobs) for different characteristic radii and values of the stellar mass-to-light ratio (M/L) at [3.6]. Assuming M/L=0.5 Msun/Lsun (as suggested by stellar population models) we find that (i) the gas fraction linearly correlates with total luminosity, (ii) the transition from star-dominated to gas-dominated galaxies roughly correspond...

  3. Nephron Toxicity Profiling via Untargeted Metabolome Analysis Employing a High Performance Liquid Chromatography-Mass Spectrometry-based Experimental and Computational Pipeline.

    Science.gov (United States)

    Ranninger, Christina; Rurik, Marc; Limonciel, Alice; Ruzek, Silke; Reischl, Roland; Wilmes, Anja; Jennings, Paul; Hewitt, Philip; Dekant, Wolfgang; Kohlbacher, Oliver; Huber, Christian G

    2015-07-31

    Untargeted metabolomics has the potential to improve the predictivity of in vitro toxicity models and therefore may aid the replacement of expensive and laborious animal models. Here we describe a long term repeat dose nephrotoxicity study conducted on the human renal proximal tubular epithelial cell line, RPTEC/TERT1, treated with 10 and 35 μmol·liter(-1) of chloroacetaldehyde, a metabolite of the anti-cancer drug ifosfamide. Our study outlines the establishment of an automated and easy to use untargeted metabolomics workflow for HPLC-high resolution mass spectrometry data. Automated data analysis workflows based on open source software (OpenMS, KNIME) enabled a comprehensive and reproducible analysis of the complex and voluminous metabolomics data produced by the profiling approach. Time- and concentration-dependent responses were clearly evident in the metabolomic profiles. To obtain a more comprehensive picture of the mode of action, transcriptomics and proteomics data were also integrated. For toxicity profiling of chloroacetaldehyde, 428 and 317 metabolite features were detectable in positive and negative modes, respectively, after stringent removal of chemical noise and unstable signals. Changes upon treatment were explored using principal component analysis, and statistically significant differences were identified using linear models for microarray assays. The analysis revealed toxic effects only for the treatment with 35 μmol·liter(-1) for 3 and 14 days. The most regulated metabolites were glutathione and metabolites related to the oxidative stress response of the cells. These findings are corroborated by proteomics and transcriptomics data, which show, among other things, an activation of the Nrf2 and ATF4 pathways. PMID:26055719

  4. [Exploring the mechanism of rhizoma coptidis in treating type II diabetes mellitus based on metabolomics by gas chromatography-mass spectrometry].

    Science.gov (United States)

    Wang, Jing; Yuan, Zimin; Kong, Hongwei; Li, Yong; Lu, Xin; Xu, Guowang

    2012-01-01

    Metabolomics was used to explore the mechanism of Rhizoma coptidis in treating type II diabetes mellitus. The rat model of type II diabetes mellitus was constructed by an injection of streptozocin (40 mg/kg), along with diets of fat emulsion. The rats were divided into four groups, the control group, the model group, the Rhizoma coptidis group (10 g/kg) and the metformin group (0.08 g/kg). After the treatment for 30 d, blood samples were collected to test biomedical indexes, and 24 h urine samples were collected for the metabolomics experiment. In the Rhizoma coptidis group, fasting blood glucose (FBG), total cholesterol (TC) and total plasma triglycerides (TG) were significantly decreased by 59.26%, 58.66% and 42.18%, respectively, compared with those in the model group. Based on gas chromatography-mass spectrometry, a urinary metabolomics method was used to study the mechanism of Rhizoma coptidis in treating diabetes mellitus. Based on the principal component analysis, it was found that the model group and control group were separated into two different clusters. The Rhizoma coptidis group was located between the model group and the control group, closer to the control group. Twelve significantly changed metabolites of diabetes mellitus were detected and identified, including 4-methyl phenol, benzoic acid, aminomalonic acid, and so on. After diabetic rats were administered with Rhizoma coptidis, 7 metabolites were significantly changed, and L-ascorbic acid and aminomalonic acid which related with the oxidative stress were significantly regulated to normal. The pharmacological results showed that Rhizoma coptidis could display anti-hyperglycemic and anti-hyperlipidemic effects. The Rhizoma coptidis had antioxidation function in preventing the occurrence of complications with diabetes mellitus to some extent. The work illustrates that the metabolomics method is a useful tool to study the treatment mechanism of traditional Chinese medicine.

  5. Pattern Recognition and Pathway Analysis with Genetic Algorithms in Mass Spectrometry Based Metabolomics

    OpenAIRE

    Wei Zou; Vladimir V. Tolstikov

    2009-01-01

    A robust and complete workflow for metabolic profiling and data mining was described in detail. Three independent and complementary analytical techniques for metabolic profiling were applied: hydrophilic interaction chromatography (HILIC–LC–ESI–MS), reversed-phase liquid chromatography (RP–LC–ESI–MS), and gas chromatography (GC–TOF–MS) all coupled to mass spectrometry (MS). Unsupervised methods, such as principle component analysis (PCA) and clustering, and supervised methods, such as classif...

  6. Chemical Derivatization and Ultrahigh Resolution and Accurate Mass Spectrometry Strategies for "Shotgun" Lipidome Analysis.

    Science.gov (United States)

    Ryan, Eileen; Reid, Gavin E

    2016-09-20

    Lipids play critical structural and functional roles in the regulation of cellular homeostasis, and it is increasingly recognized that the disruption of lipid metabolism or signaling or both is associated with the onset and progression of certain metabolically linked diseases. As a result, the field of lipidomics has emerged to comprehensively identify and structurally characterize the diverse range of lipid species within a sample of interest and to quantitatively monitor their abundances under different physiological or pathological conditions. Mass spectrometry (MS) has become a critical enabling platform technology for lipidomic researchers. However, the presence of isobaric (i.e., same nominal mass) and isomeric (i.e., same exact mass) lipids within complex lipid extracts means that MS-based identification and quantification of individual lipid species remains a significant analytical challenge. Ultrahigh resolution and accurate mass spectrometry (UHRAMS) offers a convenient solution to the isobaric mass overlap problem, while a range of chromatographic separation, differential extraction, intrasource separation and selective ionization methods, or tandem mass spectrometry (MS/MS) strategies may be used to address some types of isomeric mass lipid overlaps. Alternatively, chemical derivatization strategies represent a more recent approach for the separation of lipids within complex mixtures, including for isomeric lipids. In this Account, we highlight the key components of a lipidomics workflow developed in our laboratory, whereby certain lipid classes or subclasses, namely, aminophospholipids and O-alk-1'-enyl (i.e., plasmalogen) ether-containing lipids, are shifted in mass following sequential functional group selective chemical derivatization reactions prior to "shotgun" nano-ESI-UHRAMS analysis, "targeted" MS/MS, and automated database searching. This combined derivatization and UHRAMS approach resolves both isobaric mass lipids and certain categories of

  7. Post-acquisition filtering of salt cluster artefacts for LC-MS based human metabolomic studies.

    Science.gov (United States)

    McMillan, A; Renaud, J B; Gloor, G B; Reid, G; Sumarah, M W

    2016-01-01

    Liquid chromatography-high resolution mass spectrometry (LC-MS) has emerged as one of the most widely used platforms for untargeted metabolomics due to its unparalleled sensitivity and metabolite coverage. Despite its prevalence of use, the proportion of true metabolites identified in a given experiment compared to background contaminants and ionization-generated artefacts remains poorly understood. Salt clusters are well documented artefacts of electrospray ionization MS, recognized by their characteristically high mass defects (for this work simply generalized as the decimal numbers after the nominal mass). Exploiting this property, we developed a method to identify and remove salt clusters from LC-MS-based human metabolomics data using mass defect filtering. By comparing the complete set of endogenous metabolites in the human metabolome database to actual plasma, urine and stool samples, we demonstrate that up to 28.5 % of detected features are likely salt clusters. These clusters occur irrespective of ionization mode, column type, sweep gas and sample type, but can be easily removed post-acquisition using a set of R functions presented here. Our mass defect filter removes unwanted noise from LC-MS metabolomics datasets, while retaining true metabolites, and requires only a list of m/z and retention time values. Reducing the number of features prior to statistical analyses will result in more accurate multivariate modeling and differential feature selection, as well as decreased reporting of unknowns that often constitute the largest proportion of human metabolomics data. PMID:27606010

  8. Identification of "Known Unknowns" Utilizing Accurate Mass Data and ChemSpider

    Science.gov (United States)

    Little, James L.; Williams, Antony J.; Pshenichnov, Alexey; Tkachenko, Valery

    2012-01-01

    In many cases, an unknown to an investigator is actually known in the chemical literature, a reference database, or an internet resource. We refer to these types of compounds as "known unknowns." ChemSpider is a very valuable internet database of known compounds useful in the identification of these types of compounds in commercial, environmental, forensic, and natural product samples. The database contains over 26 million entries from hundreds of data sources and is provided as a free resource to the community. Accurate mass mass spectrometry data is used to query the database by either elemental composition or a monoisotopic mass. Searching by elemental composition is the preferred approach. However, it is often difficult to determine a unique elemental composition for compounds with molecular weights greater than 600 Da. In these cases, searching by the monoisotopic mass is advantageous. In either case, the search results are refined by sorting the number of references associated with each compound in descending order. This raises the most useful candidates to the top of the list for further evaluation. These approaches were shown to be successful in identifying "known unknowns" noted in our laboratory and for compounds of interest to others.

  9. A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Stanley, Jeffrey R.; Adkins, Joshua N.; Slysz, Gordon W.; Monroe, Matthew E.; Purvine, Samuel O.; Karpievitch, Yuliya V.; Anderson, Gordon A.; Smith, Richard D.; Dabney, Alan R.

    2011-07-15

    High-throughput proteomics is rapidly evolving to require high mass measurement accuracy for a variety of different applications. Increased mass measurement accuracy in bottom-up proteomics specifically allows for an improved ability to distinguish and characterize detected MS features, which may in turn be identified by, e.g., matching to entries in a database for both precursor and fragmentation mass identification methods. Many tools exist with which to score the identification of peptides from LC-MS/MS measurements or to assess matches to an accurate mass and time (AMT) tag database, but these two calculations remain distinctly unrelated. Here we present a statistical method, Statistical Tools for AMT tag Confidence (STAC), which extends our previous work incorporating prior probabilities of correct sequence identification from LC-MS/MS, as well as the quality with which LC-MS features match AMT tags, to evaluate peptide identification confidence. Compared to existing tools, we are able to obtain significantly more high-confidence peptide identifications at a given false discovery rate and additionally assign confidence estimates to individual peptide identifications. Freely available software implementations of STAC are available in both command line and as a Windows graphical application.

  10. ACCURATE UNIVERSAL MODELS FOR THE MASS ACCRETION HISTORIES AND CONCENTRATIONS OF DARK MATTER HALOS

    International Nuclear Information System (INIS)

    A large amount of observations have constrained cosmological parameters and the initial density fluctuation spectrum to a very high accuracy. However, cosmological parameters change with time and the power index of the power spectrum dramatically varies with mass scale in the so-called concordance ΛCDM cosmology. Thus, any successful model for its structural evolution should work well simultaneously for various cosmological models and different power spectra. We use a large set of high-resolution N-body simulations of a variety of structure formation models (scale-free, standard CDM, open CDM, and ΛCDM) to study the mass accretion histories, the mass and redshift dependence of concentrations, and the concentration evolution histories of dark matter halos. We find that there is significant disagreement between the much-used empirical models in the literature and our simulations. Based on our simulation results, we find that the mass accretion rate of a halo is tightly correlated with a simple function of its mass, the redshift, parameters of the cosmology, and of the initial density fluctuation spectrum, which correctly disentangles the effects of all these factors and halo environments. We also find that the concentration of a halo is strongly correlated with the universe age when its progenitor on the mass accretion history first reaches 4% of its current mass. According to these correlations, we develop new empirical models for both the mass accretion histories and the concentration evolution histories of dark matter halos, and the latter can also be used to predict the mass and redshift dependence of halo concentrations. These models are accurate and universal: the same set of model parameters works well for different cosmological models and for halos of different masses at different redshifts, and in the ΛCDM case the model predictions match the simulation results very well even though halo mass is traced to about 0.0005 times the final mass, when

  11. Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance

    Science.gov (United States)

    Alves, Gelio; Wang, Guanghui; Ogurtsov, Aleksey Y.; Drake, Steven K.; Gucek, Marjan; Suffredini, Anthony F.; Sacks, David B.; Yu, Yi-Kuo

    2016-02-01

    Correct and rapid identification of microorganisms is the key to the success of many important applications in health and safety, including, but not limited to, infection treatment, food safety, and biodefense. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is challenging correct microbial identification because of the large number of choices present. To properly disentangle candidate microbes, one needs to go beyond apparent morphology or simple `fingerprinting'; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptidome profiles of microbes to better separate them and by designing an analysis method that yields accurate statistical significance. Here, we present an analysis pipeline that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using MS/MS data of 81 samples, each composed of a single known microorganism, that the proposed pipeline can correctly identify microorganisms at least at the genus and species levels. We have also shown that the proposed pipeline computes accurate statistical significances, i.e., E-values for identified peptides and unified E-values for identified microorganisms. The proposed analysis pipeline has been implemented in MiCId, a freely available software for Microorganism Classification and Identification. MiCId is available for download at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.

  12. SPECT-OPT multimodal imaging enables accurate evaluation of radiotracers for β-cell mass assessments.

    Science.gov (United States)

    Eter, Wael A; Parween, Saba; Joosten, Lieke; Frielink, Cathelijne; Eriksson, Maria; Brom, Maarten; Ahlgren, Ulf; Gotthardt, Martin

    2016-01-01

    Single Photon Emission Computed Tomography (SPECT) has become a promising experimental approach to monitor changes in β-cell mass (BCM) during diabetes progression. SPECT imaging of pancreatic islets is most commonly cross-validated by stereological analysis of histological pancreatic sections after insulin staining. Typically, stereological methods do not accurately determine the total β-cell volume, which is inconvenient when correlating total pancreatic tracer uptake with BCM. Alternative methods are therefore warranted to cross-validate β-cell imaging using radiotracers. In this study, we introduce multimodal SPECT - optical projection tomography (OPT) imaging as an accurate approach to cross-validate radionuclide-based imaging of β-cells. Uptake of a promising radiotracer for β-cell imaging by SPECT, (111)In-exendin-3, was measured by ex vivo-SPECT and cross evaluated by 3D quantitative OPT imaging as well as with histology within healthy and alloxan-treated Brown Norway rat pancreata. SPECT signal was in excellent linear correlation with OPT data as compared to histology. While histological determination of islet spatial distribution was challenging, SPECT and OPT revealed similar distribution patterns of (111)In-exendin-3 and insulin positive β-cell volumes between different pancreatic lobes, both visually and quantitatively. We propose ex vivo SPECT-OPT multimodal imaging as a highly accurate strategy for validating the performance of β-cell radiotracers. PMID:27080529

  13. Insulin sensitivity is reflected by characteristic metabolic fingerprints--a Fourier transform mass spectrometric non-targeted metabolomics approach.

    Directory of Open Access Journals (Sweden)

    Marianna Lucio

    Full Text Available BACKGROUND: A decline in body insulin sensitivity in apparently healthy individuals indicates a high risk to develop type 2 diabetes. Investigating the metabolic fingerprints of individuals with different whole body insulin sensitivity according to the formula of Matsuda, et al. (ISI(Matsuda by a non-targeted metabolomics approach we aimed a to figure out an unsuspicious and altered metabolic pattern, b to estimate a threshold related to these changes based on the ISI, and c to identify the metabolic pathways responsible for the discrimination of the two patterns. METHODOLOGY AND PRINCIPAL FINDINGS: By applying infusion ion cyclotron resonance Fourier transform mass spectrometry, we analyzed plasma of 46 non-diabetic subjects exhibiting high to low insulin sensitivities. The orthogonal partial least square model revealed a cluster of 28 individuals with alterations in their metabolic fingerprints associated with a decline in insulin sensitivity. This group could be separated from 18 subjects with an unsuspicious metabolite pattern. The orthogonal signal correction score scatter plot suggests a threshold of an ISI(Matsuda of 15 for the discrimination of these two groups. Of note, a potential subgroup represented by eight individuals (ISI(Matsuda value between 8.5 and 15 was identified in different models. This subgroup may indicate a metabolic transition state, since it is already located within the cluster of individuals with declined insulin sensitivity but the metabolic fingerprints still show some similarities with unaffected individuals (ISI >15. Moreover, the highest number of metabolite intensity differences between unsuspicious and altered metabolic fingerprints was detected in lipid metabolic pathways (arachidonic acid metabolism, metabolism of essential fatty acids and biosynthesis of unsaturated fatty acids, steroid hormone biosyntheses and bile acid metabolism, based on data evaluation using the metabolic annotation interface Mass

  14. Comprehensive and Comparative Metabolomic Profiling of Wheat, Barley, Oat and Rye Using Gas Chromatography-Mass Spectrometry and Advanced Chemometrics

    Directory of Open Access Journals (Sweden)

    Bekzod Khakimov

    2014-10-01

    Full Text Available Beyond the main bulk components of cereals such as the polysaccharides and proteins, lower concentration secondary metabolites largely contribute to the nutritional value. This paper outlines a comprehensive protocol for GC-MS metabolomic profiling of phenolics and organic acids in grains, the performance of which is demonstrated through a comparison of the metabolite profiles of the main northern European cereal crops: wheat, barley, oat and rye. Phenolics and organic acids were extracted using acidic hydrolysis, trimethylsilylated using a new method based on trimethylsilyl cyanide and analyzed by GC-MS. In order to extract pure metabolite peaks, the raw chromatographic data were processed by a multi-way decomposition method, Parallel Factor Analysis 2. This approach lead to the semi-quantitative detection of a total of 247 analytes, out of which 89 were identified based on RI and EI-MS library match. The cereal metabolome included 32 phenolics, 30 organic acids, 10 fatty acids, 11 carbohydrates and 6 sterols. The metabolome of the four cereals were compared in detail, including low concentration phenolics and organic acids. Rye and oat displayed higher total concentration of phenolic acids, but ferulic, caffeic and sinapinic acids and their esters were found to be the main phenolics in all four cereals. Compared to the previously reported methods, the outlined protocol provided an efficient and high throughput analysis of the cereal metabolome and the acidic hydrolysis improved the detection of conjugated phenolics.

  15. Cluster abundance in chameleon $f(R)$ gravity I: toward an accurate halo mass function prediction

    CERN Document Server

    Cataneo, Matteo; Lombriser, Lucas; Li, Baojiu

    2016-01-01

    We refine the mass and environment dependent spherical collapse model of chameleon $f(R)$ gravity by calibrating a phenomenological correction inspired by the parameterized post-Friedmann framework against high-resolution $N$-body simulations. We employ our method to predict the corresponding modified halo mass function, and provide fitting formulas to calculate the fractional enhancement of the $f(R)$ halo abundance with respect to that of General Relativity (GR) within a precision of $\\lesssim 5\\%$ from the results obtained in the simulations. Similar accuracy can be achieved for the full $f(R)$ mass function on the condition that the modeling of the reference GR abundance of halos is accurate at the percent level. We use our fits to forecast constraints on the additional scalar degree of freedom of the theory, finding that upper bounds competitive with current Solar System tests are within reach of cluster number count analyses from ongoing and upcoming surveys at much larger scales. Importantly, the flexi...

  16. Inductively-coupled plasma mass spectrometry in proteomics, metabolomics and metallomics studies.

    Science.gov (United States)

    Mounicou, Sandra; Szpunar, Joanna; Lobinski, Ryszard

    2010-01-01

    The potential of inductively-coupled plasma mass spectrometry (ICP-MS) and its complementarity to soft- ionization MS techniques are discussed in the context of the analysis for biomolecules. ICP-MS offers detection limits in the attomolar range, regardless of the molecular environment of the target element. The sensitivity is hardly affected by the sample matrix, chromatographic mobile phase, or co-eluted compounds. The abundance sensitivity over six decades and the linear dynamic range over nine decades make simultaneous multi-isotopic analysis routinely possible. The manuscript discusses the state-of-the-art of ICP-MS for the detection of proteins in gel electrophoresis and of peptides in 2D high-performance liquid chromatography. The possibilities of quantification to the degree of some post-translational modifications are highlighted. Attention is also paid to the role of ICP-MS in protein quantification via metal-coded labeling and to the use of differentially-labeled antibodies for the multiplexed biomarker analysis. The key role of ICP-MS in the emerging area of metallomics is briefly discussed.

  17. In-depth glycoproteomic characterization of γ-conglutin by high-resolution accurate mass spectrometry.

    Directory of Open Access Journals (Sweden)

    Silvia Schiarea

    Full Text Available The molecular characterization of bioactive food components is necessary for understanding the mechanisms of their beneficial or detrimental effects on human health. This study focused on γ-conglutin, a well-known lupin seed N-glycoprotein with health-promoting properties and controversial allergenic potential. Given the importance of N-glycosylation for the functional and structural characteristics of proteins, we studied the purified protein by a mass spectrometry-based glycoproteomic approach able to identify the structure, micro-heterogeneity and attachment site of the bound N-glycan(s, and to provide extensive coverage of the protein sequence. The peptide/N-glycopeptide mixtures generated by enzymatic digestion (with or without N-deglycosylation were analyzed by high-resolution accurate mass liquid chromatography-multi-stage mass spectrometry. The four main micro-heterogeneous variants of the single N-glycan bound to γ-conglutin were identified as Man2(Xyl (Fuc GlcNAc2, Man3(Xyl (Fuc GlcNAc2, GlcNAcMan3(Xyl (Fuc GlcNAc2 and GlcNAc 2Man3(Xyl (Fuc GlcNAc2. These carry both core β1,2-xylose and core α1-3-fucose (well known Cross-Reactive Carbohydrate Determinants, but corresponding fucose-free variants were also identified as minor components. The N-glycan was proven to reside on Asn131, one of the two potential N-glycosylation sites. The extensive coverage of the γ-conglutin amino acid sequence suggested three alternative N-termini of the small subunit, that were later confirmed by direct-infusion Orbitrap mass spectrometry analysis of the intact subunit.

  18. In-Depth Glycoproteomic Characterization of γ-Conglutin by High-Resolution Accurate Mass Spectrometry

    Science.gov (United States)

    Schiarea, Silvia; Arnoldi, Lolita; Fanelli, Roberto; De Combarieu, Eric; Chiabrando, Chiara

    2013-01-01

    The molecular characterization of bioactive food components is necessary for understanding the mechanisms of their beneficial or detrimental effects on human health. This study focused on γ-conglutin, a well-known lupin seed N-glycoprotein with health-promoting properties and controversial allergenic potential. Given the importance of N-glycosylation for the functional and structural characteristics of proteins, we studied the purified protein by a mass spectrometry-based glycoproteomic approach able to identify the structure, micro-heterogeneity and attachment site of the bound N-glycan(s), and to provide extensive coverage of the protein sequence. The peptide/N-glycopeptide mixtures generated by enzymatic digestion (with or without N-deglycosylation) were analyzed by high-resolution accurate mass liquid chromatography–multi-stage mass spectrometry. The four main micro-heterogeneous variants of the single N-glycan bound to γ-conglutin were identified as Man2(Xyl) (Fuc) GlcNAc2, Man3(Xyl) (Fuc) GlcNAc2, GlcNAcMan3(Xyl) (Fuc) GlcNAc2 and GlcNAc 2Man3(Xyl) (Fuc) GlcNAc2. These carry both core β1,2-xylose and core α1-3-fucose (well known Cross-Reactive Carbohydrate Determinants), but corresponding fucose-free variants were also identified as minor components. The N-glycan was proven to reside on Asn131, one of the two potential N-glycosylation sites. The extensive coverage of the γ-conglutin amino acid sequence suggested three alternative N-termini of the small subunit, that were later confirmed by direct-infusion Orbitrap mass spectrometry analysis of the intact subunit. PMID:24069245

  19. Response to weaning and dietary L-glutamine supplementation:metabolomic analysis in piglets by gas chromatography/mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    Ying-ping XIAO; Tian-xing WU; Qi-hua HONG; Jiang-ming SUN; An-guo CHEN; Cai-mei YANG; Xiao-yan LI

    2012-01-01

    A novel metabolomic method based on gas chromatography/mass spectrometry (GC-MS) was applied to determine the metabolites in the serum of piglets in response to weaning and dietary L-glutamine (Gln) supplementation.Thirty six 21-d-old piglets were randomly assigned into three groups.One group continued to suckle from the sows (suckling group),whereas the other two groups were weaned and their diets were supplemented with 1% (w/w) Gln or isonitrogenous L-alanine,respectively,representing Gin group or control group.Serum samples were collected to characterize metabolites after a 7-d treatment.Results showed that twenty metabolites were down-regulated signifi cantly (P<0.05) in control piglets compared with suckling ones.These data demonstrated that early weaning causes a wide range of metabolic changes across arginine and proline metabolism,aminosugar and nucleotide metabolism,galactose metabolism,glycerophospholipid metabolism,biosynthesis of unsaturated fatty acid,and fatty acid metabo lism.Dietary Gin supplementation increased the levels of creatinine,o-xylose,2-hydroxybutyric acid,palmitelaidic acid,and α-L- galactofuranose (P<0.05) in early weaned piglets,and were involved in the arginine and proline metabolism,carbohydrate metabolism,and fatty acid metabolism.A leave one out cross validation of random forest analysis indi cated that creatinine was the most important metabolite among the three groups.Notably,the concentration of craatinine in control piglets was decreased (P=0.00001) compared to the suckling piglets,and increased (P=0.0003) in Gin-supplemented piglets.A correlation network for weaned and suckling piglets revealed that eady weaning changed the metabolic pathways,leading to the abnormality of carbohydrate metabolism,amino acid metabolism,and lipid metabolism,which could be partially improved by dietary Gin supplementation.These findings provide fresh insight into the complex metabolic changes in response to early weaning and dietary Gin

  20. A Comprehensive Workflow of Mass Spectrometry-Based Untargeted Metabolomics in Cancer Metabolic Biomarker Discovery Using Human Plasma and Urine

    Directory of Open Access Journals (Sweden)

    Jianwen She

    2013-09-01

    Full Text Available Current available biomarkers lack sensitivity and/or specificity for early detection of cancer. To address this challenge, a robust and complete workflow for metabolic profiling and data mining is described in details. Three independent and complementary analytical techniques for metabolic profiling are applied: hydrophilic interaction liquid chromatography (HILIC–LC, reversed-phase liquid chromatography (RP–LC, and gas chromatography (GC. All three techniques are coupled to a mass spectrometer (MS in the full scan acquisition mode, and both unsupervised and supervised methods are used for data mining. The univariate and multivariate feature selection are used to determine subsets of potentially discriminative predictors. These predictors are further identified by obtaining accurate masses and isotopic ratios using selected ion monitoring (SIM and data-dependent MS/MS and/or accurate mass MSn ion tree scans utilizing high resolution MS. A list combining all of the identified potential biomarkers generated from different platforms and algorithms is used for pathway analysis. Such a workflow combining comprehensive metabolic profiling and advanced data mining techniques may provide a powerful approach for metabolic pathway analysis and biomarker discovery in cancer research. Two case studies with previous published data are adapted and included in the context to elucidate the application of the workflow.

  1. Fatty acids composition of Caenorhabditis elegans using accurate mass GCMS-QTOF.

    Science.gov (United States)

    Henry, Parise; Owopetu, Olufunmilayo; Adisa, Demilade; Nguyen, Thao; Anthony, Kevin; Ijoni-Animadu, David; Jamadar, Sakha; Abdel-Rahman, Fawzia; Saleh, Mahmoud A

    2016-08-01

    The free living nematode Caenorhabditis elegans is a proven model organism for lipid metabolism research. Total lipids of C. elegans were extracted using chloroform and methanol in 2:1 ratio (v/v). Fatty acids composition of the extracted total lipids was converted to their corresponding fatty acids methyl esters (FAMEs) and analyzed by gas chromatography/accurate mass quadrupole time of flight mass spectrometry using both electron ionization and chemical ionization techniques. Twenty-eight fatty acids consisting of 12 to 22 carbon atoms were identified, 65% of them were unsaturated. Fatty acids containing 12 to17 carbons were mostly saturated with stearic acid (18:0) as the major constituent. Several branched-chain fatty acids were identified. Methyl-14-methylhexadecanoate (iso- 17:0) was the major identified branched fatty acid. This is the first report to detect the intact molecular parent ions of the identified fatty acids in C. elegans using chemical ionization compared to electron ionization which produced fragmentations of the FAMEs. PMID:27166662

  2. Fatty acids composition of Caenorhabditis elegans using accurate mass GCMS-QTOF.

    Science.gov (United States)

    Henry, Parise; Owopetu, Olufunmilayo; Adisa, Demilade; Nguyen, Thao; Anthony, Kevin; Ijoni-Animadu, David; Jamadar, Sakha; Abdel-Rahman, Fawzia; Saleh, Mahmoud A

    2016-08-01

    The free living nematode Caenorhabditis elegans is a proven model organism for lipid metabolism research. Total lipids of C. elegans were extracted using chloroform and methanol in 2:1 ratio (v/v). Fatty acids composition of the extracted total lipids was converted to their corresponding fatty acids methyl esters (FAMEs) and analyzed by gas chromatography/accurate mass quadrupole time of flight mass spectrometry using both electron ionization and chemical ionization techniques. Twenty-eight fatty acids consisting of 12 to 22 carbon atoms were identified, 65% of them were unsaturated. Fatty acids containing 12 to17 carbons were mostly saturated with stearic acid (18:0) as the major constituent. Several branched-chain fatty acids were identified. Methyl-14-methylhexadecanoate (iso- 17:0) was the major identified branched fatty acid. This is the first report to detect the intact molecular parent ions of the identified fatty acids in C. elegans using chemical ionization compared to electron ionization which produced fragmentations of the FAMEs.

  3. Assessment of two complementary liquid chromatography coupled to high resolution mass spectrometry metabolomics strategies for the screening of anabolic steroid treatment in calves

    International Nuclear Information System (INIS)

    Anabolic steroids are banned in food producing livestock in Europe. Efficient methods based on mass spectrometry detection have been developed to ensure the control of such veterinary drug residues. Nevertheless, the use of 'cocktails' composed of mixtures of low amounts of several substances as well as the synthesis of new compounds of unknown structure prevent efficient prevention. New analytical tools able to detect such abuse are today mandatory. In this context, metabolomics may represent new emerging strategies for investigating the global physiological effects associated to a family of substances and therefore, to suspect the administration of steroids. The purpose of the present study was to set up, assess and compare two complementary mass spectrometry-based metabolomic strategies as new tools to screen for steroid abuse in cattle and demonstrate the feasibility of such approaches. The protocols were developed in two European laboratories in charge of residues analysis in the field of food safety. Apart from sample preparation, the global process was different in both laboratories from LC-HRMS fingerprinting to multivariate data analysis through data processing and involved both LC-Orbitrap-XCMS and UPLC-ToF-MS-MetAlign strategies. The reproducibility of both sample preparation and MS measurements were assessed in order to guarantee that any differences in the acquired fingerprints were not caused by analytical variability but reflect metabolome modifications upon steroids administration. The protocols were then applied to urine samples collected on a large group of animals consisting of 12 control calves and 12 calves administrated with a mixture of 17β-estradiol 3-benzoate and 17β-nandrolone laureate esters according to a protocol reflecting likely illegal practices. The modifications in urine profiles as indicators of steroid administration have been evaluated in this context and proved the suitability of the approach for discriminating anabolic

  4. Assessment of two complementary liquid chromatography coupled to high resolution mass spectrometry metabolomics strategies for the screening of anabolic steroid treatment in calves

    Energy Technology Data Exchange (ETDEWEB)

    Dervilly-Pinel, Gaud, E-mail: laberca@oniris-nantes.fr [ONIRIS, Ecole nationale veterinaire, agroalimentaire et de l' alimentation Nantes-Atlantique, Laboratoire d' Etude des Residus et Contaminants dans les Aliments (LABERCA), Atlanpole - La Chantrerie, BP 40706, Nantes F-44307 (France); Weigel, Stefan; Lommen, Arjen [RIKILT - Institute of Food Safety, Wageningen UR, P.O. Box 230, 6700 AE Wageningen (Netherlands); Chereau, Sylvain; Rambaud, Lauriane [ONIRIS, Ecole nationale veterinaire, agroalimentaire et de l' alimentation Nantes-Atlantique, Laboratoire d' Etude des Residus et Contaminants dans les Aliments (LABERCA), Atlanpole - La Chantrerie, BP 40706, Nantes F-44307 (France); Essers, Martien [RIKILT - Institute of Food Safety, Wageningen UR, P.O. Box 230, 6700 AE Wageningen (Netherlands); Antignac, Jean-Philippe [ONIRIS, Ecole nationale veterinaire, agroalimentaire et de l' alimentation Nantes-Atlantique, Laboratoire d' Etude des Residus et Contaminants dans les Aliments (LABERCA), Atlanpole - La Chantrerie, BP 40706, Nantes F-44307 (France); Nielen, Michel W.F. [RIKILT - Institute of Food Safety, Wageningen UR, P.O. Box 230, 6700 AE Wageningen (Netherlands); Wageningen University, Laboratory of Organic Chemistry, Wageningen (Netherlands); Le Bizec, Bruno [ONIRIS, Ecole nationale veterinaire, agroalimentaire et de l' alimentation Nantes-Atlantique, Laboratoire d' Etude des Residus et Contaminants dans les Aliments (LABERCA), Atlanpole - La Chantrerie, BP 40706, Nantes F-44307 (France)

    2011-08-26

    Anabolic steroids are banned in food producing livestock in Europe. Efficient methods based on mass spectrometry detection have been developed to ensure the control of such veterinary drug residues. Nevertheless, the use of 'cocktails' composed of mixtures of low amounts of several substances as well as the synthesis of new compounds of unknown structure prevent efficient prevention. New analytical tools able to detect such abuse are today mandatory. In this context, metabolomics may represent new emerging strategies for investigating the global physiological effects associated to a family of substances and therefore, to suspect the administration of steroids. The purpose of the present study was to set up, assess and compare two complementary mass spectrometry-based metabolomic strategies as new tools to screen for steroid abuse in cattle and demonstrate the feasibility of such approaches. The protocols were developed in two European laboratories in charge of residues analysis in the field of food safety. Apart from sample preparation, the global process was different in both laboratories from LC-HRMS fingerprinting to multivariate data analysis through data processing and involved both LC-Orbitrap-XCMS and UPLC-ToF-MS-MetAlign strategies. The reproducibility of both sample preparation and MS measurements were assessed in order to guarantee that any differences in the acquired fingerprints were not caused by analytical variability but reflect metabolome modifications upon steroids administration. The protocols were then applied to urine samples collected on a large group of animals consisting of 12 control calves and 12 calves administrated with a mixture of 17{beta}-estradiol 3-benzoate and 17{beta}-nandrolone laureate esters according to a protocol reflecting likely illegal practices. The modifications in urine profiles as indicators of steroid administration have been evaluated in this context and proved the suitability of the approach for

  5. Quantitative analysis of amino acids and acylcarnitines combined with untargeted metabolomics using ultra-high performance liquid chromatography and quadrupole time-of-flight mass spectrometry.

    Science.gov (United States)

    Roy, Cynthia; Tremblay, Pierre-Yves; Bienvenu, Jean-François; Ayotte, Pierre

    2016-08-01

    Metabolomics is an "omic" technique being increasingly used in epidemiological and clinical studies. We developed a method combining untargeted metabolomics with the quantitative determination of eight amino acids (AA) and eight acylcarnitines (AC) in plasma using ultra-high pressure liquid chromatography (UHPLC), electrospray ionization (ESI) and quadrupole time-of-flight mass spectrometry (QTOFMS). Separation of metabolites is performed by ion-pair reverse phase UHPLC using a HSS T3 column (2.1×100mm, 100Å, 1.8μm particle size) and formic acid-ammonium acetate-heptafluorobutyric acid in water and formic acid-ammonium acetate in methanol as mobile phases. Metabolite identification and quantification are achieved using a QTOFMS operating in ESI-positive and full-scan mode along with MS(E) acquisition of fragmentation patterns. Targeted metabolites are quantified using the appropriate labeled standards and include branched-chain AA (leucine, isoleucine, valine), aromatic AA (phenylalanine, tyrosine) as well as acetylcarnitine and propionylcarnitine, which have been identified as biomarkers of future cardiometabolic disease risk. The inter-day precision (relative standard deviation) for the targeted method was <15% for all but one metabolite and accuracy (bias) of amino acids ranged from 0.5% to 13.9% using SRM 1950 as the external standard. Untargeted metabolomics in 30 plasma samples from the general Canadian population revealed 5018 features, of which 48 metabolites were identified using the MZmine 2.19 software including 23 by our in-house library that comprises 671 annotated metabolites. SRM 1950 analysis revealed 11,684 features, among which 154 metabolites were identified. Our method is currently applied in several epidemiological studies to better characterize cardiometabolic diseases and identify new biomarkers for disease prevention. PMID:27240302

  6. Galaxy And Mass Assembly: accurate panchromatic photometry from optical priors using LAMBDAR

    Science.gov (United States)

    Wright, A. H.; Robotham, A. S. G.; Bourne, N.; Driver, S. P.; Dunne, L.; Maddox, S. J.; Alpaslan, M.; Andrews, S. K.; Bauer, A. E.; Bland-Hawthorn, J.; Brough, S.; Brown, M. J. I.; Clarke, C.; Cluver, M.; Davies, L. J. M.; Grootes, M. W.; Holwerda, B. W.; Hopkins, A. M.; Jarrett, T. H.; Kafle, P. R.; Lange, R.; Liske, J.; Loveday, J.; Moffett, A. J.; Norberg, P.; Popescu, C. C.; Smith, M.; Taylor, E. N.; Tuffs, R. J.; Wang, L.; Wilkins, S. M.

    2016-07-01

    We present the Lambda Adaptive Multi-Band Deblending Algorithm in R (LAMBDAR), a novel code for calculating matched aperture photometry across images that are neither pixel- nor PSF-matched, using prior aperture definitions derived from high-resolution optical imaging. The development of this program is motivated by the desire for consistent photometry and uncertainties across large ranges of photometric imaging, for use in calculating spectral energy distributions. We describe the program, specifically key features required for robust determination of panchromatic photometry: propagation of apertures to images with arbitrary resolution, local background estimation, aperture normalization, uncertainty determination and propagation, and object deblending. Using simulated images, we demonstrate that the program is able to recover accurate photometric measurements in both high-resolution, low-confusion, and low-resolution, high-confusion, regimes. We apply the program to the 21-band photometric data set from the Galaxy And Mass Assembly (GAMA) Panchromatic Data Release (PDR; Driver et al. 2016), which contains imaging spanning the far-UV to the far-IR. We compare photometry derived from LAMBDAR with that presented in Driver et al. (2016), finding broad agreement between the data sets. None the less, we demonstrate that the photometry from LAMBDAR is superior to that from the GAMA PDR, as determined by a reduction in the outlier rate and intrinsic scatter of colours in the LAMBDAR data set. We similarly find a decrease in the outlier rate of stellar masses and star formation rates using LAMBDAR photometry. Finally, we note an exceptional increase in the number of UV and mid-IR sources able to be constrained, which is accompanied by a significant increase in the mid-IR colour-colour parameter-space able to be explored.

  7. A powerful methodological approach combining headspace solid phase microextraction, mass spectrometry and multivariate analysis for profiling the volatile metabolomic pattern of beer starting raw materials.

    Science.gov (United States)

    Gonçalves, João L; Figueira, José A; Rodrigues, Fátima P; Ornelas, Laura P; Branco, Ricardo N; Silva, Catarina L; Câmara, José S

    2014-10-01

    The volatile metabolomic patterns from different raw materials commonly used in beer production, namely barley, corn and hop-derived products - such as hop pellets, hop essential oil from Saaz variety and tetra-hydro isomerized hop extract (tetra hop), were established using a suitable analytical procedure based on dynamic headspace solid-phase microextraction (HS-SPME) followed by thermal desorption gas chromatography-quadrupole mass spectrometry detection (GC-qMS). Some SPME extraction parameters were optimized. The best results, in terms of maximum signal recorded and number of isolated metabolites, were obtained with a 50/30 μm DVB/CAR/PDMS coating fiber at 40 °C for 30 min. A set of 152 volatile metabolites comprising ketones (27), sesquiterpenes (26), monoterpenes (19), aliphatic esters (19), higher alcohols (15), aldehydes (11), furan compounds (11), aliphatic fatty acids (9), aliphatic hydrocarbons (8), sulphur compounds (5) and nitrogen compounds (2) were positively identified. Each raw material showed a specific volatile metabolomic profile. Monoterpenes in hop essential oil and corn, sesquiterpenes in hop pellets, ketones in tetra hop and aldehydes and sulphur compounds in barley were the predominant chemical families in the targeted beer raw materials. β-Myrcene was the most dominant volatile metabolite in hop essential oil, hop pellets and corn samples while, in barley, the predominant volatile metabolites were dimethyl sulphide and 3-methylbutanal and, in tetra hop, 6-methyl-2-pentanone and 4-methyl-2-pentanone. Principal component analysis (PCA) showed natural sample grouping among beer raw materials.

  8. Application of a novel metabolomic approach based on atmospheric pressure photoionization mass spectrometry using flow injection analysis for the study of Alzheimer's disease.

    Science.gov (United States)

    González-Domínguez, Raúl; García-Barrera, Tamara; Gómez-Ariza, José Luis

    2015-01-01

    The use of atmospheric pressure photoionization is not widespread in metabolomics, despite its considerable potential for the simultaneous analysis of compounds with diverse polarities. This work considers the development of a novel analytical approach based on flow injection analysis and atmospheric pressure photoionization mass spectrometry for rapid metabolic screening of serum samples. Several experimental parameters were optimized, such as type of dopant, flow injection solvent, and their flows, given that a careful selection of these variables is mandatory for a comprehensive analysis of metabolites. Toluene and methanol were the most suitable dopant and flow injection solvent, respectively. Moreover, analysis in negative mode required higher solvent and dopant flows (100 µl min(-1) and 40 µl min(-1), respectively) compared to positive mode (50 µl min(-1) and 20 µl min(-1)). Then, the optimized approach was used to elucidate metabolic alterations associated with Alzheimer's disease. Thereby, results confirm the increase of diacylglycerols, ceramides, ceramide-1-phosphate and free fatty acids, indicating membrane destabilization processes, and reduction of fatty acid amides and several neurotransmitters related to impairments in neuronal transmission, among others. Therefore, it could be concluded that this metabolomic tool presents a great potential for analysis of biological samples, considering its high-throughput screening capability, fast analysis and comprehensive metabolite coverage.

  9. The Megamaser Cosmology Project. III. Accurate Masses of Seven Supermassive Black Holes in Active Galaxies with Circumnuclear Megamaser Disks

    Science.gov (United States)

    Kuo, C. Y.; Braatz, J. A.; Condon, J. J.; Impellizzeri, C. M. V.; Lo, K. Y.; Zaw, I.; Schenker, M.; Henkel, C.; Reid, M. J.; Greene, J. E.

    2011-01-01

    Observations of H2O masers from circumnuclear disks in active galaxies for the Megamaser Cosmology Project (MCP) allow accurate measurement of the mass of supermassive black holes (BH) in these galaxies. We present the Very Long Baseline Interferometry images and kinematics of water maser emission in six active galaxies: NGC 1194, NGC 2273, NGC 2960 (Mrk 1419), NGC 4388, NGC 6264 and NGC 6323. We use the Keplerian rotation curves of these six megamaser galaxies, plus a seventh previously published, to determine accurate enclosed masses within the central ~0.3 pc of these galaxies, smaller than the radius of the sphere of influence of the central mass in all cases. We also set lower limits to the central mass densities of between 0.12 × 1010 and 61 × 1010 M sun pc-3. For six of the seven disks, the high central densities rule out clusters of stars or stellar remnants as the central objects, and this result further supports our assumption that the enclosed mass can be attributed predominantly to a supermassive BH. The seven BHs have masses ranging between 0.75 × 107 and 6.5 × 107 M sun, with the mass errors dominated by the uncertainty of the Hubble constant. We compare the megamaser BH mass determination with BH mass measured from the virial estimation method. The virial estimation BH mass in four galaxies is consistent with the megamaser BH mass, but the virial mass uncertainty is much greater. Circumnuclear megamaser disks allow the best mass determination of the central BH mass in external galaxies and significantly improve the observational basis at the low-mass end of the M-σsstarf relation. The M-σsstarf relation may not be a single, low-scatter power law as originally proposed. MCP observations continue and we expect to obtain more maser BH masses in the future.

  10. Screening and confirmation criteria for hormone residue analysis using liquid chromatography accurate mass time-of-flight, Fourier transform ion cyclotron resonance and orbitrap mass spectrometry techniques

    NARCIS (Netherlands)

    Nielen, M.W.F.; Engelen, M.C. van; Zuiderent, R.; Ramaker, R.

    2007-01-01

    An emerging trend is recognised in hormone and veterinary drug residue analysis from liquid chromatography tandem mass spectrometry (LC/MS/MS) based screening and confirmation towards accurate mass alternatives such as LC coupled with time-of-flight (TOF), Fourier transform ion cyclotron resonance (

  11. Gas chromatography-mass spectrometry metabolomics of goat milk with different polymorphism at the αS1-casein genotype locus.

    Science.gov (United States)

    Caboni, Pierluigi; Murgia, Antonio; Porcu, Alessandra; Demuru, Martina; Pulina, Giuseppe; Nudda, Anna

    2016-08-01

    Hyphenated gas chromatography-mass spectrometry (GC-MS) and multivariate data analysis techniques were used to uncover milk metabolite differences in different αS1-casein genotypes of goats. By a discriminant GC-MS metabolomics approach, we characterized milk polar metabolites of 28 goats. Animals were selected on the basis of their genotypes as 7 goats classified heterozygous for weak or null alleles, 5 for the genotype EE, 9 for the genotypes AE and BE, and finally 7 for the strong genotype AA. Low molecular weight polar metabolite profile was tightly related to the different goat genotypes, milk production, and protein levels. Results of multivariate statistical analysis of GC-MS data demonstrate that different heterozygous and homozygous genotypes expressed different metabolites such as citric and aconitic acid for the strong allele class with different sugars and polyols for the weak class. PMID:27289154

  12. Accurate Quantification of Lipid Species by Electrospray Ionization Mass Spectrometry — Meets a Key Challenge in Lipidomics

    Directory of Open Access Journals (Sweden)

    Kui Yang

    2011-11-01

    Full Text Available Electrospray ionization mass spectrometry (ESI-MS has become one of the most popular and powerful technologies to identify and quantify individual lipid species in lipidomics. Meanwhile, quantitative analysis of lipid species by ESI-MS has also become a major obstacle to meet the challenges of lipidomics. Herein, we discuss the principles, advantages, and possible limitations of different mass spectrometry-based methodologies for lipid quantification, as well as a few practical issues important for accurate quantification of individual lipid species. Accordingly, accurate quantification of individual lipid species, one of the key challenges in lipidomics, can be practically met.

  13. Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients.

    Science.gov (United States)

    Tsuruoka, Mayuko; Hara, Junko; Hirayama, Akiyoshi; Sugimoto, Masahiro; Soga, Tomoyoshi; Shankle, William R; Tomita, Masaru

    2013-10-01

    Despite increasing global prevalence, the precise pathogenesis and terms for objective diagnosis of neurodegenerative dementias remain controversial, and comprehensive understanding of the disease remains lacking. Here, we conducted metabolomic analysis of serum and saliva obtained from patients with neurodegenerative dementias (n = 10), including Alzheimer's disease, frontotemporal lobe dementia, and Lewy body disease, as well as from age-matched healthy controls (n = 9). Using CE-TOF-MS, six metabolites in serum (β-alanine, creatinine, hydroxyproline, glutamine, iso-citrate, and cytidine) and two in saliva (arginine and tyrosine) were significantly different between dementias and controls. Using multivariate analysis, serum was confirmed as a more efficient biological fluid for diagnosis compared to saliva; additionally, 45 metabolites in total were identified as candidate markers that could discriminate at least one pair of diagnostic groups from the healthy control group. These metabolites possibly provide an objective method for diagnosing dementia-type by multiphase screening. Moreover, diagnostic-type-dependent differences were observed in several tricarboxylic acid cycle compounds detected in serum, indicating that some pathways in glucose metabolism may be altered in dementia patients. This pilot study revealed novel alterations in metabolomic profiles between various neurodegenerative dementias, which would contribute to etiological investigations.

  14. Simultaneous measurement in mass and mass/mass mode for accurate qualitative and quantitative screening analysis of pharmaceuticals in river water.

    Science.gov (United States)

    Martínez Bueno, M J; Ulaszewska, Maria M; Gomez, M J; Hernando, M D; Fernández-Alba, A R

    2012-09-21

    A new approach for the analysis of pharmaceuticals (target and non-target) in water by LC-QTOF-MS is described in this work. The study has been designed to assess the performance of the simultaneous quantitative screening of target compounds, and the qualitative analysis of non-target analytes, in just one run. The features of accurate mass full scan mass spectrometry together with high MS/MS spectral acquisition rates - by means of information dependent acquisition (IDA) - have demonstrated their potential application in this work. Applying this analytical strategy, an identification procedure is presented based on library searching for compounds which were not included a priori in the analytical method as target compounds, thus allowing their characterization by data processing of accurate mass measurements in MS and MS/MS mode. The non-target compounds identified in river water samples were ketorolac, trazodone, fluconazole, metformin and venlafaxine. Simultaneously, this strategy allowed for the identification of other compounds which were not included in the library by screening the highest intensity peaks detected in the samples and by analysis of the full scan TOF-MS, isotope pattern and MS/MS spectra - the example of loratadine (histaminergic) is described. The group of drugs of abuse selected as target compounds for evaluation included analgesics, opioids and psychostimulants. Satisfactory results regarding sensitivity and linearity of the developed method were obtained. Limits of detection for the selected target compounds were from 0.003 to 0.01 μg/L and 0.01 to 0.5 μg/L, in MS and MS/MS mode, respectively - by direct sample injection of 100 μL.

  15. Accurate screening for synthetic preservatives in beverage using high performance liquid chromatography with time-of-flight mass spectrometry.

    Science.gov (United States)

    Li, Xiu Qin; Zhang, Feng; Sun, Yan Yan; Yong, Wei; Chu, Xiao Gang; Fang, Yan Yan; Zweigenbaum, Jerry

    2008-02-11

    In this study, liquid chromatography time-of-flight mass spectrometry (HPLC/TOF-MS) is applied to qualitation and quantitation of 18 synthetic preservatives in beverage. The identification by HPLC/TOF-MS is accomplished with the accurate mass (the subsequent generated empirical formula) of the protonated molecules [M+H]+ or the deprotonated molecules [M-H]-, along with the accurate mass of their main fragment ions. In order to obtain sufficient sensitivity for quantitation purposes (using the protonated or deprotonated molecule) and additional qualitative mass spectrum information provided by the fragments ions, segment program of fragmentor voltages is designed in positive and negative ion mode, respectively. Accurate mass measurements are highly useful in the complex sample analyses since they allow us to achieve a high degree of specificity, often needed when other interferents are present in the matrix. The mass accuracy typically obtained is routinely better than 3 ppm. The 18 compounds behave linearly in the 0.005-5.0mg.kg(-1) concentration range, with correlation coefficient >0.996. The recoveries at the tested concentrations of 1.0mg.kg(-1)-100mg.kg(-1) are 81-106%, with coefficients of variation preservatives in foodstuff. The method is suitable for routine quantitative and qualitative analyses of synthetic preservatives in foodstuff.

  16. Accurate screening for synthetic preservatives in beverage using high performance liquid chromatography with time-of-flight mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Li Xiuqin; Zhang Feng; Sun Yanyan; Yong Wei [Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Jia 3, Gaobeidian North Road, Beijing 100025 (China); Chu Xiaogang [Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Jia 3, Gaobeidian North Road, Beijing 100025 (China)], E-mail: lixq_sypu@yahoo.com; Fang Yanyan; Zweigenbaum, Jerry [Agilent Technologies, Inc., 2850 Centerville Road, Wilmington, Delaware (United States)

    2008-02-11

    In this study, liquid chromatography time-of-flight mass spectrometry (HPLC/TOF-MS) is applied to qualitation and quantitation of 18 synthetic preservatives in beverage. The identification by HPLC/TOF-MS is accomplished with the accurate mass (the subsequent generated empirical formula) of the protonated molecules [M + H]+ or the deprotonated molecules [M - H]-, along with the accurate mass of their main fragment ions. In order to obtain sufficient sensitivity for quantitation purposes (using the protonated or deprotonated molecule) and additional qualitative mass spectrum information provided by the fragments ions, segment program of fragmentor voltages is designed in positive and negative ion mode, respectively. Accurate mass measurements are highly useful in the complex sample analyses since they allow us to achieve a high degree of specificity, often needed when other interferents are present in the matrix. The mass accuracy typically obtained is routinely better than 3 ppm. The 18 compounds behave linearly in the 0.005-5.0 mg.kg{sup -1} concentration range, with correlation coefficient >0.996. The recoveries at the tested concentrations of 1.0 mg.kg{sup -1}-100 mg.kg{sup -1} are 81-106%, with coefficients of variation <7.5%. Limits of detection (LODs) range from 0.0005 to 0.05 mg.kg{sup -1}, which are far below the required maximum residue level (MRL) for these preservatives in foodstuff. The method is suitable for routine quantitative and qualitative analyses of synthetic preservatives in foodstuff.

  17. Metabolomics in transfusion medicine.

    Science.gov (United States)

    Nemkov, Travis; Hansen, Kirk C; Dumont, Larry J; D'Alessandro, Angelo

    2016-04-01

    Biochemical investigations on the regulatory mechanisms of red blood cell (RBC) and platelet (PLT) metabolism have fostered a century of advances in the field of transfusion medicine. Owing to these advances, storage of RBCs and PLT concentrates has become a lifesaving practice in clinical and military settings. There, however, remains room for improvement, especially with regard to the introduction of novel storage and/or rejuvenation solutions, alternative cell processing strategies (e.g., pathogen inactivation technologies), and quality testing (e.g., evaluation of novel containers with alternative plasticizers). Recent advancements in mass spectrometry-based metabolomics and systems biology, the bioinformatics integration of omics data, promise to speed up the design and testing of innovative storage strategies developed to improve the quality, safety, and effectiveness of blood products. Here we review the currently available metabolomics technologies and briefly describe the routine workflow for transfusion medicine-relevant studies. The goal is to provide transfusion medicine experts with adequate tools to navigate through the otherwise overwhelming amount of metabolomics data burgeoning in the field during the past few years. Descriptive metabolomics data have represented the first step omics researchers have taken into the field of transfusion medicine. However, to up the ante, clinical and omics experts will need to merge their expertise to investigate correlative and mechanistic relationships among metabolic variables and transfusion-relevant variables, such as 24-hour in vivo recovery for transfused RBCs. Integration with systems biology models will potentially allow for in silico prediction of metabolic phenotypes, thus streamlining the design and testing of alternative storage strategies and/or solutions.

  18. Accurate and precise 40Ar/39Ar dating by high-resolution, multi-collection, mass spectrometry

    DEFF Research Database (Denmark)

    Storey, Michael; Rivera, Tiffany; Flude, Stephanie

    analog enabling precise measurement of very small 36Ar signals for accurate correction for atmospheric-derived 40Ar; (iii) higher mass resolution allows pseudo resolution of hydrocarbon isobaric interferences from 36Ar through to 40Ar; (iv) multi-collection, allowing more data to be gathered in a fixed...

  19. Discrimination of Citrus reticulata Blanco and Citrus reticulata 'Chachi' by gas chromatograph-mass spectrometry based metabolomics approach.

    Science.gov (United States)

    Duan, Li; Guo, Long; Dou, Li-Li; Zhou, Chang-Lin; Xu, Feng-Guo; Zheng, Guo-Dong; Li, Ping; Liu, E-Hu

    2016-12-01

    Citri Reticulatae Pericarpium, mainly including the pericarp of Citrus reticulata Blanco and the pericarp of Citrus reticulata 'Chachi', has been consumed daily as food and dietary supplement for centuries. In this study, GC-MS based metabolomics was employed to compare comprehensively the volatile constituents in Citrus reticulata Blanco and Citrus reticulata 'Chachi'. Principal component analysis and orthogonal partial least squares discrimination analysis indicated that samples could be distinguished effectively from one another. Fifteen metabolites were finally identified for use as chemical markers in discrimination of Citri Reticulatae Pericarpium samples. The antimicrobial activity against Gram-negative and Gram-positive bacteria of the volatile oil from Citrus reticulata Blanco and Citrus reticulata 'Chachi' was investigated preliminarily. PMID:27374515

  20. A powerful methodological approach combining headspace solid phase microextraction, mass spectrometry and multivariate analysis for profiling the volatile metabolomic pattern of beer starting raw materials.

    Science.gov (United States)

    Gonçalves, João L; Figueira, José A; Rodrigues, Fátima P; Ornelas, Laura P; Branco, Ricardo N; Silva, Catarina L; Câmara, José S

    2014-10-01

    The volatile metabolomic patterns from different raw materials commonly used in beer production, namely barley, corn and hop-derived products - such as hop pellets, hop essential oil from Saaz variety and tetra-hydro isomerized hop extract (tetra hop), were established using a suitable analytical procedure based on dynamic headspace solid-phase microextraction (HS-SPME) followed by thermal desorption gas chromatography-quadrupole mass spectrometry detection (GC-qMS). Some SPME extraction parameters were optimized. The best results, in terms of maximum signal recorded and number of isolated metabolites, were obtained with a 50/30 μm DVB/CAR/PDMS coating fiber at 40 °C for 30 min. A set of 152 volatile metabolites comprising ketones (27), sesquiterpenes (26), monoterpenes (19), aliphatic esters (19), higher alcohols (15), aldehydes (11), furan compounds (11), aliphatic fatty acids (9), aliphatic hydrocarbons (8), sulphur compounds (5) and nitrogen compounds (2) were positively identified. Each raw material showed a specific volatile metabolomic profile. Monoterpenes in hop essential oil and corn, sesquiterpenes in hop pellets, ketones in tetra hop and aldehydes and sulphur compounds in barley were the predominant chemical families in the targeted beer raw materials. β-Myrcene was the most dominant volatile metabolite in hop essential oil, hop pellets and corn samples while, in barley, the predominant volatile metabolites were dimethyl sulphide and 3-methylbutanal and, in tetra hop, 6-methyl-2-pentanone and 4-methyl-2-pentanone. Principal component analysis (PCA) showed natural sample grouping among beer raw materials. PMID:24799238

  1. Physical consequences of the alpha/beta rule which accurately calculates particle masses

    International Nuclear Information System (INIS)

    Using the fine structure constant α (=1/137.036), the proton vs. electron mass ratio β (= 1836.2) and the integers m and n, the α/β rule: mparticle = α-n x β m x 27.2 eV/c2 allows almost exact calculation of particle masses. (K.O.Greulich, DPG Spring meeting 2014, Mainz, T99.4) With n=2, m=0 the electron mass becomes 510.79 keV/c2 (experimental 511 keV/c2) With n=2, m=1 the proton mass is 937.9 MeV/c2 (literature 938.3 MeV/c2). For n=3 and m=1 a particle with 128.6 GeV/c2 close to the reported Higgs mass, is expected. For n=14 and m=-1 the Planck mass results. The calculated masses for gauge bosons and for quarks have similar accuracy. All masses fit into the same scheme (the alpha/beta rule), indicating that non of these particle masses play an extraordinary role. Particularly, the Higgs Boson, often termed the *God particle* plays in this sense no extraordinary role. In addition, particle masses are intimately correlated with the fine structure constant α. If particle masses have been constant over all times, α must have been constant over these times. In addition, the ionization energy of the hydrogen atom (13.6 eV) needs to have been constant if particle masses have been unchanged or vice versa. In conclusion, the α/β rule needs to be taken into account when cosmological models are developed.

  2. Physical consequences of the alpha/beta rule which accurately calculates particle masses

    Energy Technology Data Exchange (ETDEWEB)

    Greulich, Karl Otto [Fritz Lipmann Institute, Beutenbergstr.11, D07745 Jena (Germany)

    2015-07-01

    Using the fine structure constant α (=1/137.036), the proton vs. electron mass ratio β (= 1836.2) and the integers m and n, the α/β rule: m{sub particle} = α{sup -n} x β m x 27.2 eV/c{sup 2} allows almost exact calculation of particle masses. (K.O.Greulich, DPG Spring meeting 2014, Mainz, T99.4) With n=2, m=0 the electron mass becomes 510.79 keV/c{sup 2} (experimental 511 keV/c{sup 2}) With n=2, m=1 the proton mass is 937.9 MeV/c{sup 2} (literature 938.3 MeV/c{sup 2}). For n=3 and m=1 a particle with 128.6 GeV/c{sup 2} close to the reported Higgs mass, is expected. For n=14 and m=-1 the Planck mass results. The calculated masses for gauge bosons and for quarks have similar accuracy. All masses fit into the same scheme (the alpha/beta rule), indicating that non of these particle masses play an extraordinary role. Particularly, the Higgs Boson, often termed the *God particle* plays in this sense no extraordinary role. In addition, particle masses are intimately correlated with the fine structure constant α. If particle masses have been constant over all times, α must have been constant over these times. In addition, the ionization energy of the hydrogen atom (13.6 eV) needs to have been constant if particle masses have been unchanged or vice versa. In conclusion, the α/β rule needs to be taken into account when cosmological models are developed.

  3. Polyphenol Identification Based on Systematic and Robust High-Resolution Accurate Mass Spectroscopy Fragmentation

    NARCIS (Netherlands)

    Hooft, van der J.J.J.; Vervoort, J.J.M.; Bino, R.J.; Beekwilder, M.J.; Vos, de R.C.H.

    2011-01-01

    High-mass resolution multi-stage mass spectrometry (MSn) fragmentation was tested for differentiation and identification of metabolites, using a series of 121 polyphenolic molecules. The MSn fragmentation approach is based on the systematic breakdown of compounds, forming a so-called spectral tree.

  4. Identification of Plasma Metabolomic Profiling for Diagnosis of Esophageal Squamous-Cell Carcinoma Using an UPLC/TOF/MS Platform

    OpenAIRE

    Lihong Yin; Enchun Pan; Wei Guo; Yuepu Pu; Yi Wang; Xiaobo Li; Yuan Peng; Ran Liu

    2013-01-01

    Epidemiological studies indicated that esophageal squamous-cell carcinoma (ESCC) is still one of the most common causes of cancer incidence in the world. Searching for valuable markers including circulating endogenous metabolites associated with the risk of esophageal cancer, is extremely important A comparative metabolomics study was performed by using ultraperformance liquid chromatography-electrospray ionization-accurate mass time-of-flight mass spectrometry to analyze 53 pairs of plasma s...

  5. A simple and accurate model for Love wave based sensors: Dispersion equation and mass sensitivity

    OpenAIRE

    Jiansheng Liu

    2014-01-01

    Dispersion equation is an important tool for analyzing propagation properties of acoustic waves in layered structures. For Love wave (LW) sensors, the dispersion equation with an isotropic-considered substrate is too rough to get accurate solutions; the full dispersion equation with a piezoelectric-considered substrate is too complicated to get simple and practical expressions for optimizing LW-based sensors. In this work, a dispersion equation is introduced for Love waves in a layered struct...

  6. Comparative evaluation of eight software programs for alignment of gas chromatography-mass spectrometry chromatograms in metabolomics experiments.

    Science.gov (United States)

    Niu, Weihuan; Knight, Elisa; Xia, Qingyou; McGarvey, Brian D

    2014-12-29

    Since retention times of compounds in GC-MS chromatograms always vary slightly from chromatogram to chromatogram, it is necessary to align chromatograms before comparing them in metabolomics experiments. Several software programs have been developed to automate this process. Here we report a comparative evaluation of the performance of eight programs using prepared samples of mixtures of chemicals, and an extract of tomato vines spiked with three concentrations of a mixture of alkanes. The programs included in the comparison were SpectConnect, MetaboliteDetector 2.01a, MetAlign 041012, MZmine 2.0, TagFinder 04, XCMS Online 1.21.01, MeltDB and GAVIN. Samples were analyzed by GC-MS, chromatograms were aligned using the selected programs, and the resulting data matrices were preprocessed and submitted to principal components analysis. In the first trial, SpectConnect, MetAlign and MetaboliteDetector correctly identified ≥90% of the true positives. In the second trial, MetAlign and MetaboliteDetector correctly identified 87% and 81% of the true positives, respectively. In addition, in both trials >90% of the peaks identified by MetAlign and MetaboliteDetector were true positives. PMID:25435458

  7. The Megamaser Cosmology Project. III. Accurate Masses of Seven Supermassive Black Holes in Active Galaxies with Circumnuclear Megamaser Disks

    CERN Document Server

    Kuo, C Y; Condon, J J; Impellizzeri, C M V; Lo, K Y; Zaw, I; Schenker, M; Henkel, C; Reid, M J; Greene, J E

    2010-01-01

    Observations of H$_2$O masers from circumnuclear disks in active galaxies for the Megamaser Cosmology Project allow accurate measurement of the mass of supermassive black holes (BH) in these galaxies. We present the Very Long Baseline Interferometry (VLBI) images and kinematics of water maser emission in six active galaxies: NGC~1194, NGC~2273, NGC~2960 (Mrk~1419), NGC~4388, NGC~6264 and NGC~6323. We use the Keplerian rotation curves of these six megamaser galaxies, plus a seventh previously published, to determine accurate enclosed masses within the central $\\sim0.3$ pc of these galaxies, smaller than the radius of the sphere of influence of the central mass in all cases. We also set lower limits to the central mass densities of between 0.12 and 60 $\\times 10^{10} M_{\\odot}$~pc$^{-3}$. For six of the seven disks, the high central densities rule out clusters of stars or stellar remnants as the central objects, and this result further supports our assumption that the enclosed mass can be attributed predominant...

  8. Improving global feature detectabilities through scan range splitting for untargeted metabolomics by high-performance liquid chromatography-Orbitrap mass spectrometry.

    Science.gov (United States)

    Ranninger, Christina; Schmidt, Lukas E; Rurik, Marc; Limonciel, Alice; Jennings, Paul; Kohlbacher, Oliver; Huber, Christian G

    2016-08-01

    Untargeted metabolomics aims at obtaining quantitative information on the highest possible number of low-molecular biomolecules present in a biological sample. Rather small changes in mass spectrometric spectrum acquisition parameters may have a significant influence on the detectabilities of metabolites in untargeted global-scale studies by means of high-performance liquid chromatography-mass spectrometry (HPLC-MS). Employing whole cell lysates of human renal proximal tubule cells, we present a systematic global-scale study of the influence of mass spectrometric scan parameters and post-acquisition data treatment on the number and intensity of metabolites detectable in whole cell lysates. Ion transmission and ion collection efficiencies in an Orbitrap-based mass spectrometer basically depend on the m/z range scanned, which, ideally, requires different instrument settings for the respective mass ranges investigated. Therefore, we split a full scan range of m/z 50-1000 relevant for metabolites into two separate segments (m/z 50-200 and m/z 200-1,000), allowing an independent tuning of the ion transmission parameters for both mass ranges. Three different implementations, involving either scanning from m/z 50-1000 in a single scan, or scanning from m/z 50-200 and from m/z 200-1000 in two alternating scans, or performing two separate HPLC-MS runs with m/z 50-200 and m/z 200-1000 scan ranges were critically assessed. The detected features were subjected to rigorous background filtering and quality control in order to obtain reliable metabolite features for subsequent differential quantification. The most efficient approach in terms of feature number, which forms the basis for statistical analysis, identification, and for generating biological hypotheses, was the separate analysis of two different mass ranges. This lead to an increase in the number of detectable metabolite features, especially in the higher mass range (m/z greater than 400), by 2.5 (negative mode) to 6

  9. Metabolomic Heterogeneity of Pulmonary Arterial Hypertension

    OpenAIRE

    Zhao, Yidan; Peng, Jenny; Lu, Catherine; Hsin, Michael; Mura, Marco; Wu, Licun; Chu, Lei; Zamel, Ricardo; Machuca, Tiago; Waddell, Thomas; Liu, Mingyao; Keshavjee, Shaf; Granton, John; de Perrot, Marc

    2014-01-01

    Although multiple gene and protein expression have been extensively profiled in human pulmonary arterial hypertension (PAH), the mechanism for the development and progression of pulmonary hypertension remains elusive. Analysis of the global metabolomic heterogeneity within the pulmonary vascular system leads to a better understanding of disease progression. Using a combination of high-throughput liquid-and-gas-chromatography-based mass spectrometry, we showed unbiased metabolomic profiles of ...

  10. Rapid yet accurate measurement of mass diffusion coefficients by phase shifting interferometer

    CERN Document Server

    Guo Zhi Xiong; Komiya, A

    1999-01-01

    The technique of using a phase-shifting interferometer is applied to the study of diffusion in transparent liquid mixtures. A quick method is proposed for determining the diffusion coefficient from the measurements of the location of fringes on a grey level picture. The measurement time is very short (within 100 s) and a very small transient diffusion field can be observed and recorded accurately with a rate of 30 frames per second. The measurement can be completed using less than 0.12 cc of solutions. The influence of gravity on the measurement of the diffusion coefficient is eliminated in the present method. Results on NaCl-water diffusion systems are presented and compared with the reference data. (author)

  11. Galaxy And Mass Assembly (GAMA): Accurate Panchromatic Photometry from Optical Priors using LAMBDAR

    CERN Document Server

    Wright, A H; Bourne, N; Driver, S P; Dunne, L; Maddox, S J; Alpaslan, M; Andrews, S K; Bauer, A E; Bland-Hawthorn, J; Brough, S; Brown, M J I; Cluver, M; Davies, L J M; Holwerda, B W; Hopkins, A M; Jarrett, T H; Kafle, P R; Lange, R; Liske, J; Loveday, J; Moffett, A J; Norberg, P; Popescu, C C; Smith, M; Taylor, E N; Tuffs, R J; Wang, L; Wilkins, S M

    2016-01-01

    We present the Lambda Adaptive Multi-Band Deblending Algorithm in R (LAMBDAR), a novel code for calculating matched aperture photometry across images that are neither pixel- nor PSF-matched, using prior aperture definitions derived from high resolution optical imaging. The development of this program is motivated by the desire for consistent photometry and uncertainties across large ranges of photometric imaging, for use in calculating spectral energy distributions. We describe the program, specifically key features required for robust determination of panchromatic photometry: propagation of apertures to images with arbitrary resolution, local background estimation, aperture normalisation, uncertainty determination and propagation, and object deblending. Using simulated images, we demonstrate that the program is able to recover accurate photometric measurements in both high-resolution, low-confusion, and low-resolution, high-confusion, regimes. We apply the program to the 21-band photometric dataset from the ...

  12. Accurate mass measurements of $^{26}$Ne, $^{26-30}$Na, $^{29-33}$Mg performed with the MISTRAL spectrometer

    CERN Document Server

    Gaulard, C; Bachelet, C; De Simon, M S; Lunney, M D; Thibault, C; Vieira, N

    2006-01-01

    The minuteness of the nuclear binding energy requires that mass measurements be highly precise and accurate. Here we report on new measurements $^{29-33}$Mg and $^{26}$Na performed with the Mistral mass spectrometer at CERN's Isolde facility. Since mass measurements are prone to systematic errors, considerable effort has been devoted to their evaluation and elimination in order to achieve accuracy and not only precision. We have therefore conducted a campaign of measurements for calibration and error evaluation. As a result, we now have a satisfactory description of the Mistral calibration laws and error budget. We have applied our new understanding to previous measurements of $^{26}$Ne, $^{26-30}$Na and $^{29,32}$Mg for which re-evaluated values are reported.

  13. Metabolomics in food science.

    Science.gov (United States)

    Cevallos-Cevallos, Juan Manuel; Reyes-De-Corcuera, José Ignacio

    2012-01-01

    Metabolomics, the newest member of the omics techniques, has become an important tool in agriculture, pharmacy, and environmental sciences. Advances in compound extraction, separation, detection, identification, and data analysis have allowed metabolomics applications in food sciences including food processing, quality, and safety. This chapter discusses recent advances and applications of metabolomics in food science.

  14. Automated resolution of chromatographic signals by independent component analysis-orthogonal signal deconvolution in comprehensive gas chromatography/mass spectrometry-based metabolomics.

    Science.gov (United States)

    Domingo-Almenara, Xavier; Perera, Alexandre; Ramírez, Noelia; Brezmes, Jesus

    2016-07-01

    Comprehensive gas chromatography-mass spectrometry (GC×GC-MS) provides a different perspective in metabolomics profiling of samples. However, algorithms for GC×GC-MS data processing are needed in order to automatically process the data and extract the purest information about the compounds appearing in complex biological samples. This study shows the capability of independent component analysis-orthogonal signal deconvolution (ICA-OSD), an algorithm based on blind source separation and distributed in an R package called osd, to extract the spectra of the compounds appearing in GC×GC-MS chromatograms in an automated manner. We studied the performance of ICA-OSD by the quantification of 38 metabolites through a set of 20 Jurkat cell samples analyzed by GC×GC-MS. The quantification by ICA-OSD was compared with a supervised quantification by selective ions, and most of the R(2) coefficients of determination were in good agreement (R(2)>0.90) while up to 24 cases exhibited an excellent linear relation (R(2)>0.95). We concluded that ICA-OSD can be used to resolve co-eluted compounds in GC×GC-MS.

  15. Gas Chromatography/Mass Spectrometry-Based Metabolomic Profiling Reveals Alterations in Mouse Plasma and Liver in Response to Fava Beans.

    Science.gov (United States)

    Xiao, Man; Du, Guankui; Zhong, Guobing; Yan, Dongjing; Zeng, Huazong; Cai, Wangwei

    2016-01-01

    Favism is a life-threatening hemolytic anemia resulting from the intake of fava beans by susceptible individuals with low erythrocytic glucose 6-phosphate dehydrogenase (G6PD) activity. However, little is known about the metabolomic changes in plasma and liver after the intake of fava beans in G6PD normal and deficient states. In this study, gas chromatography/mass spectrometry was used to analyze the plasma and liver metabolic alterations underlying the effects of fava beans in C3H- and G6PD-deficient (G6PDx) mice, and to find potential biomarkers and metabolic changes associated with favism. Our results showed that fava beans induced oxidative stress in both C3H and G6PDx mice. Significantly, metabolomic differences were observed in plasma and liver between the control and fava bean treated groups of both C3H and G6PDx mice. The levels of 7 and 21 metabolites in plasma showed significant differences between C3H-control (C3H-C)- and C3H fava beans-treated (C3H-FB) mice, and G6PDx-control (G6PDx-C)- and G6PDx fava beans-treated (G6PDx-FB) mice, respectively. Similarly, the levels of 7 and 25 metabolites in the liver showed significant differences between C3H and C3H-FB, and G6PDx and G6PDx-FB, respectively. The levels of oleic acid, linoleic acid, and creatinine were significantly increased in the plasma of both C3H-FB and G6PDx-FB mice. In the liver, more metabolic alterations were observed in G6PDx-FB mice than in C3H-FB mice, and were involved in a sugar, fatty acids, amino acids, cholesterol biosynthesis, the urea cycle, and the nucleotide metabolic pathway. These findings suggest that oleic acid, linoleic acid, and creatinine may be potential biomarkers of the response to fava beans in C3H and G6PDx mice and therefore that oleic acid and linoleic acid may be involved in oxidative stress induced by fava beans. This study demonstrates that G6PD activity in mice can affect their metabolic pathways in response to fava beans.

  16. Stellar mass-to-light ratios from galaxy spectra: how accurate can they be?

    CERN Document Server

    Gallazzi, Anna

    2009-01-01

    Stellar masses play a crucial role in the exploration of galaxy properties and the evolution of the galaxy population. In this paper, we explore the minimum possible uncertainties in stellar mass-to-light (M/L) ratios from the assumed star formation history (SFH) and metallicity distribution, with the goals of providing a minimum set of requirements for observational studies. We use a large Monte Carlo library of SFHs to study as a function of galaxy spectral type and signal-to-noise ratio (S/N) the statistical uncertainties of M/L values using either absorption-line data or broad band colors. The accuracy of M/L estimates can be significantly improved by using metal-sensitive indices in combination with age-sensitive indices, in particular for galaxies with intermediate-age or young stellar populations. While M/L accuracy clearly depends on the spectral S/N ratio, there is no significant gain in improving the S/N much above 50/pix and limiting uncertainties of 0.03 dex are reached. Assuming that dust is accu...

  17. Dynamic Bayesian Network for Accurate Detection of Peptides from Tandem Mass Spectra.

    Science.gov (United States)

    Halloran, John T; Bilmes, Jeff A; Noble, William S

    2016-08-01

    A central problem in mass spectrometry analysis involves identifying, for each observed tandem mass spectrum, the corresponding generating peptide. We present a dynamic Bayesian network (DBN) toolkit that addresses this problem by using a machine learning approach. At the heart of this toolkit is a DBN for Rapid Identification (DRIP), which can be trained from collections of high-confidence peptide-spectrum matches (PSMs). DRIP's score function considers fragment ion matches using Gaussians rather than fixed fragment-ion tolerances and also finds the optimal alignment between the theoretical and observed spectrum by considering all possible alignments, up to a threshold that is controlled using a beam-pruning algorithm. This function not only yields state-of-the art database search accuracy but also can be used to generate features that significantly boost the performance of the Percolator postprocessor. The DRIP software is built upon a general purpose DBN toolkit (GMTK), thereby allowing a wide variety of options for user-specific inference tasks as well as facilitating easy modifications to the DRIP model in future work. DRIP is implemented in Python and C++ and is available under Apache license at http://melodi-lab.github.io/dripToolkit . PMID:27397138

  18. Metabolomics Analysis of Health Functions of Physalis Pubescens L. using by Ultra-performance Liquid Chromatography/Electrospray Ionization Quadruple Time-of-Flight Mass Spectrometry

    OpenAIRE

    Hang Chu; Hui Sun; Guang-Li Yan; Ai-Hua Zhang; Chang Liu; Hui Dong; Xiang-Cai Meng; Xi-Jun Wang

    2015-01-01

    Herbal medicines may benefit from metabolomics studies, and applying metabolomics may provide answers about which herbal interventions may be effective for individuals, which metabolic processes are triggered, and the subsequent chemical pathways of activity. Physalis pubescens L (PPL) is an herbal fruit for one year living plant and has been developed into healthy function's food. However, the mechanisms of health functions are still unclear. To comprehensively and holistically assess its an...

  19. Screening of the polyphenol content of tomato-based products through accurate-mass spectrometry (HPLC-ESI-QTOF).

    Science.gov (United States)

    Vallverdú-Queralt, Anna; Jáuregui, Olga; Di Lecce, Giuseppe; Andrés-Lacueva, Cristina; Lamuela-Raventós, Rosa M

    2011-12-01

    Tomatoes, the second most important vegetable crop worldwide, are a key component in the so-called "Mediterranean diet" and its consumption has greatly increased worldwide over the past 2 decades, mostly due to a growing demand for tomato-based products such as ketchups, gazpachos and tomato juices. In this work, tomato-based products were analysed after a suitable work-up extraction procedure using liquid chromatography/electrospray ionisation-time of flight-mass spectrometry (HPLC-ESI-QTOF) with negative ion detection using information-dependent acquisition (IDA) to determine their phenolic composition. The compounds were confirmed by accurate mass measurements in MS and MS(2) modes. The elemental composition was selected according to the accurate masses and isotopic pattern. In this way, 47 compounds (simple phenolic and hydroxycinnamoylquinic acids and flavone, flavonol, flavanone and dihydrochalcone derivatives) were identified in tomato-based products, five of them, as far as was known, were previously unreported in tomatoes. The phenolic fingerprint showed that tomato-based products differ in phenolic composition, principally in protocatechuic acid-O-hexoside, apigenin and its glycosylated forms, quercetin-O-dihexoside, kaempferol-C-hexoside and eriodictyol-O-dihexoside. Gazpacho showed the highest number of phenolic compounds due to the vegetables added for its production. PMID:25212313

  20. A feasibility study of UHPLC-HRMS accurate-mass screening methods for multiclass testing of organic contaminants in food.

    Science.gov (United States)

    Pérez-Ortega, Patricia; Lara-Ortega, Felipe J; García-Reyes, Juan F; Gilbert-López, Bienvenida; Trojanowicz, Marek; Molina-Díaz, Antonio

    2016-11-01

    The feasibility of accurate-mass multi-residue screening methods using liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS) using time-of-flight mass spectrometry has been evaluated, including over 625 multiclass food contaminants as case study. Aspects such as the selectivity and confirmation capability provided by HRMS with different acquisition modes (full-scan or full-scan combined with collision induced dissociation (CID) with no precursor ion isolation), and chromatographic separation along with main limitations such as sensitivity or automated data processing have been examined. Compound identification was accomplished with retention time matching and accurate mass measurements of the targeted ions for each analyte (mainly (de)protonated molecules). Compounds with the same nominal mass (isobaric species) were very frequent due to the large number of compounds included. Although 76% of database compounds were involved in isobaric groups, they were resolved in most cases (99% of these isobaric species were distinguished by retention time, resolving power, isotopic profile or fragment ions). Only three pairs could not be resolved with these tools. In-source CID fragmentation was evaluated in depth, although the results obtained in terms of information provided were not as thorough as those obtained using fragmentation experiments without precursor ion isolation (all ion mode). The latter acquisition mode was found to be the best suited for this type of large-scale screening method instead of classic product ion scan, as provided excellent fragmentation information for confirmatory purposes for an unlimited number of compounds. Leaving aside the sample treatment limitations, the main weaknesses noticed are basically the relatively low sensitivity for compounds which does not map well against electrospray ionization and also quantitation issues such as those produced by signal suppression due to either matrix effects from coeluting matrix or from

  1. A Facility for Accurate Heat Load and Mass Leak Measurements on Superfluid Helium Valves

    CERN Document Server

    Bézaguet, Alain-Arthur; Ferlin, G; Losserand-Madoux, R; Perin, A; Vandoni, Giovanna; Van Weelderen, R

    1999-01-01

    The superconducting magnets of the Large Hadron Collider (LHC) will be protected by safety relief valves operating at 1.9 K in superfluid helium (HeII). A test facility was developed to precisely determine the heat load and the mass leakage of cryogenic valves with HeII at their inlet. The temperature of the valve inlet can be varied from 1.8 K to 2 K for pressures up to 3.5 bar. The valve outlet pipe temperature can be regulated between 5 K and 20 K. The heat flow is measured with high precision using a Kapitza-resistance heatmeter and is also crosschecked by a vaporization measurement. After calibration, a precision of 10 mW for heat flows up to 1.1 W has been achieved. The helium leak can be measured up to 15 mg/s with an accuracy of 0.2 mg/s. We present a detailed description of the test facility and the measurements showing its performances.

  2. Accurate determination of silver nanoparticles in animal tissues by inductively coupled plasma mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Veverková, Lenka [Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacky University, 17.listopadu 12, CZ 771 46 Olomouc (Czech Republic); Hradilová, Šárka [Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17.listopadu 12, CZ 771 46 Olomouc (Czech Republic); Milde, David, E-mail: david.mlde@upol.cz [Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacky University, 17.listopadu 12, CZ 771 46 Olomouc (Czech Republic); Panáček, Aleš [Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17.listopadu 12, CZ 771 46 Olomouc (Czech Republic); Skopalová, Jana [Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacky University, 17.listopadu 12, CZ 771 46 Olomouc (Czech Republic); Kvítek, Libor [Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17.listopadu 12, CZ 771 46 Olomouc (Czech Republic); Petrželová, Kamila [Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacky University, 17.listopadu 12, CZ 771 46 Olomouc (Czech Republic); National Reference Laboratory for Chemical Elements, Department of Residues in Kroměříž, State Veterinary Institute Olomouc, Hulínská 2286, CZ 767 60 Kroměříž (Czech Republic); and others

    2014-12-01

    This study examined recoveries of silver determination in animal tissues after wet digestion by inductively coupled plasma mass spectrometry. The composition of the mineralization mixture for microwave assisted digestion was optimized and the best recoveries were obtained for mineralization with HNO{sub 3} and addition of HCl promptly after digestion. The optimization was performed on model samples of chicken meat spiked with silver nanoparticles and a solution of ionic silver. Basic calculations of theoretical distribution of Ag among various silver-containing species were implemented and the results showed that most of the silver is in the form of soluble complexes AgCl{sub 2}{sup −} and AgCl{sub 3}{sup 2−} for the optimized composition of the mineralization mixture. Three animal tissue certified reference materials were then analyzed to verify the trueness and precision of the results. - Highlights: • We performed detailed optimization of microwave assisted digestion procedure of animal tissue used prior to Ag determination by ICP-MS. • We provide basic equilibrium calculations to give theoretical explanation of results from optimization of tested mineralization mixtures. • Results from method validation that was done by analysis of several matrix CRMs are presented.

  3. Accurate nuclear masses from a three parameter Kohn-Sham DFT approach (BCPM)

    CERN Document Server

    Baldo, M; Schuck, P; Viñas, X

    2012-01-01

    Given the promising features of the recently proposed Barcelona-Catania-Paris (BCP) functional \\cite{Baldo.08}, it is the purpose of this paper to still improve on it. It is, for instance, shown that the number of open parameters can be reduced from 4-5 to 2-3, i.e. by practically a factor of two. One parameter is tightly fixed by a fine-tuning of the bulk, a second by the surface energy. The third is the strength of the spin-orbit potential on which the final result does not depend within the scatter of the values used in Skyrme and Gogny like functionals. An energy rms value of 1.58 MeV is obtained from a fit of these three parameters to the 579 measured masses reported in the Audi and Waspra 2003 compilation. This rms value compares favorably with the one obtained using other successful mean field theories. Charge radii are also well reproduced when compared with experiment. The energies of some excited states, mostly the isoscalar giant monopole resonances, are studied within this model as well.

  4. Accurate determination of silver nanoparticles in animal tissues by inductively coupled plasma mass spectrometry

    International Nuclear Information System (INIS)

    This study examined recoveries of silver determination in animal tissues after wet digestion by inductively coupled plasma mass spectrometry. The composition of the mineralization mixture for microwave assisted digestion was optimized and the best recoveries were obtained for mineralization with HNO3 and addition of HCl promptly after digestion. The optimization was performed on model samples of chicken meat spiked with silver nanoparticles and a solution of ionic silver. Basic calculations of theoretical distribution of Ag among various silver-containing species were implemented and the results showed that most of the silver is in the form of soluble complexes AgCl2− and AgCl32− for the optimized composition of the mineralization mixture. Three animal tissue certified reference materials were then analyzed to verify the trueness and precision of the results. - Highlights: • We performed detailed optimization of microwave assisted digestion procedure of animal tissue used prior to Ag determination by ICP-MS. • We provide basic equilibrium calculations to give theoretical explanation of results from optimization of tested mineralization mixtures. • Results from method validation that was done by analysis of several matrix CRMs are presented

  5. Bioprospecting of microalgae: Proper extraction followed by high performance liquid chromatographic-high resolution mass spectrometric fingerprinting as key tools for successful metabolom characterization.

    Science.gov (United States)

    Stranska-Zachariasova, Milena; Kastanek, Petr; Dzuman, Zbynek; Rubert, Josep; Godula, Michal; Hajslova, Jana

    2016-03-15

    Currently, the interest in microalgae as a source of biologically active components exploitable as supplementary ingredients to food/feed or in cosmetics continues to increase. Existing research mainly aims to focus on revealing and recovering the rare, cost competitive components of the algae metabolom. Because these components could be of very different physicochemical character, a universal approach for their isolation and characterization should be developed. This study demonstrates the systematic development of the extraction strategy that represents one of the key challenges in effective algae bioprospecting, which predefines their further industrial application. By using of Trachydiscus minutus as a model microalgae biomass, following procedures were tested and critically evaluated in order to develop the generic procedure for microalgae bioprospecting: (i) various ways of mechanical disintegration of algae cells enabling maximum extraction efficiency, (ii) the use of a wide range of extraction solvents/solvent mixtures suitable for optimal extraction yields of polar, medium-polar, and non-polar compounds, (iii) the use of consecutive extractions as a fractionation approach. Within the study, targeted screening of selected compounds representing broad range of polarities was realized by ultra-high performance liquid chromatography coupled with high resolution tandem mass spectrometric detection (UHPLC-HRMS/MS), to assess the effectiveness of undertaken isolation steps. As a result, simple and high-throughput extraction-fractionation strategy based on consecutive extraction with water-aqueous methanol-hexane/isopropanol was developed. Moreover, to demonstrate the potential of the UHPLC-HRMS/MS for the retrospective non-target screening and compounds identification, the collected mass spectra have been evaluated to characterize the pattern of extracted metabolites. Attention was focused on medium-/non-polar extracts and characterization of lipid species

  6. Liquid chromatography-quadrupole time of flight tandem mass spectrometry-based targeted metabolomic study for varietal discrimination of grapes according to plant sterols content.

    Science.gov (United States)

    Millán, Laura; Sampedro, M Carmen; Sánchez, Alicia; Delporte, Cédric; Van Antwerpen, Pierre; Goicolea, M Aranzazu; Barrio, Ramón J

    2016-07-01

    Grapevine and derived products are rich in a wide range of compounds and its quality mainly depends on its metabolites, as a result of viticulture practices. Plant sterols, also called phytosterols (PS), are secondary metabolites regarded as bioactive substance present in grape berries and other plant-based food. The present study deals with a metabolomic approach focusing on phytosterols family in six varieties of Rioja grapes (Cabernet Sauvignon, Tempranillo, Graciano, Garnacha, White Garnacha and Viura), in order to find significant differences among them. Liquid chromatography- mass spectrometry with a quadrupole-time of flight mass analyzer (LC-QTOF) was used to find as many metabolites as possible in the different grape berry fractions, and using statistics to help finding significant clustering of the metabolic profile of pulp, peel and seeds in relation to the variety. The best chromatographic and detection conditions were achieved by gas phase ionization via atmospheric pressure chemical ionization (APCI) in positive mode. Furthermore, analysis with electrospray (ESI) is also needed for phytosterol derivatives confirmation. Putative compounds of interest in the analyzed samples were found by an automated compound extraction algorithm (Molecular Feature Extraction, MFE) and an initial differential expression from the data was created with the aid of commercial software. Once the data were collected, the results were filtered, aligned and normalized, and evaluating applying one-way analysis of variance (ANOVA) with a 95% significance level. For sample class prediction, partial least square-discriminant analysis (PLS-DA) is used as a supervised pattern recognition method and excellent separation among the grape varieties is shown. An overall accuracy of 93.3% (pulp samples), 100.0% (peel) or 96.7% (seeds) in discriminating between grape varieties was achieved when comparing the different fractions. In general, 7 PS derivatives were identified with ID scores

  7. Bioprospecting of microalgae: Proper extraction followed by high performance liquid chromatographic-high resolution mass spectrometric fingerprinting as key tools for successful metabolom characterization.

    Science.gov (United States)

    Stranska-Zachariasova, Milena; Kastanek, Petr; Dzuman, Zbynek; Rubert, Josep; Godula, Michal; Hajslova, Jana

    2016-03-15

    Currently, the interest in microalgae as a source of biologically active components exploitable as supplementary ingredients to food/feed or in cosmetics continues to increase. Existing research mainly aims to focus on revealing and recovering the rare, cost competitive components of the algae metabolom. Because these components could be of very different physicochemical character, a universal approach for their isolation and characterization should be developed. This study demonstrates the systematic development of the extraction strategy that represents one of the key challenges in effective algae bioprospecting, which predefines their further industrial application. By using of Trachydiscus minutus as a model microalgae biomass, following procedures were tested and critically evaluated in order to develop the generic procedure for microalgae bioprospecting: (i) various ways of mechanical disintegration of algae cells enabling maximum extraction efficiency, (ii) the use of a wide range of extraction solvents/solvent mixtures suitable for optimal extraction yields of polar, medium-polar, and non-polar compounds, (iii) the use of consecutive extractions as a fractionation approach. Within the study, targeted screening of selected compounds representing broad range of polarities was realized by ultra-high performance liquid chromatography coupled with high resolution tandem mass spectrometric detection (UHPLC-HRMS/MS), to assess the effectiveness of undertaken isolation steps. As a result, simple and high-throughput extraction-fractionation strategy based on consecutive extraction with water-aqueous methanol-hexane/isopropanol was developed. Moreover, to demonstrate the potential of the UHPLC-HRMS/MS for the retrospective non-target screening and compounds identification, the collected mass spectra have been evaluated to characterize the pattern of extracted metabolites. Attention was focused on medium-/non-polar extracts and characterization of lipid species

  8. Accurate mass fragment library for rapid analysis of pesticides on produce using ambient pressure desorption ionization with high-resolution mass spectrometry.

    Science.gov (United States)

    Kern, Sara E; Lin, Lora A; Fricke, Frederick L

    2014-08-01

    U.S. food imports have been increasing steadily for decades, intensifying the need for a rapid and sensitive screening technique. A method has been developed that uses foam disks to sample the surface of incoming produce. This work provides complimentary information to the extensive amount of published pesticide fragmentation data collected using LCMS systems (Sack et al. Journal of Agricultural and Food Chemistry, 59, 6383-6411, 2011; Mol et al. Analytical and Bioanalytical Chemistry, 403, 2891-2908, 2012). The disks are directly analyzed using transmission-mode direct analysis in real time (DART) ambient pressure desorption ionization coupled to a high resolution accurate mass-mass spectrometer (HRAM-MS). In order to provide more certainty in the identification of the pesticides detected, a library of accurate mass fragments and isotopes of the protonated parent molecular ion (the [M+H]⁺) has been developed. The HRAM-MS is equipped with a quadrupole mass filter, providing the capability of "data-dependent" fragmentation, as opposed to "all -ion" fragmentation (where all of the ions enter a collision chamber and are fragmented at once). A temperature gradient for the DART helium stream and multiple collision energies were employed to detect and fragment 164 pesticides of varying chemical classes, sizes, and polarities. The accurate mass information of precursor ([M+H]⁺ ion) and fragment ions is essential in correctly identifying chemical contaminants on the surface of imported produce. Additionally, the inclusion of isotopes of the [M+H]⁺ in the database adds another metric to the confirmation process. The fragmentation data were collected using a Q-Exactive mass spectrometer and were added to a database used to process data collected with an Exactive mass spectrometer, an instrument that is more readily available for this screening application. The commodities investigated range from smooth-skinned produce such as apples to rougher surfaces like broccoli

  9. Accurate Mass Fragment Library for Rapid Analysis of Pesticides on Produce Using Ambient Pressure Desorption Ionization with High-Resolution Mass Spectrometry

    Science.gov (United States)

    Kern, Sara E.; Lin, Lora A.; Fricke, Frederick L.

    2014-08-01

    U.S. food imports have been increasing steadily for decades, intensifying the need for a rapid and sensitive screening technique. A method has been developed that uses foam disks to sample the surface of incoming produce. This work provides complimentary information to the extensive amount of published pesticide fragmentation data collected using LCMS systems (Sack et al. Journal of Agricultural and Food Chemistry, 59, 6383-6411, 2011; Mol et al. Analytical and Bioanalytical Chemistry, 403, 2891-2908, 2012). The disks are directly analyzed using transmission-mode direct analysis in real time (DART) ambient pressure desorption ionization coupled to a high resolution accurate mass-mass spectrometer (HRAM-MS). In order to provide more certainty in the identification of the pesticides detected, a library of accurate mass fragments and isotopes of the protonated parent molecular ion (the [M+H]+) has been developed. The HRAM-MS is equipped with a quadrupole mass filter, providing the capability of "data-dependent" fragmentation, as opposed to "all -ion" fragmentation (where all of the ions enter a collision chamber and are fragmented at once). A temperature gradient for the DART helium stream and multiple collision energies were employed to detect and fragment 164 pesticides of varying chemical classes, sizes, and polarities. The accurate mass information of precursor ([M+H]+ ion) and fragment ions is essential in correctly identifying chemical contaminants on the surface of imported produce. Additionally, the inclusion of isotopes of the [M+H]+ in the database adds another metric to the confirmation process. The fragmentation data were collected using a Q-Exactive mass spectrometer and were added to a database used to process data collected with an Exactive mass spectrometer, an instrument that is more readily available for this screening application. The commodities investigated range from smooth-skinned produce such as apples to rougher surfaces like broccoli. The

  10. Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide

    Science.gov (United States)

    Ross, Charles W.; Simonsick, William J.; Bogusky, Michael J.; Celikay, Recep W.; Guare, James P.; Newton, Randall C.

    2016-01-01

    Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI), sheath flow electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and high-field nuclear magnetic resonance (NMR) analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry. PMID:27367671

  11. Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide

    Directory of Open Access Journals (Sweden)

    Charles W. Ross

    2016-06-01

    Full Text Available Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI, sheath flow electrospray ionization (ESI Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS and high-field nuclear magnetic resonance (NMR analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry.

  12. Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide.

    Science.gov (United States)

    Ross, Charles W; Simonsick, William J; Bogusky, Michael J; Celikay, Recep W; Guare, James P; Newton, Randall C

    2016-01-01

    Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI), sheath flow electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and high-field nuclear magnetic resonance (NMR) analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry.

  13. Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide.

    Science.gov (United States)

    Ross, Charles W; Simonsick, William J; Bogusky, Michael J; Celikay, Recep W; Guare, James P; Newton, Randall C

    2016-01-01

    Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI), sheath flow electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and high-field nuclear magnetic resonance (NMR) analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry. PMID:27367671

  14. Gas Chromatography Time-Of-Flight Mass Spectrometry (GC-TOF-MS)-Based Metabolomics for Comparison of Caffeinated and Decaffeinated Coffee and Its Implications for Alzheimer’s Disease

    Science.gov (United States)

    Chang, Kai Lun; Ho, Paul C.

    2014-01-01

    Findings from epidemiology, preclinical and clinical studies indicate that consumption of coffee could have beneficial effects against dementia and Alzheimer’s disease (AD). The benefits appear to come from caffeinated coffee, but not decaffeinated coffee or pure caffeine itself. Therefore, the objective of this study was to use metabolomics approach to delineate the discriminant metabolites between caffeinated and decaffeinated coffee, which could have contributed to the observed therapeutic benefits. Gas chromatography time-of-flight mass spectrometry (GC-TOF-MS)-based metabolomics approach was employed to characterize the metabolic differences between caffeinated and decaffeinated coffee. Orthogonal partial least squares discriminant analysis (OPLS-DA) showed distinct separation between the two types of coffee (cumulative Q2 = 0.998). A total of 69 discriminant metabolites were identified based on the OPLS-DA model, with 37 and 32 metabolites detected to be higher in caffeinated and decaffeinated coffee, respectively. These metabolites include several benzoate and cinnamate-derived phenolic compounds, organic acids, sugar, fatty acids, and amino acids. Our study successfully established GC-TOF-MS based metabolomics approach as a highly robust tool in discriminant analysis between caffeinated and decaffeinated coffee samples. Discriminant metabolites identified in this study are biologically relevant and provide valuable insights into therapeutic research of coffee against AD. Our data also hint at possible involvement of gut microbial metabolism to enhance therapeutic potential of coffee components, which represents an interesting area for future research. PMID:25098597

  15. Accurate mass screening and identification of emerging contaminants in environmental samples by liquid chromatography-hybrid linear ion trap Orbitrap mass spectrometry.

    Science.gov (United States)

    Hogenboom, A C; van Leerdam, J A; de Voogt, P

    2009-01-16

    The European Reach legislation will possibly drive producers to develop newly designed chemicals that will be less persistent, bioaccumulative or toxic. If this innovation leads to an increased use of more hydrophilic chemicals it may result in higher mobilities of chemicals in the aqueous environment. As a result, the drinking water companies may face stronger demands on removal processes as the hydrophilic compounds inherently are more difficult to remove. Monitoring efforts will also experience a shift in focus to more water-soluble compounds. Screening source waters on the presence of (emerging) contaminants is an essential step in the control of the water cycle from source to tap water. In this article, some of our experiences are presented with the hybrid linear ion trap (LTQ) FT Orbitrap mass spectrometer, in the area of chemical water analysis. A two-pronged strategy in mass spectrometric research was employed: (i) exploring effluent, surface, ground- and drinking-water samples searching for accurate masses corresponding to target compounds (and their product ions) known from, e.g. priority lists or the scientific literature and (ii) full-scan screening of water samples in search of 'unknown' or unexpected masses, followed by MS(n) experiments to elucidate the structure of the unknowns. Applications of both approaches to emerging water contaminants are presented and discussed. Results are presented for target analysis search for pharmaceuticals, benzotriazoles, illicit drugs and for the identification of unknown compounds in a groundwater sample and in a polar extract of a landfill soil sample (a toxicity identification evaluation bioassay sample). The applications of accurate mass screening and identification described in this article demonstrate that the LC-LTQ FT Orbitrap MS is well equipped to meet the challenges posed by newly emerging polar contaminants. PMID:18771771

  16. Metabolomics and Epidemiology Working Group

    Science.gov (United States)

    The Metabolomics and Epidemiology (MetEpi) Working Group promotes metabolomics analyses in population-based studies, as well as advancement in the field of metabolomics for broader biomedical and public health research.

  17. Metabolomic Profiling of the Effects of Melittin on Cisplatin Resistant and Cisplatin Sensitive Ovarian Cancer Cells Using Mass Spectrometry and Biolog Microarray Technology

    Directory of Open Access Journals (Sweden)

    Sanad Alonezi

    2016-10-01

    Full Text Available In the present study, liquid chromatography-mass spectrometry (LC-MS was employed to characterise the metabolic profiles of two human ovarian cancer cell lines A2780 (cisplatin-sensitive and A2780CR (cisplatin-resistant in response to their exposure to melittin, a cytotoxic peptide from bee venom. In addition, the metabolomics data were supported by application of Biolog microarray technology to examine the utilisation of carbon sources by the two cell lines. Data extraction with MZmine 2.14 and database searching were applied to provide metabolite lists. Principal component analysis (PCA gave clear separation between the cisplatin-sensitive and resistant strains and their respective controls. The cisplatin-resistant cells were slightly more sensitive to melittin than the sensitive cells with IC50 values of 4.5 and 6.8 μg/mL respectively, although the latter cell line exhibited the greatest metabolic perturbation upon treatment. The changes induced by melittin in the cisplatin-sensitive cells led mostly to reduced levels of amino acids in the proline/glutamine/arginine pathway, as well as to decreased levels of carnitines, polyamines, adenosine triphosphate (ATP and nicotinamide adenine dinucleotide (NAD+. The effects on energy metabolism were supported by the data from the Biolog assays. The lipid compositions of the two cell lines were quite different with the A2780 cells having higher levels of several ether lipids than the A2780CR cells. Melittin also had some effect on the lipid composition of the cells. Overall, this study suggests that melittin might have some potential as an adjuvant therapy in cancer treatment.

  18. Investigations on the cell metabolomics basis of multidrug resistance from tumor cells by ultra-performance liquid chromatography-mass spectrometry.

    Science.gov (United States)

    Zhang, Ruixing; Zhuang, Xiaoyu; Zong, Li; Liu, Shu; Liu, Zhiqiang; Song, Fengrui

    2016-08-01

    Although anticancer drug resistance has been linked to high expression of P-glycoprotein and the enhanced DNA repair ability, the biochemical process and the underlying mechanisms of drug resistance are not clear. In order to clarify the biochemical mechanisms of drug resistance during anticancer drug treatment, we studied the metabolomics of MCF-7/S and MCF-7/Adr cell lines, the COC1 and COC1/DDP cell lines, including the metabolic pathways of multidrug-resistant tumor cells and the changes of endogenous substances in cells. The intracellular metabolites were profiled using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). In this study, 24 biomarkers in MCF-7/Adr cells and 15 biomarkers in COC1/DDP cells that are involved in some important metabolic pathways were putatively identified. Several metabolic pathways are changed in tumor cells showing drug resistance, such as protein synthesis pathways, cysteine synthesis, the glutamine metabolic pathway, and the ammonia cycle; the first of these are involved in the synthesis of some important proteins including membrane proteins, multidrug resistance-associated proteins, and P-glycoprotein (P-gp). Proteins related to drug resistance were overexpressed in multidrug-resistant tumor cells. These proteins depended on energy and play important roles in the emergence of drug resistance. The changes in glutathione and cysteine metabolic pathways showed that the cells can activate related metabolic pathways and reduce the cell apoptosis when they encounter oxidative damage. These findings indicate that drug resistance is likely associated with increased P-gp synthesis and reduced apoptosis of tumor cells. Graphical Abstract Drug resistance was charactered in the changing of genomics and proteomics. Like enhancing DNA repair, reducing uptake, high P-g protein expression. Here, we studied the changes of metabolite pathway which could be also play an imported role in drug resistance. PMID

  19. Systemic Metabolomic Changes in Blood Samples of Lung Cancer Patients Identified by Gas Chromatography Time-of-Flight Mass Spectrometry

    OpenAIRE

    Suzanne Miyamoto; Taylor, Sandra L.; Barupal, Dinesh K; Ayumu Taguchi; Gert Wohlgemuth; Wikoff, William R.; Yoneda, Ken Y.; Gandara, David R.; Samir M. Hanash; Kyoungmi Kim; Oliver Fiehn

    2015-01-01

    Lung cancer is a leading cause of cancer deaths worldwide. Metabolic alterations in tumor cells coupled with systemic indicators of the host response to tumor development have the potential to yield blood profiles with clinical utility for diagnosis and monitoring of treatment. We report results from two separate studies using gas chromatography time-of-flight mass spectrometry (GC-TOF MS) to profile metabolites in human blood samples that significantly differ from non-small cell lung cancer ...

  20. A Comprehensive Workflow of Mass Spectrometry-Based Untargeted Metabolomics in Cancer Metabolic Biomarker Discovery Using Human Plasma and Urine

    OpenAIRE

    Jianwen She; Wei Zou; Vladimir V. Tolstikov

    2013-01-01

    Current available biomarkers lack sensitivity and/or specificity for early detection of cancer. To address this challenge, a robust and complete workflow for metabolic profiling and data mining is described in details. Three independent and complementary analytical techniques for metabolic profiling are applied: hydrophilic interaction liquid chromatography (HILIC–LC), reversed-phase liquid chromatography (RP–LC), and gas chromatography (GC). All three techniques are coupled to a mass spectro...

  1. ECMDB: the E. coli Metabolome Database.

    Science.gov (United States)

    Guo, An Chi; Jewison, Timothy; Wilson, Michael; Liu, Yifeng; Knox, Craig; Djoumbou, Yannick; Lo, Patrick; Mandal, Rupasri; Krishnamurthy, Ram; Wishart, David S

    2013-01-01

    The Escherichia coli Metabolome Database (ECMDB, http://www.ecmdb.ca) is a comprehensively annotated metabolomic database containing detailed information about the metabolome of E. coli (K-12). Modelled closely on the Human and Yeast Metabolome Databases, the ECMDB contains >2600 metabolites with links to ∼1500 different genes and proteins, including enzymes and transporters. The information in the ECMDB has been collected from dozens of textbooks, journal articles and electronic databases. Each metabolite entry in the ECMDB contains an average of 75 separate data fields, including comprehensive compound descriptions, names and synonyms, chemical taxonomy, compound structural and physicochemical data, bacterial growth conditions and substrates, reactions, pathway information, enzyme data, gene/protein sequence data and numerous hyperlinks to images, references and other public databases. The ECMDB also includes an extensive collection of intracellular metabolite concentration data compiled from our own work as well as other published metabolomic studies. This information is further supplemented with thousands of fully assigned reference nuclear magnetic resonance and mass spectrometry spectra obtained from pure E. coli metabolites that we (and others) have collected. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of E. coli's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers but also to molecular biologists, systems biologists and individuals in the biotechnology industry.

  2. Bridging the gap between comprehensive extraction protocols in plant metabolomics studies and method validation.

    Science.gov (United States)

    Bijttebier, Sebastiaan; Van der Auwera, Anastasia; Foubert, Kenn; Voorspoels, Stefan; Pieters, Luc; Apers, Sandra

    2016-09-01

    It is vital to pay much attention to the design of extraction methods developed for plant metabolomics, as any non-extracted or converted metabolites will greatly affect the overall quality of the metabolomics study. Method validation is however often omitted in plant metabolome studies, as the well-established methodologies for classical targeted analyses such as recovery optimization cannot be strictly applied. The aim of the present study is to thoroughly evaluate state-of-the-art comprehensive extraction protocols for plant metabolomics with liquid chromatography-photodiode array-accurate mass mass spectrometry (LC-PDA-amMS) by bridging the gap with method validation. Validation of an extraction protocol in untargeted plant metabolomics should ideally be accomplished by validating the protocol for all possible outcomes, i.e. for all secondary metabolites potentially present in the plant. In an effort to approach this ideal validation scenario, two plant matrices were selected based on their wide versatility of phytochemicals: meadowsweet (Filipendula ulmaria) for its polyphenols content, and spicy paprika powder (from the genus Capsicum) for its apolar phytochemicals content (carotenoids, phytosterols, capsaicinoids). These matrices were extracted with comprehensive extraction protocols adapted from literature and analysed with a generic LC-PDA-amMS characterization platform that was previously validated for broad range phytochemical analysis. The performance of the comprehensive sample preparation protocols was assessed based on extraction efficiency, repeatability and intermediate precision and on ionization suppression/enhancement evaluation. The manuscript elaborates on the finding that none of the extraction methods allowed to exhaustively extract the metabolites. Furthermore, it is shown that depending on the extraction conditions enzymatic degradation mechanisms can occur. Investigation of the fractions obtained with the different extraction methods

  3. Analysis of liposoluble carboxylic acids metabolome in human serum by stable isotope labeling coupled with liquid chromatography-mass spectrometry.

    Science.gov (United States)

    Zhu, Quan-Fei; Zhang, Zheng; Liu, Ping; Zheng, Shu-Jian; Peng, Ke; Deng, Qian-Yun; Zheng, Fang; Yuan, Bi-Feng; Feng, Yu-Qi

    2016-08-19

    Fatty acids (FAs) are groups of liposoluble carboxylic acids (LCAs) and play important roles in various physiological processes. Abnormal contents or changes of FAs are associated with a series of diseases. Here we developed a strategy with stable isotope labeling combined with liquid chromatography-tandem mass spectrometry (IL-LC-MS) analysis for comprehensive profiling and relative quantitation of LCAs in human serum. In this strategy, a pair of isotope labeling reagents (2-dimethylaminoethylamine (DMED)) and d4-2-dimethylaminoethylamine (d4-DMED) were employed to selectively label carboxyl groups of LCAs. The DMED and d4-DMED labeled products can lose four characteristic neutral fragments of 45 and 49Da or 63 and 67Da in collision-induced dissociation. Therefore, quadruple neutral loss scan (QNLS) mode was established and used for non-targeted profiling of LCAs. The peak pairs of DMED and d4-DMED labeling with the same retention time, intensity and characteristic mass differences were extracted from the two NLS spectra respectively, and assigned as potential LCA candidates. Using this strategy, 241 LCA candidates were discovered in the human serum; 156 carboxylic acid compounds could be determined by searching HMDB and METLIN databases (FAs are over 90%) and 21 of these LCAs were successfully identified by standards. Subsequently, a modified pseudo-targeted method with multiple reaction monitoring (MRM) detection mode was developed and used for relative quantification of LCAs in human serum from type 2 diabetes mellitus (T2DM) patients and healthy controls. As a result, 81 LCAs were found to have significant difference between T2DM patients and healthy controls. Taken together, the isotope labeling combined with tandem mass spectrometry analysis demonstrated to be a powerful strategy for identification and quantification of LCA compounds in serum samples. PMID:27432792

  4. Cancer Metabolomics and the Human Metabolome Database

    Directory of Open Access Journals (Sweden)

    David S. Wishart

    2016-03-01

    Full Text Available The application of metabolomics towards cancer research has led to a renewed appreciation of metabolism in cancer development and progression. It has also led to the discovery of metabolite cancer biomarkers and the identification of a number of novel cancer causing metabolites. The rapid growth of metabolomics in cancer research is also leading to challenges. In particular, with so many cancer-associate metabolites being identified, it is often difficult to keep track of which compounds are associated with which cancers. It is also challenging to track down information on the specific pathways that particular metabolites, drugs or drug metabolites may be affecting. Even more frustrating are the difficulties associated with identifying metabolites from NMR or MS spectra. Fortunately, a number of metabolomics databases are emerging that are designed to address these challenges. One such database is the Human Metabolome Database (HMDB. The HMDB is currently the world’s largest and most comprehensive, organism-specific metabolomics database. It contains more than 40,000 metabolite entries, thousands of metabolite concentrations, >700 metabolic and disease-associated pathways, as well as information on dozens of cancer biomarkers. This review is intended to provide a brief summary of the HMDB and to offer some guidance on how it can be used in metabolomic studies of cancer.

  5. High resolution/accurate mass (HRMS) detection of anatoxin-a in lake water using LDTD-APCI coupled to a Q-Exactive mass spectrometer.

    Science.gov (United States)

    Roy-Lachapelle, Audrey; Solliec, Morgan; Sinotte, Marc; Deblois, Christian; Sauvé, Sébastien

    2015-01-01

    A new innovative analytical method combining ultra-fast analysis time with high resolution/accurate mass detection was developed to eliminate the misidentification of anatoxin-a (ANA-a), a cyanobacterial toxin, from the natural amino acid phenylalanine (PHE). This was achieved by using the laser diode thermal desorption-atmospheric pressure chemical ionization (LDTD-APCI) coupled to the Q-Exactive, a high resolution/accurate mass spectrometer (HRMS). This novel combination, the LDTD-APCI-HRMS, allowed for an ultra-fast analysis time (0.999). Enhancement of signal to noise ratios relative to a standard triple-quadrupole method was demonstrated with lower detection and quantification limit values of 0.2 and 0.6 μg/L using the Q-Exactive. Accuracy and interday/intraday relative standard deviations were below 15%. The new method was applied to 8 different lake water samples with signs of cyanobacterial blooms. This work demonstrates the possibility of using an ultra-fast LDTD-APCI sample introduction system with an HRMS hybrid instrument for quantitative purposes with high selectivity in complex environmental matrices. PMID:25476385

  6. Metabolomic and mass isotopomer analysis of liver gluconeogenesis and citric acid cycle: II. Heterogeneity of metabolite labeling pattern.

    Science.gov (United States)

    Yang, Lili; Kasumov, Takhar; Kombu, Rajan S; Zhu, Shu-Han; Cendrowski, Andrea V; David, France; Anderson, Vernon E; Kelleher, Joanne K; Brunengraber, Henri

    2008-08-01

    In this second of two companion articles, we compare the mass isotopomer distribution of metabolites of liver gluconeogenesis and citric acid cycle labeled from NaH(13)CO(3) or dimethyl [1,4-(13)C(2)]succinate. The mass isotopomer distribution of intermediates reveals the reversibility of the isocitrate dehydrogenase + aconitase reactions, even in the absence of a source of alpha-ketoglutarate. In addition, in many cases, a number of labeling incompatibilities were found as follows: (i) glucose versus triose phosphates and phosphoenolpyruvate; (ii) differences in the labeling ratios C-4/C-3 of glucose versus (glyceraldehyde 3-phosphate)/(dihydroxyacetone phosphate); and (iii) labeling of citric acid cycle intermediates in tissue versus effluent perfusate. Overall, our data show that gluconeogenic and citric acid cycle intermediates cannot be considered as sets of homogeneously labeled pools. This probably results from the zonation of hepatic metabolism and, in some cases, from differences in the labeling pattern of mitochondrial versus extramitochondrial metabolites. Our data have implications for the use of labeling patterns for the calculation of metabolic rates or fractional syntheses in liver, as well as for modeling liver intermediary metabolism.

  7. Multiclass semi-volatile compounds determination in wine by gas chromatography accurate time-of-flight mass spectrometry.

    Science.gov (United States)

    Rodríguez-Cabo, T; Rodríguez, I; Ramil, M; Silva, A; Cela, R

    2016-04-15

    The performance of gas chromatography (GC) with accurate, high resolution mass spectrometry (HRMS) for the determination of a group of 39 semi-volatile compounds related to wine quality (pesticide residues, phenolic off-flavours, phenolic pollutants and bioactive stilbenes) is investigated. Solid-phase extraction (SPE) was used as extraction technique, previously to acetylation (phenolic compounds) and dispersive liquid-liquid microextraction (DLLME) concentration. Compounds were determined by GC coupled to a quadrupole time-of-flight (QTOF) MS system through an electron ionization (EI) source. The final method attained limits of quantification (LOQs) at the very low ng mL(-1) level, covering the range of expected concentrations for target compounds in red and white wines. For 38 out of 39 compounds, performance of sample preparation and determination steps were hardly affected by the wine matrix; thus, accurate recoveries were achieved by using pseudo-external calibration. Levels of target compounds in a set of 25 wine samples are reported. The capabilities of the described approach for the post-run identification of species not considered during method development, without retention time information, are illustrated and discussed with selected examples of compounds from different classes. PMID:26971021

  8. Multiclass semi-volatile compounds determination in wine by gas chromatography accurate time-of-flight mass spectrometry.

    Science.gov (United States)

    Rodríguez-Cabo, T; Rodríguez, I; Ramil, M; Silva, A; Cela, R

    2016-04-15

    The performance of gas chromatography (GC) with accurate, high resolution mass spectrometry (HRMS) for the determination of a group of 39 semi-volatile compounds related to wine quality (pesticide residues, phenolic off-flavours, phenolic pollutants and bioactive stilbenes) is investigated. Solid-phase extraction (SPE) was used as extraction technique, previously to acetylation (phenolic compounds) and dispersive liquid-liquid microextraction (DLLME) concentration. Compounds were determined by GC coupled to a quadrupole time-of-flight (QTOF) MS system through an electron ionization (EI) source. The final method attained limits of quantification (LOQs) at the very low ng mL(-1) level, covering the range of expected concentrations for target compounds in red and white wines. For 38 out of 39 compounds, performance of sample preparation and determination steps were hardly affected by the wine matrix; thus, accurate recoveries were achieved by using pseudo-external calibration. Levels of target compounds in a set of 25 wine samples are reported. The capabilities of the described approach for the post-run identification of species not considered during method development, without retention time information, are illustrated and discussed with selected examples of compounds from different classes.

  9. Incentives Increase Participation in Mass Dog Rabies Vaccination Clinics and Methods of Coverage Estimation Are Assessed to Be Accurate.

    Directory of Open Access Journals (Sweden)

    Abel B Minyoo

    2015-12-01

    Full Text Available In this study we show that incentives (dog collars and owner wristbands are effective at increasing owner participation in mass dog rabies vaccination clinics and we conclude that household questionnaire surveys and the mark-re-sight (transect survey method for estimating post-vaccination coverage are accurate when all dogs, including puppies, are included. Incentives were distributed during central-point rabies vaccination clinics in northern Tanzania to quantify their effect on owner participation. In villages where incentives were handed out participation increased, with an average of 34 more dogs being vaccinated. Through economies of scale, this represents a reduction in the cost-per-dog of $0.47. This represents the price-threshold under which the cost of the incentive used must fall to be economically viable. Additionally, vaccination coverage levels were determined in ten villages through the gold-standard village-wide census technique, as well as through two cheaper and quicker methods (randomized household questionnaire and the transect survey. Cost data were also collected. Both non-gold standard methods were found to be accurate when puppies were included in the calculations, although the transect survey and the household questionnaire survey over- and under-estimated the coverage respectively. Given that additional demographic data can be collected through the household questionnaire survey, and that its estimate of coverage is more conservative, we recommend this method. Despite the use of incentives the average vaccination coverage was below the 70% threshold for eliminating rabies. We discuss the reasons and suggest solutions to improve coverage. Given recent international targets to eliminate rabies, this study provides valuable and timely data to help improve mass dog vaccination programs in Africa and elsewhere.

  10. Incentives Increase Participation in Mass Dog Rabies Vaccination Clinics and Methods of Coverage Estimation Are Assessed to Be Accurate.

    Science.gov (United States)

    Minyoo, Abel B; Steinmetz, Melissa; Czupryna, Anna; Bigambo, Machunde; Mzimbiri, Imam; Powell, George; Gwakisa, Paul; Lankester, Felix

    2015-12-01

    In this study we show that incentives (dog collars and owner wristbands) are effective at increasing owner participation in mass dog rabies vaccination clinics and we conclude that household questionnaire surveys and the mark-re-sight (transect survey) method for estimating post-vaccination coverage are accurate when all dogs, including puppies, are included. Incentives were distributed during central-point rabies vaccination clinics in northern Tanzania to quantify their effect on owner participation. In villages where incentives were handed out participation increased, with an average of 34 more dogs being vaccinated. Through economies of scale, this represents a reduction in the cost-per-dog of $0.47. This represents the price-threshold under which the cost of the incentive used must fall to be economically viable. Additionally, vaccination coverage levels were determined in ten villages through the gold-standard village-wide census technique, as well as through two cheaper and quicker methods (randomized household questionnaire and the transect survey). Cost data were also collected. Both non-gold standard methods were found to be accurate when puppies were included in the calculations, although the transect survey and the household questionnaire survey over- and under-estimated the coverage respectively. Given that additional demographic data can be collected through the household questionnaire survey, and that its estimate of coverage is more conservative, we recommend this method. Despite the use of incentives the average vaccination coverage was below the 70% threshold for eliminating rabies. We discuss the reasons and suggest solutions to improve coverage. Given recent international targets to eliminate rabies, this study provides valuable and timely data to help improve mass dog vaccination programs in Africa and elsewhere. PMID:26633821

  11. Incentives Increase Participation in Mass Dog Rabies Vaccination Clinics and Methods of Coverage Estimation Are Assessed to Be Accurate

    Science.gov (United States)

    Steinmetz, Melissa; Czupryna, Anna; Bigambo, Machunde; Mzimbiri, Imam; Powell, George; Gwakisa, Paul

    2015-01-01

    In this study we show that incentives (dog collars and owner wristbands) are effective at increasing owner participation in mass dog rabies vaccination clinics and we conclude that household questionnaire surveys and the mark-re-sight (transect survey) method for estimating post-vaccination coverage are accurate when all dogs, including puppies, are included. Incentives were distributed during central-point rabies vaccination clinics in northern Tanzania to quantify their effect on owner participation. In villages where incentives were handed out participation increased, with an average of 34 more dogs being vaccinated. Through economies of scale, this represents a reduction in the cost-per-dog of $0.47. This represents the price-threshold under which the cost of the incentive used must fall to be economically viable. Additionally, vaccination coverage levels were determined in ten villages through the gold-standard village-wide census technique, as well as through two cheaper and quicker methods (randomized household questionnaire and the transect survey). Cost data were also collected. Both non-gold standard methods were found to be accurate when puppies were included in the calculations, although the transect survey and the household questionnaire survey over- and under-estimated the coverage respectively. Given that additional demographic data can be collected through the household questionnaire survey, and that its estimate of coverage is more conservative, we recommend this method. Despite the use of incentives the average vaccination coverage was below the 70% threshold for eliminating rabies. We discuss the reasons and suggest solutions to improve coverage. Given recent international targets to eliminate rabies, this study provides valuable and timely data to help improve mass dog vaccination programs in Africa and elsewhere. PMID:26633821

  12. Alterations of the exo- and endometabolite profiles in breast cancer cell lines: A mass spectrometry-based metabolomics approach.

    Science.gov (United States)

    Willmann, Lucas; Schlimpert, Manuel; Hirschfeld, Marc; Erbes, Thalia; Neubauer, Hans; Stickeler, Elmar; Kammerer, Bernd

    2016-06-21

    In recent years, knowledge about metabolite changes which are characteristic for the physiologic state of cancer cells has been acquired by liquid chromatography coupled to mass spectrometry. Distinct molecularly characterized breast cancer cell lines provide an unbiased and standardized in vitro tumor model reflecting the heterogeneity of the disease. Tandem mass spectrometry is a widely applied analytical platform and highly sensitive technique for analysis of complex biological samples. Endo- and exometabolite analysis of the breast cancer cell lines MDA-MB-231, -453 and BT-474 as well as the breast epithelial cell line MCF-10A has been performed using two different analytical platforms: UPLC-ESI-Q-TOF based on a scheduled precursor list has been applied for highlighting of significant differences between cell lines and HPLC-ESI-QqQ using multiple reaction monitoring has been utilized for a targeted approach focusing on RNA metabolism and interconnected pathways, respectively. Statistical analysis enabled a clear discrimination of the breast epithelial from the breast cancer cell lines. As an effect of oxidative stress, a decreased GSH/GSSG ratio has been detected in breast cancer cell lines. The triple negative breast cancer cell line MDA-MB-231 showed an elevation in nicotinamide, 1-ribosyl-nicotinamide and NAD+ reflecting the increased energy demand in triple negative breast cancer, which has a more aggressive clinical course than other forms of breast cancer. Obtained distinct metabolite pattern could be correlated with distinct molecular characteristics of breast cancer cells. Results and methodology of this preliminary in vitro study could be transferred to in vivo studies with breast cancer patients. PMID:27188315

  13. Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools.

    Science.gov (United States)

    Sud, Manish; Fahy, Eoin; Cotter, Dawn; Azam, Kenan; Vadivelu, Ilango; Burant, Charles; Edison, Arthur; Fiehn, Oliver; Higashi, Richard; Nair, K Sreekumaran; Sumner, Susan; Subramaniam, Shankar

    2016-01-01

    The Metabolomics Workbench, available at www.metabolomicsworkbench.org, is a public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. It provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies. The Metabolomics Workbench, part of the data coordinating effort of the National Institute of Health (NIH) Common Fund's Metabolomics Program, provides data from the Common Fund's Metabolomics Resource Cores, metabolite standards, and analysis tools to the wider metabolomics community and seeks data depositions from metabolomics researchers across the world. PMID:26467476

  14. Development and evaluation of a liquid chromatography-mass spectrometry method for rapid, accurate quantitation of malondialdehyde in human plasma.

    Science.gov (United States)

    Sobsey, Constance A; Han, Jun; Lin, Karen; Swardfager, Walter; Levitt, Anthony; Borchers, Christoph H

    2016-09-01

    Malondialdhyde (MDA) is a commonly used marker of lipid peroxidation in oxidative stress. To provide a sensitive analytical method that is compatible with high throughput, we developed a multiple reaction monitoring-mass spectrometry (MRM-MS) approach using 3-nitrophenylhydrazine chemical derivatization, isotope-labeling, and liquid chromatography (LC) with electrospray ionization (ESI)-tandem mass spectrometry assay to accurately quantify MDA in human plasma. A stable isotope-labeled internal standard was used to compensate for ESI matrix effects. The assay is linear (R(2)=0.9999) over a 20,000-fold concentration range with a lower limit of quantitation of 30fmol (on-column). Intra- and inter-run coefficients of variation (CVs) were 36h at 5°C. Standards spiked into plasma had recoveries of 92-98%. When compared to a common LC-UV method, the LC-MS method found near-identical MDA concentrations. A pilot project to quantify MDA in patient plasma samples (n=26) in a study of major depressive disorder with winter-type seasonal pattern (MDD-s) confirmed known associations between MDA concentrations and obesity (p<0.02). The LC-MS method provides high sensitivity and high reproducibility for quantifying MDA in human plasma. The simple sample preparation and rapid analysis time (5x faster than LC-UV) offers high throughput for large-scale clinical applications. PMID:27437618

  15. Accurate determination of selected pesticides in soya beans by liquid chromatography coupled to isotope dilution mass spectrometry.

    Science.gov (United States)

    Huertas Pérez, J F; Sejerøe-Olsen, B; Fernández Alba, A R; Schimmel, H; Dabrio, M

    2015-05-01

    A sensitive, accurate and simple liquid chromatography coupled with mass spectrometry method for the determination of 10 selected pesticides in soya beans has been developed and validated. The method is intended for use during the characterization of selected pesticides in a reference material. In this process, high accuracy and appropriate uncertainty levels associated to the analytical measurements are of utmost importance. The analytical procedure is based on sample extraction by the use of a modified QuEChERS (quick, easy, cheap, effective, rugged, safe) extraction and subsequent clean-up of the extract with C18, PSA and Florisil. Analytes were separated on a C18 column using gradient elution with water-methanol/2.5 mM ammonium acetate mobile phase, and finally identified and quantified by triple quadrupole mass spectrometry in the multiple reaction monitoring mode (MRM). Reliable and accurate quantification of the analytes was achieved by means of stable isotope-labelled analogues employed as internal standards (IS) and calibration with pure substance solutions containing both, the isotopically labelled and native compounds. Exceptions were made for thiodicarb and malaoxon where the isotopically labelled congeners were not commercially available at the time of analysis. For the quantification of those compounds methomyl-(13)C2(15)N and malathion-D10 were used respectively. The method was validated according to the general principles covered by DG SANCO guidelines. However, validation criteria were set more stringently. Mean recoveries were in the range of 86-103% with RSDs lower than 8.1%. Repeatability and intermediate precision were in the range of 3.9-7.6% and 1.9-8.7% respectively. LODs were theoretically estimated and experimentally confirmed to be in the range 0.001-0.005 mg kg(-1) in the matrix, while LOQs established as the lowest spiking mass fractionation level were in the range 0.01-0.05 mg kg(-1). The method reliably identifies and quantifies the

  16. Plasma metabolomics in human pulmonary tuberculosis disease: a pilot study.

    Directory of Open Access Journals (Sweden)

    Jennifer K Frediani

    Full Text Available We aimed to characterize metabolites during tuberculosis (TB disease and identify new pathophysiologic pathways involved in infection as well as biomarkers of TB onset, progression and resolution. Such data may inform development of new anti-tuberculosis drugs. Plasma samples from adults with newly diagnosed pulmonary TB disease and their matched, asymptomatic, sputum culture-negative household contacts were analyzed using liquid chromatography high-resolution mass spectrometry (LC-MS to identify metabolites. Statistical and bioinformatics methods were used to select accurate mass/charge (m/z ions that were significantly different between the two groups at a false discovery rate (FDR of q<0.05. Two-way hierarchical cluster analysis (HCA was used to identify clusters of ions contributing to separation of cases and controls, and metabolomics databases were used to match these ions to known metabolites. Identity of specific D-series resolvins, glutamate and Mycobacterium tuberculosis (Mtb-derived trehalose-6-mycolate was confirmed using LC-MS/MS analysis. Over 23,000 metabolites were detected in untargeted metabolomic analysis and 61 metabolites were significantly different between the two groups. HCA revealed 8 metabolite clusters containing metabolites largely upregulated in patients with TB disease, including anti-TB drugs, glutamate, choline derivatives, Mycobacterium tuberculosis-derived cell wall glycolipids (trehalose-6-mycolate and phosphatidylinositol and pro-resolving lipid mediators of inflammation, known to stimulate resolution, efferocytosis and microbial killing. The resolvins were confirmed to be RvD1, aspirin-triggered RvD1, and RvD2. This study shows that high-resolution metabolomic analysis can differentiate patients with active TB disease from their asymptomatic household contacts. Specific metabolites upregulated in the plasma of patients with active TB disease, including Mtb-derived glycolipids and resolvins, have potential as

  17. Quantitative profiling of bile acids in biofluids and tissues based on accurate mass high resolution LC-FT-MS: Compound class targeting in a metabolomics workflow

    NARCIS (Netherlands)

    Bobeldijk, I.; Hekman, M.; Vries de- Weij, J.van der; Coulier, L.; Ramaker, R.; Kleemann, R.; Kooistra, T.; Rubingh, C.; Freidig, A.; Verheij, E.

    2008-01-01

    We report a sensitive, generic method for quantitative profiling of bile acids and other endogenous metabolites in small quantities of various biological fluids and tissues. The method is based on a straightforward sample preparation, separation by reversed-phase high performance liquid-chromatograp

  18. Untargeted Metabolomics Strategies—Challenges and Emerging Directions

    Science.gov (United States)

    Schrimpe-Rutledge, Alexandra C.; Codreanu, Simona G.; Sherrod, Stacy D.; McLean, John A.

    2016-09-01

    Metabolites are building blocks of cellular function. These species are involved in enzyme-catalyzed chemical reactions and are essential for cellular function. Upstream biological disruptions result in a series of metabolomic changes and, as such, the metabolome holds a wealth of information that is thought to be most predictive of phenotype. Uncovering this knowledge is a work in progress. The field of metabolomics is still maturing; the community has leveraged proteomics experience when applicable and developed a range of sample preparation and instrument methodology along with myriad data processing and analysis approaches. Research focuses have now shifted toward a fundamental understanding of the biology responsible for metabolomic changes. There are several types of metabolomics experiments including both targeted and untargeted analyses. While untargeted, hypothesis generating workflows exhibit many valuable attributes, challenges inherent to the approach remain. This Critical Insight comments on these challenges, focusing on the identification process of LC-MS-based untargeted metabolomics studies—specifically in mammalian systems. Biological interpretation of metabolomics data hinges on the ability to accurately identify metabolites. The range of confidence associated with identifications that is often overlooked is reviewed, and opportunities for advancing the metabolomics field are described.

  19. Metabolomics across the globe

    NARCIS (Netherlands)

    Summer, L.W.; Hall, R.D.

    2013-01-01

    This article highlights some of the larger and more recent metabolomics activities which are funded and organised at local (mostly national) level. While being just a snap-shot, and far from exhaustive, the details clearly illustrate the extent to which metabolomics has already become established an

  20. The food metabolome

    DEFF Research Database (Denmark)

    Scalbert, Augustin; Brennan, Lorraine; Manach, Claudine;

    2014-01-01

    The food metabolome is defined as the part of the human metabolome directly derived from the digestion and biotransformation of foods and their constituents. With >25,000 compounds known in various foods, the food metabolome is extremely complex, with a composition varying widely according to the......; development of new databases, software tools, and chemical libraries for the food metabolome; and shared repositories of metabolomic data. Once achieved, major progress can be expected toward a better understanding of the complex interactions between diet and human health.......The food metabolome is defined as the part of the human metabolome directly derived from the digestion and biotransformation of foods and their constituents. With >25,000 compounds known in various foods, the food metabolome is extremely complex, with a composition varying widely according...... to the diet. By its very nature it represents a considerable and still largely unexploited source of novel dietary biomarkers that could be used to measure dietary exposures with a high level of detail and precision. Most dietary biomarkers currently have been identified on the basis of our knowledge of food...

  1. Effect of a traditional Chinese medicine prescription Quzhuotongbi decoction on hyperuricemia model rats studied by using serum metabolomics based on gas chromatography-mass spectrometry.

    Science.gov (United States)

    Chen, Jiao; Zhou, Jia; Wei, Shuangshuang; Xie, Zhijun; Wen, Chengping; Xu, Guowang

    2016-07-15

    Morbidity of hyperuricemia has constantly increased in population in decades, and hyperuricemia has proved to be an important risk factor for gout, cardiovascular diseases and others. Many urate-lowering drugs have unfavorable side effects and drug interactions. Quzhuotongbi decoction (QZTBD) is an empirical traditional Chinese medicine prescription for clinical therapy of hyperuricemia without serious adverse effects. In the study, we investigated the effects of QZTBD on urate and other metabolites in the sera of hyperuricemia model rats. Hyperuricemia model was established by orally administering yeast extract paste, and allopurinol served as a positive control drug. Serum metabolomics was performed by using a gas chromatography-mass spectrometry (GC-MS) method. Student's t-test and the principal component analysis (PCA) were employed to find the metabolic perturbations in hyperuricemia model rats. The levels of urate, lactate, pyruvate and ornithine were significantly increased, and xanthine, glyconic acids (ribonate, galactonate), amino acids (aspartate, proline, glutamine, serine, pyroglutamate, glutamate) and glucose were down-regulated greatly in the model rats. It demonstrated that nucleotide metabolism, amino acid metabolism and glycolytic pathway were disturbed by yeast administration. An orthogonal signal correction-partial least-squares discriminant analysis (OSC-PLS DA) was performed to assess the effects of yeast administering and drug treatment. 11 significantly distinctive metabolites among four groups were defined according to the variable importance for project values (VIP>1) and univariate ANOVA (p value<0.05). As compared to the model rats, the serum uric acid levels were lowered markedly under the treatment of allopurinol or QZTBD. Aspartate and glutamine involved in purine metabolism, were raised to normal level as well. The different influences on xanthine, glutamate pyroglutamate and galactonate suggested there were different mechanisms of

  2. Critical evaluation of screening techniques for emerging environmental contaminants based on accurate mass measurements with time-of-flight mass spectrometry.

    Science.gov (United States)

    Nurmi, Joonas; Pellinen, Jukka; Rantalainen, Anna-Lea

    2012-03-01

    Emerging contaminants from wastewater effluent samples were analysed, using posttarget and nontarget analysis techniques. The samples were analysed with an ultra performance liquid chromatograph-time-of-flight mass spectrometer (UPLC-TOF-MS), and the resulting data were processed with commercial deconvolution software. The method works well for posttarget analysis with prior information about the retention times of the compounds of interest. With positive polarity, 63 of 66 compounds and with negative polarity, 18 of 20 compounds were correctly identified in a spiked sample, while two compounds of a total of 88 fell out of the mass range. Furthermore, a four-stage process for identification was developed for the posttarget analysis lacking the retention time data. In the process, the number of candidate compounds was reduced by using the accurate mass of selected compounds in two steps (stages 1 and 2), structure-property relationships (stage 3) and isotope patterns of the analytes (stage 4). The process developed was validated by analysing wastewater samples spiked with 88 compounds. This procedure can be used to gain a preliminary indication of the presence of certain analytes in the samples. Nontarget analysis was tested by applying a theoretical mass spectra library for a wastewater sample spiked with six pharmaceuticals. The results showed a high number of false identifications. In addition, manual processing of the data was considered laborious and ineffective. Finally, the posttarget analysis was applied to a real wastewater sample. The analysis revealed the presence of six compounds that were afterwards confirmed with standard compounds as being correct. Three psycholeptics (nordiazepam, oxazepam and temazepam) could be tentatively identified, using the identification process developed. Posttarget analysis with UPLC-TOF-MS proved to be a promising method for analysing wastewater samples, while we concluded that the software for nontarget analysis will need

  3. Development of a metabolomic radiation signature in urine from patients undergoing total body irradiation.

    Science.gov (United States)

    Laiakis, Evagelia C; Mak, Tytus D; Anizan, Sebastien; Amundson, Sally A; Barker, Christopher A; Wolden, Suzanne L; Brenner, David J; Fornace, Albert J

    2014-04-01

    The emergence of the threat of radiological terrorism and other radiological incidents has led to the need for development of fast, accurate and noninvasive methods for detection of radiation exposure. The purpose of this study was to extend radiation metabolomic biomarker discovery to humans, as previous studies have focused on mice. Urine was collected from patients undergoing total body irradiation at Memorial Sloan-Kettering Cancer Center prior to hematopoietic stem cell transplantation at 4-6 h postirradiation (a single dose of 1.25 Gy) and 24 h (three fractions of 1.25 Gy each). Global metabolomic profiling was obtained through analysis with ultra performance liquid chromatography coupled to time-of-flight mass spectrometry (TOFMS). Prior to further analyses, each sample was normalized to its respective creatinine level. Statistical analysis was conducted by the nonparametric Kolmogorov-Smirnov test and the Fisher's exact test and markers were validated against pure standards. Seven markers showed distinct differences between pre- and post-exposure samples. Of those, trimethyl-l-lysine and the carnitine conjugates acetylcarnitine, decanoylcarnitine and octanoylcarnitine play an important role in the transportation of fatty acids across mitochondria for subsequent fatty acid β-oxidation. The remaining metabolites, hypoxanthine, xanthine and uric acid are the final products of the purine catabolism pathway, and high levels of excretion have been associated with increased oxidative stress and radiation induced DNA damage. Further analysis revealed sex differences in the patterns of excretion of the markers, demonstrating that generation of a sex-specific metabolomic signature will be informative and can provide a quick and reliable assessment of individuals in a radiological scenario. This is the first radiation metabolomics study in human urine laying the foundation for the use of metabolomics in biodosimetry and providing confidence in biomarker

  4. Quality classification of Spanish olive oils by untargeted gas chromatography coupled to hybrid quadrupole-time of flight mass spectrometry with atmospheric pressure chemical ionization and metabolomics-based statistical approach.

    Science.gov (United States)

    Sales, C; Cervera, M I; Gil, R; Portolés, T; Pitarch, E; Beltran, J

    2017-02-01

    The novel atmospheric pressure chemical ionization (APCI) source has been used in combination with gas chromatography (GC) coupled to hybrid quadrupole time-of-flight (QTOF) mass spectrometry (MS) for determination of volatile components of olive oil, enhancing its potential for classification of olive oil samples according to their quality using a metabolomics-based approach. The full-spectrum acquisition has allowed the detection of volatile organic compounds (VOCs) in olive oil samples, including Extra Virgin, Virgin and Lampante qualities. A dynamic headspace extraction with cartridge solvent elution was applied. The metabolomics strategy consisted of three different steps: a full mass spectral alignment of GC-MS data using MzMine 2.0, a multivariate analysis using Ez-Info and the creation of the statistical model with combinations of responses for molecular fragments. The model was finally validated using blind samples, obtaining an accuracy in oil classification of 70%, taking the official established method, "PANEL TEST", as reference. PMID:27596432

  5. Rapid and accurate U-Th dating of ancient carbonates using inductively coupled plasma-quadrupole mass spectrometry

    International Nuclear Information System (INIS)

    Here, the potential for rapid and accurate U-Th dating technique of marine aragonite skeletons (deep-sea corals, Lophelia pertusa) and secondary calcite deposits (speleothems and stalagmites) has been explored using inductively coupled plasma-quadrupole mass spectrometry (ICP-QMS). The analytical procedure includes a largely simplified chemical separation technique for uranium (U) and thorium (Th) using UTEVA resin. The developed technique permits simultaneous quantification of uranium [238U] and thorium [232Th] concentrations and their respective isotopic composition, required for U-series disequilibrium dating. Up to 50 U-Th dates per day can be achieved through ICP-QMS with δ234U and δ230Th reproducibility (2 σ) of 3-4 parts per thousand and 1%, respectively. The high sensitivity (≥3.0 x 105 cps/ppb) together with low background (≤0.5 cps) on each mass between 228 and 236 amu allowed U-Th dating of ancient deep-water corals (15-260 kyr) and stalagmites (30-85 kyr) at precision levels of less than 2%. Consequently, the combination of simplified chemistry using UTEVA with state-of-the-art ICP-QMS isotopic measurements that do not require a U-Th separation step now provides an extremely rapid and low-cost U-series dating technology. The level of precision is most convenient for numerous geochronological applications, such as the determination of climatic influences on ecosystem development and carbonate precipitation. As a first-example application we present ICP-QMS U-Th dates of North Atlantic deep-water coral fragments retrieved in the southeastern Porcupine Seabight (MD01-2463G. Mound Therese), indicating a purely interglacial growth of deep-water corals on so-called carbonate mounds over several climate cycles. (authors)

  6. Rapid and Accurate U-Th Dating of Ancient Carbonates using Inductively Coupled Plasma-Quadrupole Mass Spectrometry

    Science.gov (United States)

    Douville, Eric; Sallé, Eline; Frank, Norbert; Eisele, Markus; Pons-Branchu, Edwige; Ayrault, Sophie

    2010-05-01

    Here, the potential for rapid and accurate U-Th dating technique of marine aragonite skeletons (deep-sea corals, Lophelia pertusa) and secondary calcite deposits (speleothems and stalagmites) has been explored using inductively-coupled plasma-quadrupole mass spectrometry (ICP-QMS). The analytical procedure includes a largely simplified chemical separation technique for uranium (U) and thorium (Th) using UTEVA resin. The developed technique permits simultaneous quantification of uranium [238U] and thorium [232Th] concentrations and their respective isotopic composition, required for U-series disequilibrium dating. Up to 50 U-Th dates per day can be achieved through ICP-QMS with 234U and 230Th reproducibility (2sigma) of 3-4 permil and 1 percent, respectively. The high sensitivity (> 300 000 cps/ppb) together with low background (<0.5 cps) on each mass between 228-236 amu allowed U-Th dating of ancient deep water corals (15-260 kyrs) and stalagmites (30-85 kyrs) at precision levels of less than 2%. Consequently, the combination of simplified chemistry using UTEVA with state-of-the-art ICP-QMS isotopic measurements that do not require a U-Th separation step now provides an extremely rapid and low-cost U-series dating technology. The level of precision is most convenient for numerous geochronological applications, such as the determination of climatic influences on ecosystem development and carbonate precipitation. As a first-example application we present ICP-QMS U-Th dates of North Atlantic deep-water coral fragments retrieved in the southeastern Porcupine Seabight (MD01-2463G, Mound Thérèse), indicating a purely interglacial growth of deep-water corals on so-called carbonate mounds over several climate cycles.

  7. Metabolomics data normalization with EigenMS.

    Directory of Open Access Journals (Sweden)

    Yuliya V Karpievitch

    Full Text Available Liquid chromatography mass spectrometry has become one of the analytical platforms of choice for metabolomics studies. However, LC-MS metabolomics data can suffer from the effects of various systematic biases. These include batch effects, day-to-day variations in instrument performance, signal intensity loss due to time-dependent effects of the LC column performance, accumulation of contaminants in the MS ion source and MS sensitivity among others. In this study we aimed to test a singular value decomposition-based method, called EigenMS, for normalization of metabolomics data. We analyzed a clinical human dataset where LC-MS serum metabolomics data and physiological measurements were collected from thirty nine healthy subjects and forty with type 2 diabetes and applied EigenMS to detect and correct for any systematic bias. EigenMS works in several stages. First, EigenMS preserves the treatment group differences in the metabolomics data by estimating treatment effects with an ANOVA model (multiple fixed effects can be estimated. Singular value decomposition of the residuals matrix is then used to determine bias trends in the data. The number of bias trends is then estimated via a permutation test and the effects of the bias trends are eliminated. EigenMS removed bias of unknown complexity from the LC-MS metabolomics data, allowing for increased sensitivity in differential analysis. Moreover, normalized samples better correlated with both other normalized samples and corresponding physiological data, such as blood glucose level, glycated haemoglobin, exercise central augmentation pressure normalized to heart rate of 75, and total cholesterol. We were able to report 2578 discriminatory metabolite peaks in the normalized data (p<0.05 as compared to only 1840 metabolite signals in the raw data. Our results support the use of singular value decomposition-based normalization for metabolomics data.

  8. Rapid Screening of Bovine Milk Oligosaccharides in a Whey Permeate Product and Domestic Animal Milks by Accurate Mass Database and Tandem Mass Spectral Library.

    Science.gov (United States)

    Lee, Hyeyoung; Cuthbertson, Daniel J; Otter, Don E; Barile, Daniela

    2016-08-17

    A bovine milk oligosaccharide (BMO) library, prepared from cow colostrum, with 34 structures was generated and used to rapidly screen oligosaccharides in domestic animal milks and a whey permeate powder. The novel library was entered into a custom Personal Compound Database and Library (PCDL) and included accurate mass, retention time, and tandem mass spectra. Oligosaccharides in minute-sized samples were separated using nanoliquid chromatography (nanoLC) coupled to a high resolution and sensitive quadrupole-Time of Flight (Q-ToF) MS system. Using the PCDL, 18 oligosaccharides were found in a BMO-enriched product obtained from whey permeate processing. The usefulness of the analytical system and BMO library was further validated using milks from domestic sheep and buffaloes. Through BMO PCDL searching, 15 and 13 oligosaccharides in the BMO library were assigned in sheep and buffalo milks, respectively, thus demonstrating significant overlap between oligosaccharides in bovine (cow and buffalo) and ovine (sheep) milks. This method was shown to be an efficient, reliable, and rapid tool to identify oligosaccharide structures using automated spectral matching. PMID:27428379

  9. Accurate Mass MS/MS/MS Analysis of Siderophores Ferrioxamine B and E1 by Collision-Induced Dissociation Electrospray Mass Spectrometry

    Science.gov (United States)

    Sidebottom, Ashley M.; Karty, Jonathan A.; Carlson, Erin E.

    2015-11-01

    Siderophores are bacterially secreted, small molecule iron chelators that facilitate the binding of insoluble iron (III) for reuptake and use in various biological processes. These compounds are classified by their iron (III) binding geometry, as dictated by subunit composition and include groups such as the trihydroxamates (hexadentate ligand) and catecholates (bidentate). Small modifications to the core structure such as acetylation, lipid tail addition, or cyclization, make facile characterization of new siderophores difficult by molecular ion detection alone (MS1). We have expanded upon previous fragmentation-directed studies using electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS/MS) and identified diagnostic MS3 features from the trihydroxamate siderophore class for ferrioxamine B and E1 by accurate mass. Diagnostic features for MS3 include C-C, C-N, amide, and oxime cleavage events with proposed losses of water and -CO from the iron (III) coordination sites. These insights will facilitate the discovery of novel trihydroxamate siderophores from complex sample matrices.

  10. Analysis of the neurotoxic plasticizer n-butylbenzenesulfonamide by gas chromatography combined with accurate mass selected ion monitoring.

    Science.gov (United States)

    Duffield, P; Bourne, D; Tan, K; Garruto, R M; Duncan, M W

    1994-01-01

    The plasticizer, n-butylbenzenesulfonamide (NBBS), is reported to be neurotoxic when inoculated intracisternally or intraperitoneally into rabbits. Because NBBS is commonly used in the production of polyamide (nylon) plastics and is soluble in water, the disposal of NBBS-containing plastics in landfill sites could result in NBBS appearing in the leachate. Further, NBBS could also be leached from packaging into their contents. To allow us to examine the risks posed by NBBS in the environment, we have developed a quantitative assay for this compound. The assay employs a one-step extraction into dichloromethane followed by gas chromatography with accurate mass selected ion recording. The assay incorporates [13C6]NBBS as an internal standard to allow precise quantitation, and four separate ion chromatograms are recorded. NBBS was found in some Australian domestic solidwaste landfill leachate (from less than 0.3 to 94.6 ng/mL), but ground water in the vicinity of a landfill had only trace quantities of NBBS. NBBS was also quantitated in some bottled and cask wines, and levels varied from not detected to 2.17 ng/mL (n = 14). Additional studies are required to assess the public health risks associated with the use of NBBS as a plasticizer. PMID:7861748

  11. Accurate quantification of creatinine in serum by coupling a measurement standard to extractive electrospray ionization mass spectrometry.

    Science.gov (United States)

    Huang, Keke; Li, Ming; Li, Hongmei; Li, Mengwan; Jiang, You; Fang, Xiang

    2016-01-01

    Ambient ionization (AI) techniques have been widely used in chemistry, medicine, material science, environmental science, forensic science. AI takes advantage of direct desorption/ionization of chemicals in raw samples under ambient environmental conditions with minimal or no sample preparation. However, its quantitative accuracy is restricted by matrix effects during the ionization process. To improve the quantitative accuracy of AI, a matrix reference material, which is a particular form of measurement standard, was coupled to an AI technique in this study. Consequently the analyte concentration in a complex matrix can be easily quantified with high accuracy. As a demonstration, this novel method was applied for the accurate quantification of creatinine in serum by using extractive electrospray ionization (EESI) mass spectrometry. Over the concentration range investigated (0.166 ~ 1.617 μg/mL), a calibration curve was obtained with a satisfactory linearity (R(2) = 0.994), and acceptable relative standard deviations (RSD) of 4.6 ~ 8.0% (n = 6). Finally, the creatinine concentration value of a serum sample was determined to be 36.18 ± 1.08 μg/mL, which is in excellent agreement with the certified value of 35.16 ± 0.39 μg/mL. PMID:26759071

  12. Metabolomics in chemical ecology.

    Science.gov (United States)

    Kuhlisch, Constanze; Pohnert, Georg

    2015-07-01

    Chemical ecology elucidates the nature and role of natural products as mediators of organismal interactions. The emerging techniques that can be summarized under the concept of metabolomics provide new opportunities to study such environmentally relevant signaling molecules. Especially comparative tools in metabolomics enable the identification of compounds that are regulated during interaction situations and that might play a role as e.g. pheromones, allelochemicals or in induced and activated defenses. This approach helps overcoming limitations of traditional bioassay-guided structure elucidation approaches. But the power of metabolomics is not limited to the comparison of metabolic profiles of interacting partners. Especially the link to other -omics techniques helps to unravel not only the compounds in question but the entire biosynthetic and genetic re-wiring, required for an ecological response. This review comprehensively highlights successful applications of metabolomics in chemical ecology and discusses existing limitations of these novel techniques. It focuses on recent developments in comparative metabolomics and discusses the use of metabolomics in the systems biology of organismal interactions. It also outlines the potential of large metabolomics initiatives for model organisms in the field of chemical ecology.

  13. Application of Metabolomics in Thyroid Cancer Research

    Directory of Open Access Journals (Sweden)

    Anna Wojakowska

    2015-01-01

    Full Text Available Thyroid cancer is the most common endocrine malignancy with four major types distinguished on the basis of histopathological features: papillary, follicular, medullary, and anaplastic. Classification of thyroid cancer is the primary step in the assessment of prognosis and selection of the treatment. However, in some cases, cytological and histological patterns are inconclusive; hence, classification based on histopathology could be supported by molecular biomarkers, including markers identified with the use of high-throughput “omics” techniques. Beside genomics, transcriptomics, and proteomics, metabolomic approach emerges as the most downstream attitude reflecting phenotypic changes and alterations in pathophysiological states of biological systems. Metabolomics using mass spectrometry and magnetic resonance spectroscopy techniques allows qualitative and quantitative profiling of small molecules present in biological systems. This approach can be applied to reveal metabolic differences between different types of thyroid cancer and to identify new potential candidates for molecular biomarkers. In this review, we consider current results concerning application of metabolomics in the field of thyroid cancer research. Recent studies show that metabolomics can provide significant information about the discrimination between different types of thyroid lesions. In the near future, one could expect a further progress in thyroid cancer metabolomics leading to development of molecular markers and improvement of the tumor types classification and diagnosis.

  14. Metabolomic heterogeneity of pulmonary arterial hypertension.

    Directory of Open Access Journals (Sweden)

    Yidan Zhao

    Full Text Available Although multiple gene and protein expression have been extensively profiled in human pulmonary arterial hypertension (PAH, the mechanism for the development and progression of pulmonary hypertension remains elusive. Analysis of the global metabolomic heterogeneity within the pulmonary vascular system leads to a better understanding of disease progression. Using a combination of high-throughput liquid-and-gas-chromatography-based mass spectrometry, we showed unbiased metabolomic profiles of disrupted glycolysis, increased TCA cycle, and fatty acid metabolites with altered oxidation pathways in the human PAH lung. The results suggest that PAH has specific metabolic pathways contributing to increased ATP synthesis for the vascular remodeling process in severe pulmonary hypertension. These identified metabolites may serve as potential biomarkers for the diagnosis of PAH. By profiling metabolomic alterations of the PAH lung, we reveal new pathogenic mechanisms of PAH, opening an avenue of exploration for therapeutics that target metabolic pathway alterations in the progression of PAH.

  15. Metabolomics Study of Resina Draconis on Myocardial Ischemia Rats Using Ultraperformance Liquid Chromatography/Quadrupole Time-of-Flight Mass Spectrometry Combined with Pattern Recognition Methods and Metabolic Pathway Analysis

    Directory of Open Access Journals (Sweden)

    Yunpeng Qi

    2013-01-01

    Full Text Available Resina draconis (bright red resin isolated from Dracaena cochinchinensis, RD has been clinically used for treatment of myocardial ischemia (MI for many years. However, the mechanisms of its pharmacological action on MI are still poorly understood. This study aimed to characterize the plasma metabolic profiles of MI and investigate the mechanisms of RD on MI using ultraperformance liquid chromatography/quadrupole time-of-flight mass spectrometry-based metabolomics combined with pattern recognition methods and metabolic pathway analysis. Twenty metabolite markers characterizing metabolic profile of MI were revealed, which were mainly involved in aminoacyl-tRNA biosynthesis, phenylalanine, tyrosine, and tryptophan biosynthesis, vascular smooth muscle contraction, sphingolipid metabolism, and so forth. After RD treatment, however, levels of seven MI metabolite markers, including phytosphingosine, sphinganine, acetylcarnitine, cGMP, cAMP, L-tyrosine, and L-valine, were turned over, indicating that RD is likely to alleviate MI through regulating the disturbed vascular smooth muscle contraction, sphingolipid metabolism, phenylalanine metabolism, and BCAA metabolism. To our best knowledge, this is the first comprehensive study to investigate the mechanisms of RD for treating MI, from a metabolomics point of view. Our findings are very valuable to gain a better understanding of MI metabolic profiles and provide novel insights for exploring the mechanisms of RD on MI.

  16. Current metabolomics: technological advances.

    Science.gov (United States)

    Putri, Sastia P; Yamamoto, Shinya; Tsugawa, Hiroshi; Fukusaki, Eiichiro

    2013-07-01

    Metabolomics, the global quantitative assessment of metabolites in a biological system, has played a pivotal role in various fields of science in the post-genomic era. Metabolites are the result of the interaction of the system's genome with its environment and are not merely the end product of gene expression, but also form part of the regulatory system in an integrated manner. Therefore, metabolomics is often considered a powerful tool to provide an instantaneous snapshot of the physiology of a cell. The power of metabolomics lies on the acquisition of analytical data in which metabolites in a cellular system are quantified, and the extraction of the most meaningful elements of the data by using various data analysis tool. In this review, we discuss the latest development of analytical techniques and data analyses methods in metabolomics study.

  17. Metabolomics er fremtiden

    DEFF Research Database (Denmark)

    Pedersern, Birger

    2010-01-01

    Forskningen i fødevarer har fået et potent redskab i hånden. Metabolomics er vejen frem, mener professor Søren Balling Engelsen fra Københavns Universitet......Forskningen i fødevarer har fået et potent redskab i hånden. Metabolomics er vejen frem, mener professor Søren Balling Engelsen fra Københavns Universitet...

  18. COnsortium of METabolomics Studies (COMETS)

    Science.gov (United States)

    The COnsortium of METabolomics Studies (COMETS) is an extramural-intramural partnership that promotes collaboration among prospective cohort studies that follow participants for a range of outcomes and perform metabolomic profiling of individuals.

  19. Xenobiotic metabolomics: major impact on the metabolome.

    Science.gov (United States)

    Johnson, Caroline H; Patterson, Andrew D; Idle, Jeffrey R; Gonzalez, Frank J

    2012-01-01

    Xenobiotics are encountered by humans on a daily basis and include drugs, environmental pollutants, cosmetics, and even components of the diet. These chemicals undergo metabolism and detoxication to produce numerous metabolites, some of which have the potential to cause unintended effects such as toxicity. They can also block the action of enzymes or receptors used for endogenous metabolism or affect the efficacy and/or bioavailability of a coadministered drug. Therefore, it is essential to determine the full metabolic effects that these chemicals have on the body. Metabolomics, the comprehensive analysis of small molecules in a biofluid, can reveal biologically relevant perturbations that result from xenobiotic exposure. This review discusses the impact that genetic, environmental, and gut microflora variation has on the metabolome, and how these variables may interact, positively and negatively, with xenobiotic metabolism.

  20. The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets

    Directory of Open Access Journals (Sweden)

    Carroll Adam J

    2010-07-01

    Full Text Available Abstract Background Standardization of analytical approaches and reporting methods via community-wide collaboration can work synergistically with web-tool development to result in rapid community-driven expansion of online data repositories suitable for data mining and meta-analysis. In metabolomics, the inter-laboratory reproducibility of gas-chromatography/mass-spectrometry (GC/MS makes it an obvious target for such development. While a number of web-tools offer access to datasets and/or tools for raw data processing and statistical analysis, none of these systems are currently set up to act as a public repository by easily accepting, processing and presenting publicly submitted GC/MS metabolomics datasets for public re-analysis. Description Here, we present MetabolomeExpress, a new File Transfer Protocol (FTP server and web-tool for the online storage, processing, visualisation and statistical re-analysis of publicly submitted GC/MS metabolomics datasets. Users may search a quality-controlled database of metabolite response statistics from publicly submitted datasets by a number of parameters (eg. metabolite, species, organ/biofluid etc.. Users may also perform meta-analysis comparisons of multiple independent experiments or re-analyse public primary datasets via user-friendly tools for t-test, principal components analysis, hierarchical cluster analysis and correlation analysis. They may interact with chromatograms, mass spectra and peak detection results via an integrated raw data viewer. Researchers who register for a free account may upload (via FTP their own data to the server for online processing via a novel raw data processing pipeline. Conclusions MetabolomeExpress https://www.metabolome-express.org provides a new opportunity for the general metabolomics community to transparently present online the raw and processed GC/MS data underlying their metabolomics publications. Transparent sharing of these data will allow researchers to

  1. Metabolomics in the fight against malaria

    Directory of Open Access Journals (Sweden)

    Jorge L Salinas

    2014-08-01

    Full Text Available Metabolomics uses high-resolution mass spectrometry to provide a chemical fingerprint of thousands of metabolites present in cells, tissues or body fluids. Such metabolic phenotyping has been successfully used to study various biologic processes and disease states. High-resolution metabolomics can shed new light on the intricacies of host-parasite interactions in each stage of the Plasmodium life cycle and the downstream ramifications on the host’s metabolism, pathogenesis and disease. Such data can become integrated with other large datasets generated using top-down systems biology approaches and be utilised by computational biologists to develop and enhance models of malaria pathogenesis relevant for identifying new drug targets or intervention strategies. Here, we focus on the promise of metabolomics to complement systems biology approaches in the quest for novel interventions in the fight against malaria. We introduce the Malaria Host-Pathogen Interaction Center (MaHPIC, a new systems biology research coalition. A primary goal of the MaHPIC is to generate systems biology datasets relating to human and non-human primate (NHP malaria parasites and their hosts making these openly available from an online relational database. Metabolomic data from NHP infections and clinical malaria infections from around the world will comprise a unique global resource.

  2. Microbial metabolomics in open microscale platforms

    Science.gov (United States)

    Barkal, Layla J.; Theberge, Ashleigh B.; Guo, Chun-Jun; Spraker, Joe; Rappert, Lucas; Berthier, Jean; Brakke, Kenneth A.; Wang, Clay C. C.; Beebe, David J.; Keller, Nancy P.; Berthier, Erwin

    2016-01-01

    The microbial secondary metabolome encompasses great synthetic diversity, empowering microbes to tune their chemical responses to changing microenvironments. Traditional metabolomics methods are ill-equipped to probe a wide variety of environments or environmental dynamics. Here we introduce a class of microscale culture platforms to analyse chemical diversity of fungal and bacterial secondary metabolomes. By leveraging stable biphasic interfaces to integrate microculture with small molecule isolation via liquid–liquid extraction, we enable metabolomics-scale analysis using mass spectrometry. This platform facilitates exploration of culture microenvironments (including rare media typically inaccessible using established methods), unusual organic solvents for metabolite isolation and microbial mutants. Utilizing Aspergillus, a fungal genus known for its rich secondary metabolism, we characterize the effects of culture geometry and growth matrix on secondary metabolism, highlighting the potential use of microscale systems to unlock unknown or cryptic secondary metabolites for natural products discovery. Finally, we demonstrate the potential for this class of microfluidic systems to study interkingdom communication between fungi and bacteria. PMID:26842393

  3. Microbial metabolomics in open microscale platforms.

    Science.gov (United States)

    Barkal, Layla J; Theberge, Ashleigh B; Guo, Chun-Jun; Spraker, Joe; Rappert, Lucas; Berthier, Jean; Brakke, Kenneth A; Wang, Clay C C; Beebe, David J; Keller, Nancy P; Berthier, Erwin

    2016-01-01

    The microbial secondary metabolome encompasses great synthetic diversity, empowering microbes to tune their chemical responses to changing microenvironments. Traditional metabolomics methods are ill-equipped to probe a wide variety of environments or environmental dynamics. Here we introduce a class of microscale culture platforms to analyse chemical diversity of fungal and bacterial secondary metabolomes. By leveraging stable biphasic interfaces to integrate microculture with small molecule isolation via liquid-liquid extraction, we enable metabolomics-scale analysis using mass spectrometry. This platform facilitates exploration of culture microenvironments (including rare media typically inaccessible using established methods), unusual organic solvents for metabolite isolation and microbial mutants. Utilizing Aspergillus, a fungal genus known for its rich secondary metabolism, we characterize the effects of culture geometry and growth matrix on secondary metabolism, highlighting the potential use of microscale systems to unlock unknown or cryptic secondary metabolites for natural products discovery. Finally, we demonstrate the potential for this class of microfluidic systems to study interkingdom communication between fungi and bacteria. PMID:26842393

  4. Computational analysis and ratiometric comparison approaches aimed to assist column selection in hydrophilic interaction liquid chromatography-tandem mass spectrometry targeted metabolomics.

    Science.gov (United States)

    Sampsonidis, Ioannis; Witting, Michael; Koch, Wendelin; Virgiliou, Christina; Gika, Helen G; Schmitt-Kopplin, Philippe; Theodoridis, Georgios A

    2015-08-01

    In the present work two different approaches, a semi-quantitative and a Derringer function approach, were developed to assist column selection for method development in targeted metabolomics. These approaches were applied in the performance assessment of three HILIC columns with different chemistries (an amide, a diol and a zwitterionic phase). This was the first step for the development of a HILIC UPLC-MS/MS method that should be capable to analyze a large number of polar metabolites. Two gradient elution profiles and two mobile phase pH values were tested for the analysis of multi-analyte mixtures. Acquired chromatographic data were firstly treated by a ratiometric, "semi-quantitative" approach which quantifies various overall analysis parameters (e.g. the percent of detected compounds, retentivity and resolved critical pairs). These parameters were used to assess chromatographic performance in a rather conventional/traditional and cumbersome/labor-intensive way. Secondly, a comprehensive and automated comparison of the three columns was performed by monitoring several well-known chromatographic parameters (peak width, resolution, tailing factor, etc.) using a lab-built programming script which calculates overall desirability utilizing Derringer functions. Derringer functions exhibit the advantage that column performance is ultimately expressed in an objective single and quantitative value which can be easily interpreted. In summary, results show that each column exhibits unique strengths in metabolic profiling of polar compounds. The applied methodology proved useful for the selection of the most effective chromatographic system during method development for LC-MS/MS targeted metabolomics, while it could further assist in the selection of chromatographic conditions for the development of multi-analyte methods.

  5. HEASARC Astronomical Archive: GLIESE2MAS - Gliese Catalog Stars with Accurate Coordinates and 2MASS Cross-Identifications

    Data.gov (United States)

    National Aeronautics and Space Administration — This table contains precise epoch 2000 coordinates and cross-identifications to sources in the 2MASS Point Source Catalog for nearly all stars in the Gliese,...

  6. Metabolomic analysis of three Mollicute species.

    Directory of Open Access Journals (Sweden)

    Anna A Vanyushkina

    Full Text Available We present a systematic study of three bacterial species that belong to the class Mollicutes, the smallest and simplest bacteria, Spiroplasma melliferum, Mycoplasma gallisepticum, and Acholeplasma laidlawii. To understand the difference in the basic principles of metabolism regulation and adaptation to environmental conditions in the three species, we analyzed the metabolome of these bacteria. Metabolic pathways were reconstructed using the proteogenomic annotation data provided by our lab. The results of metabolome, proteome and genome profiling suggest a fundamental difference in the adaptation of the three closely related Mollicute species to stress conditions. As the transaldolase is not annotated in Mollicutes, we propose variants of the pentose phosphate pathway catalyzed by annotated enzymes for three species. For metabolite detection we employed high performance liquid chromatography coupled with mass spectrometry. We used liquid chromatography method - hydrophilic interaction chromatography with silica column - as it effectively separates highly polar cellular metabolites prior to their detection by mass spectrometer.

  7. Plasma metabolomics in human pulmonary tuberculosis disease: a pilot study.

    Science.gov (United States)

    Frediani, Jennifer K; Jones, Dean P; Tukvadze, Nestan; Uppal, Karan; Sanikidze, Eka; Kipiani, Maia; Tran, ViLinh T; Hebbar, Gautam; Walker, Douglas I; Kempker, Russell R; Kurani, Shaheen S; Colas, Romain A; Dalli, Jesmond; Tangpricha, Vin; Serhan, Charles N; Blumberg, Henry M; Ziegler, Thomas R

    2014-01-01

    We aimed to characterize metabolites during tuberculosis (TB) disease and identify new pathophysiologic pathways involved in infection as well as biomarkers of TB onset, progression and resolution. Such data may inform development of new anti-tuberculosis drugs. Plasma samples from adults with newly diagnosed pulmonary TB disease and their matched, asymptomatic, sputum culture-negative household contacts were analyzed using liquid chromatography high-resolution mass spectrometry (LC-MS) to identify metabolites. Statistical and bioinformatics methods were used to select accurate mass/charge (m/z) ions that were significantly different between the two groups at a false discovery rate (FDR) of qmetabolites. Identity of specific D-series resolvins, glutamate and Mycobacterium tuberculosis (Mtb)-derived trehalose-6-mycolate was confirmed using LC-MS/MS analysis. Over 23,000 metabolites were detected in untargeted metabolomic analysis and 61 metabolites were significantly different between the two groups. HCA revealed 8 metabolite clusters containing metabolites largely upregulated in patients with TB disease, including anti-TB drugs, glutamate, choline derivatives, Mycobacterium tuberculosis-derived cell wall glycolipids (trehalose-6-mycolate and phosphatidylinositol) and pro-resolving lipid mediators of inflammation, known to stimulate resolution, efferocytosis and microbial killing. The resolvins were confirmed to be RvD1, aspirin-triggered RvD1, and RvD2. This study shows that high-resolution metabolomic analysis can differentiate patients with active TB disease from their asymptomatic household contacts. Specific metabolites upregulated in the plasma of patients with active TB disease, including Mtb-derived glycolipids and resolvins, have potential as biomarkers and may reveal pathways involved in TB disease pathogenesis and resolution. PMID:25329995

  8. Accurate quantitation of pentaerythritol tetranitrate and its degradation products using liquid chromatography-atmospheric pressure chemical ionization-mass spectrometry

    NARCIS (Netherlands)

    Brust, H.; Asten, A. van; Koeberg, M.; Dalmolen, J.; Heijden, A.E.D.M. van der; Schoenmakers, P.

    2014-01-01

    After an explosion of pentaerythritol tetranitrate (PETN), its degradation products pentaerythritol trinitrate (PETriN), dinitrate (PEDiN) and mononitrate (PEMN) were detected using liquid chromatography-atmospheric-pressure chemical-ionization-mass spectrometry (LC-APCI-MS). Discrimination between

  9. Accurate determination of ultra-trace impurities, including europium, in ultra-pure barium carbonate materials through inductively coupled plasma-tandem mass spectrometry

    Science.gov (United States)

    Wu, Shuchao; Zeng, Xiangcheng; Dai, Xuefeng; Hu, Yongping; Li, Gang; Zheng, Cunjiang

    2016-09-01

    Impurities, especially ultra-trace europium (Eu), in ultra-pure barium carbonate materials were accurately determined through inductively coupled plasma-tandem mass spectrometry (ICP-MS/MS). Two reaction modes, namely, mass shift (with O2 as reaction gas) and on-mass modes(with NH3/He and He as reaction gases), were extensively investigated using Eu+ as target analyte. The use of Eu+ → EuO2+, instead of Eu+ → EuO+, as ion pairs in mass shift mode eliminated polyatomic interferences based on Ba matrix ions (135Ba16O2+ on 151Eu16O+ and 137Ba16O2+ on 153Eu16O+). This procedure exhibited enhanced sensitivity and selectivity. When the ICP-MS/MS was operated in NH3 on-mass mode, Eu+ can be determined in its original mass in interference-free conditions because NH3 did not react with Eu+ but with BaO+ to form a neutral product (BaO). The two reaction modes, especially NH3 on mass mode, were validated to be accurate because their resultant isotope ratios of 153Eu/151Eu matched well with that of the natural abundance ratio. The proposed ICP-MS/MS method is a sensitive technique with a limit of detection as low as 2.0 ng L- 1 for 153Eu+. Compared with conventional single-quadrupole (SQ) ICP-MS, both NH3 on-mass mode and O2 mass shift mode in ICP-MS/MS can be used to accurately determine Eu+ in ultra-pure BaCO3 materials. The detected concentration of Eu+ was 4.0 ng L- 1 to 15 ng L- 1, with spiked recoveries ranging from 100%-110%. ICP-MS/MS was also used to eliminate polyatomic interferences, particularly Ba-based interferences, prior to measurement of Gd and Sm. Impurities, including Na, Mg, Al, K, Mn, Fe, Cr, Sr, and Cs, in ultra-pure BaCO3 materials were also determined using ICP-MS/MS in conventional SQ mode.

  10. metaMS: An open-source pipeline for GC–MS-based untargeted metabolomics

    NARCIS (Netherlands)

    Wehrens, H.R.M.J.; Weingart, G.; Mattivi, F.

    2014-01-01

    Untargeted metabolomics are rapidly becoming an important tool for studying complex biological samples. Gas chromatography–mass spectrometry (GC–MS) is the most widely used analytical technology for metabolomic analysis of compounds that are volatile or can be chemically derivatised into volatile co

  11. Rapid and Accurate Identification of Animal Species in Natural Leather Goods by Liquid Chromatography/Mass Spectrometry

    Science.gov (United States)

    Izuchi, Yukari; Takashima, Tsuneo; Hatano, Naoya

    2016-01-01

    The demand for leather goods has grown globally in recent years. Industry revenue is forecast to reach $91.2 billion by 2018. There is an ongoing labelling problem in the leather items market, in that it is currently impossible to identify the species that a given piece of leather is derived from. To address this issue, we developed a rapid and simple method for the specific identification of leather derived from cattle, horses, pigs, sheep, goats, and deer by analysing peptides produced by the trypsin-digestion of proteins contained in leather goods using liquid chromatography/mass spectrometry. We determined species-specific amino acid sequences by liquid chromatography/tandem mass spectrometry analysis using the Mascot software program and demonstrated that collagen α-1(I), collagen α-2(I), and collagen α-1(III) from the dermal layer of the skin are particularly useful in species identification. PMID:27313979

  12. Rapid and Accurate Identification of Animal Species in Natural Leather Goods by Liquid Chromatography/Mass Spectrometry.

    Science.gov (United States)

    Izuchi, Yukari; Takashima, Tsuneo; Hatano, Naoya

    2016-01-01

    The demand for leather goods has grown globally in recent years. Industry revenue is forecast to reach $91.2 billion by 2018. There is an ongoing labelling problem in the leather items market, in that it is currently impossible to identify the species that a given piece of leather is derived from. To address this issue, we developed a rapid and simple method for the specific identification of leather derived from cattle, horses, pigs, sheep, goats, and deer by analysing peptides produced by the trypsin-digestion of proteins contained in leather goods using liquid chromatography/mass spectrometry. We determined species-specific amino acid sequences by liquid chromatography/tandem mass spectrometry analysis using the Mascot software program and demonstrated that collagen α-1(I), collagen α-2(I), and collagen α-1(III) from the dermal layer of the skin are particularly useful in species identification.

  13. Rapid and Accurate Identification of Animal Species in Natural Leather Goods by Liquid Chromatography/Mass Spectrometry.

    Science.gov (United States)

    Izuchi, Yukari; Takashima, Tsuneo; Hatano, Naoya

    2016-01-01

    The demand for leather goods has grown globally in recent years. Industry revenue is forecast to reach $91.2 billion by 2018. There is an ongoing labelling problem in the leather items market, in that it is currently impossible to identify the species that a given piece of leather is derived from. To address this issue, we developed a rapid and simple method for the specific identification of leather derived from cattle, horses, pigs, sheep, goats, and deer by analysing peptides produced by the trypsin-digestion of proteins contained in leather goods using liquid chromatography/mass spectrometry. We determined species-specific amino acid sequences by liquid chromatography/tandem mass spectrometry analysis using the Mascot software program and demonstrated that collagen α-1(I), collagen α-2(I), and collagen α-1(III) from the dermal layer of the skin are particularly useful in species identification. PMID:27313979

  14. CLASH-VLT: CONSTRAINTS ON THE DARK MATTER EQUATION OF STATE FROM ACCURATE MEASUREMENTS OF GALAXY CLUSTER MASS PROFILES

    Energy Technology Data Exchange (ETDEWEB)

    Sartoris, Barbara; Borgani, Stefano; Girardi, Marisa [Dipartimento di Fisica, Sezione di Astronomia, Università di Trieste, Via Tiepolo 11, I-34143 Trieste (Italy); Biviano, Andrea; Balestra, Italo; Nonino, Mario [INAF/Osservatorio Astronomico di Trieste, Via Tiepolo 11, I-34143 Trieste (Italy); Rosati, Piero [Dipartimento di Fisica e Scienze della Terra, Universita' di Ferrara, Via Saragat 1, I-44122 Ferrara (Italy); Umetsu, Keiichi; Czakon, Nicole [Institute of Astronomy and Astrophysics, Academia Sinica, P.O. Box 23-141, Taipei 10617, Taiwan (China); Bartelmann, Matthias [Zentrum für Astronomie der Universität Heidelberg, ITA, Albert-Ueberle-Str. 2, D-69120 Heidelberg (Germany); Grillo, Claudio [Dark Cosmology Centre, Niels Bohr Institute, University of Copenhagen, Juliane Maries Vej 30, DK-2100 Copenhagen (Denmark); Lemze, Doron; Medezinski, Elinor [Department of Physics and Astronomy, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 (United States); Zitrin, Adi [Cahill Center for Astronomy and Astrophysics, California Institute of Technology, MS 249-17, Pasadena, CA 91125 (United States); Mercurio, Amata [INAF/Osservatorio Astronomico di Capodimonte, Via Moiariello 16, I-80131 Napoli (Italy); Postman, Marc; Bradley, Larry; Coe, Dan [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Broadhurst, Tom [Department of Theoretical Physics, University of the Basque Country, P.O. Box 644, E-48080 Bilbao (Spain); Melchior, Peter, E-mail: sartoris@oats.inaf.it [Department of Physics, The Ohio State University, Columbus, OH 43210 (United States); and others

    2014-03-01

    A pressureless scenario for the dark matter (DM) fluid is a widely adopted hypothesis, despite the absence of direct observational evidence. According to general relativity, the total mass-energy content of a system shapes the gravitational potential well, but different test particles perceive this potential in different ways depending on their properties. Cluster galaxy velocities, being <mass. We exploit this phenomenon to constrain the equation of state (EoS) parameter of the fluid, primarily DM, contained in galaxy clusters. We use complementary information provided by the kinematic and lensing mass profiles of the galaxy cluster MACS 1206.2–0847 at z = 0.44, as obtained in an extensive imaging and spectroscopic campaign within the Cluster Lensing And Supernova survey with Hubble. The unprecedented high quality of our data set and the properties of this cluster are well suited to determine the EoS parameter of the cluster fluid. Since baryons contribute at most 15% to the total mass in clusters and their pressure is negligible, the EoS parameter we derive describes the behavior of the DM fluid. We obtain the most stringent constraint on the DM EoS parameter to date, w = (p{sub r} + 2 p{sub t} )/(3 c {sup 2}ρ) = 0.00 ± 0.15 (stat) ± 0.08 (syst), averaged over the radial range 0.5 Mpc ≤ r ≤ r {sub 200}, where p{sub r} and p{sub t} are the radial and tangential pressure, and ρ is the density. We plan to further improve our constraint by applying the same procedure to all clusters from the ongoing Cluster Lensing And Supernova Survey with Hubble-Very Large Telescope program.

  15. CLASH-VLT: Constraints on the Dark Matter Equation of State from Accurate Measurements of Galaxy Cluster Mass Profiles

    CERN Document Server

    Sartoris, Barbara; Rosati, Piero; Borgani, Stefano; Umetsu, Keiichi; Bartelmann, Matthias; Girardi, Marisa; Grillo, Claudio; Lemze, Doron; Zitrin, Adi; Balestra, Italo; Mercurio, Amata; Nonino, Mario; Postman, Marc; Czakon, Nicole; Bradley, Larry; Broadhurst, Tom; Coe, Dan; Medezinski, Elinor; Melchior, Peter; Meneghetti, Massimo; Merten, Julian; Annunziatella, Marianna; Benitez, Narciso; Czoske, Oliver; Donahue, Megan; Ettori, Stefano; Ford, Holland; Fritz, Alexander; Kelson, Dan; Koekemoer, Anton; Kuchner, Ulrike; Lombardi, Marco; Maier, Christian; Mou, Leonidas A; Munari, Emiliano; Presotto, Valentina; Scodeggio, Marco; Seitz, Stella; Tozzi, Paolo; Zheng, Wei; Ziegler, Bodo

    2014-01-01

    A pressureless scenario for the Dark Matter (DM) fluid is a widely adopted hypothesis, despite the absence of a direct observational evidence. According to general relativity, the total mass-energy content of a system shapes the gravitational potential well, but different test particles perceive this potential in different ways depending on their properties. Cluster galaxy velocities, being $\\ll$c, depend solely on the gravitational potential, whereas photon trajectories reflect the contributions from the gravitational potential plus a relativistic-pressure term that depends on the cluster mass. We exploit this phenomenon to constrain the Equation of State (EoS) parameter of the fluid, primarily DM, contained in galaxy clusters. We use the complementary information provided by the kinematic and lensing mass profiles of the galaxy cluster MACS 1206.2-0847 at $z=0.44$, as obtained in an extensive imaging and spectroscopic campaign within the CLASH survey. The unprecedented high quality of our data-set and the p...

  16. Metabolomics Research Group 2011 Study

    OpenAIRE

    Asara, J. M.; Tolstikov, V.V.; Aronov, P.; Kesler, B.; Shulaev, V.; Turck, C. W.; Wikoff, W R

    2011-01-01

    The ABRF Metabolomics Research Group (MRG) was formed in 2009 and aims to educate research scientists and resource facilities in the analytical approaches and management of data resulting from comprehensive metabolite studies and to promote the science and standardization of metabolomic analyses for a variety of applications. Last year the MRG conducted a ‘Survey Study’ on the current use of metabolomics technologies and procedures in core facilities. This year the MRG is organizing a ‘Resear...

  17. Metabolomics for Quality and food security

    International Nuclear Information System (INIS)

    By the term 'Metabolomics' means the discipline which allows you to determine the set of small molecules (metabolites) produced by an organism in a given time. The metabolomic analysis requires complex technological platforms that allow, in the first place, the separation (chromatography liquid or gaseous) of the different molecules and, subsequently, the identification of the same on the basis of characteristic ratio between their mass and charge (m / z). This study arises by estimates that, between climate change planned for the coming decades, there will also be quick increasing the concentration of Co2 in the atmosphere. In this context, it is essential to predict how these changes weather will impact on product quality plant at the base of our diet.

  18. Self-aliquoting microarray plates for accurate quantitative matrix-assisted laser desorption/ionization mass spectrometry.

    Science.gov (United States)

    Pabst, Martin; Fagerer, Stephan R; Köhling, Rudolf; Küster, Simon K; Steinhoff, Robert; Badertscher, Martin; Wahl, Fabian; Dittrich, Petra S; Jefimovs, Konstantins; Zenobi, Renato

    2013-10-15

    Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a fast analysis tool employed for the detection of a broad range of analytes. However, MALDI-MS has a reputation of not being suitable for quantitative analysis. Inhomogeneous analyte/matrix co-crystallization, spot-to-spot inhomogeneity, as well as a typically low number of replicates are the main contributing factors. Here, we present a novel MALDI sample target for quantitative MALDI-MS applications, which addresses the limitations mentioned above. The platform is based on the recently developed microarray for mass spectrometry (MAMS) technology and contains parallel lanes of hydrophilic reservoirs. Samples are not pipetted manually but deposited by dragging one or several sample droplets with a metal sliding device along these lanes. Sample is rapidly and automatically aliquoted into the sample spots due to the interplay of hydrophilic/hydrophobic interactions. With a few microliters of sample, it is possible to aliquot up to 40 replicates within seconds, each aliquot containing just 10 nL. The analyte droplet dries immediately and homogeneously, and consumption of the whole spot during MALDI-MS analysis is typically accomplished within few seconds. We evaluated these sample targets with respect to their suitability for use with different samples and matrices. Furthermore, we tested their application for generating calibration curves of standard peptides with α-cyano-4-hdydroxycinnamic acid as a matrix. For angiotensin II and [Glu(1)]-fibrinopeptide B we achieved coefficients of determination (r(2)) greater than 0.99 without the use of internal standards. PMID:24003910

  19. Comprehensive two-dimensional liquid chromatography tandem diode array detector (DAD) and accurate mass QTOF-MS for the analysis of flavonoids and iridoid glycosides in Hedyotis diffusa.

    Science.gov (United States)

    Li, Duxin; Schmitz, Oliver J

    2015-01-01

    The analysis of chemical constituents in Chinese herbal medicines (CHMs) is a challenge because of numerous compounds with various polarities and functional groups. Liquid chromatography coupled with quadrupole time-of-flight (QTOF) mass spectrometry (LC/MS) is of particular interest in the analysis of herbal components. One of the main attributes of QTOF that makes it an attractive analytical technique is its accurate mass measurement for both precursor and product ions. For the separation of CHMs, comprehensive two-dimensional chromatography (LCxLC) provides much higher resolving power than traditional one-dimensional separation. Therefore, a LCxLC-QTOF-MS system was developed and applied to the analysis of flavonoids and iridoid glycosides in aqueous extracts of Hedyotis diffusa (Rubiaceae). Shift gradient was applied in the two-dimensional separation in the LCxLC system to increase the orthogonality and effective peak distribution area of the analysis. Tentative identification of compounds was done by accurate mass interpretation and validation by UV spectrum. A clear classification of flavonol glycosides (FGs), acylated FGs, and iridoid glycosides (IGs) was shown in different regions of the LCxLC contour plot. In total, five FGs, four acylated FGs, and three IGs were tentatively identified. In addition, several novel flavonoids were found, which demonstrates that LCxLC-QTOF-MS detection also has great potential in herbal medicine analysis. PMID:25171829

  20. Using MALDI-TOF mass spectrometry as a rapid and accurate diagnostic tool in infective endocarditis: a case report of a patient with mitral valve infective endocarditis caused by Abiotrophia defectiva

    DEFF Research Database (Denmark)

    Holler, Jon Gitz; Pedersen, Line; Calum, Henrik;

    2011-01-01

    A case of infective endocarditis caused by Abiotrophia defectiva is presented. The use of MALDI-TOF mass spectrometry as a rapid and accurate diagnostic tool in infective endocarditis is discussed.......A case of infective endocarditis caused by Abiotrophia defectiva is presented. The use of MALDI-TOF mass spectrometry as a rapid and accurate diagnostic tool in infective endocarditis is discussed....

  1. Changes in the Metabolome of Picea balfouriana Embryogenic Tissues That Were Linked to Different Levels of 6-BAP by Gas Chromatography-Mass Spectrometry Approach.

    Science.gov (United States)

    Li, Q F; Wang, J H; Pulkkinen, P; Kong, L S

    2015-01-01

    Embryogenic cultures of Picea balfouriana, which is an important commercial species for reforestation in Southern China, easily lose their embryogenic ability during long-term culture. Embryogenic tissue that proliferated at lower concentrations (3.6 μM and 2.5 μM) of 6-benzylaminopurine (6-BAP) were more productive, and generated 113 ± 6 and 89 ± 3 mature embryos per 100 mg embryogenic tissue, respectively. A metabolomic approach was used to study the changes in metabolites linked to embryogenic competence related to three different 6-BAP concentrations (2.5 μM, 3.6 μM, and 5 μM). A total of 309 compounds were obtained, among which 123 metabolites mapped to Kyoto Encyclopedia of Genes and genomes (KEGG) pathways. The levels of 35 metabolites were significantly differentially regulated among the three 6-BAP treatments, and 32 metabolites differed between the 2.5 μM and 5 μM treatments. A total of 17 metabolites appeared only once among the three comparisons. The combination of a score plot and a loading plot showed that in the samples with higher embryogenic ability (3.6 μM and 2.5 μM), up-regulated metabolites were mostly amino acids and down-regulated metabolites were mostly primary carbohydrates (especially sugars). These results suggested that 6-BAP may influence embryogenic competence by nitrogen metabolism, which could cause an increase in amino acid levels and higher amounts of aspartate, isoleucine, and leucine in tissues with higher embryogenic ability. Furthermore, we speculated that 6-BAP may affect the amount of tryptophan in tissues, which would change the indole-3-acetic acid levels and influence the embryogenic ability.

  2. Changes in the Metabolome of Picea balfouriana Embryogenic Tissues That Were Linked to Different Levels of 6-BAP by Gas Chromatography-Mass Spectrometry Approach.

    Directory of Open Access Journals (Sweden)

    Q F Li

    Full Text Available Embryogenic cultures of Picea balfouriana, which is an important commercial species for reforestation in Southern China, easily lose their embryogenic ability during long-term culture. Embryogenic tissue that proliferated at lower concentrations (3.6 μM and 2.5 μM of 6-benzylaminopurine (6-BAP were more productive, and generated 113 ± 6 and 89 ± 3 mature embryos per 100 mg embryogenic tissue, respectively. A metabolomic approach was used to study the changes in metabolites linked to embryogenic competence related to three different 6-BAP concentrations (2.5 μM, 3.6 μM, and 5 μM. A total of 309 compounds were obtained, among which 123 metabolites mapped to Kyoto Encyclopedia of Genes and genomes (KEGG pathways. The levels of 35 metabolites were significantly differentially regulated among the three 6-BAP treatments, and 32 metabolites differed between the 2.5 μM and 5 μM treatments. A total of 17 metabolites appeared only once among the three comparisons. The combination of a score plot and a loading plot showed that in the samples with higher embryogenic ability (3.6 μM and 2.5 μM, up-regulated metabolites were mostly amino acids and down-regulated metabolites were mostly primary carbohydrates (especially sugars. These results suggested that 6-BAP may influence embryogenic competence by nitrogen metabolism, which could cause an increase in amino acid levels and higher amounts of aspartate, isoleucine, and leucine in tissues with higher embryogenic ability. Furthermore, we speculated that 6-BAP may affect the amount of tryptophan in tissues, which would change the indole-3-acetic acid levels and influence the embryogenic ability.

  3. CLASH-VLT: Insights on the mass substructures in the Frontier Fields Cluster MACS J0416.1-2403 through accurate strong lens modeling

    CERN Document Server

    Grillo, C; Rosati, P; Mercurio, A; Balestra, I; Munari, E; Nonino, M; Caminha, G B; Lombardi, M; De Lucia, G; Borgani, S; Gobat, R; Biviano, A; Girardi, M; Umetsu, K; Coe, D; Koekemoer, A M; Postman, M; Zitrin, A; Halkola, A; Broadhurst, T; Sartoris, B; Presotto, V; Annunziatella, M; Maier, C; Fritz, A; Vanzella, E; Frye, B

    2014-01-01

    We present a detailed mass reconstruction and a novel study on the substructure properties in the core of the CLASH and Frontier Fields galaxy cluster MACS J0416.1-2403. We show and employ our extensive spectroscopic data set taken with the VIMOS instrument as part of our CLASH-VLT program, to confirm spectroscopically 10 strong lensing systems and to select a sample of 175 plausible cluster members to a limiting stellar mass of log(M_*/M_Sun) ~ 8.6. We reproduce the measured positions of 30 multiple images with a remarkable median offset of only 0.3" by means of a comprehensive strong lensing model comprised of 2 cluster dark-matter halos, represented by cored elliptical pseudo-isothermal mass distributions, and the cluster member components. The latter have total mass-to-light ratios increasing with the galaxy HST/WFC3 near-IR (F160W) luminosities. The measurement of the total enclosed mass within the Einstein radius is accurate to ~5%, including systematic uncertainties. We emphasize that the use of multip...

  4. CYP450 phenotyping and metabolite identification of quinine by accurate mass UPLC-MS analysis: a possible metabolic link to blackwater fever

    OpenAIRE

    Marcsisin, Sean R; Jin, Xiannu; Bettger, Theresa; McCulley, Nicholas; Sousa, Jason C; Shanks, G Dennis; Tekwani, Babu L.; Sahu, Rajnish; Reichard, Gregory A; Sciotti, Richard J; Melendez, Victor; Pybus, Brandon S

    2013-01-01

    Background The naturally occurring alkaloid drug, quinine is commonly used for the treatment of severe malaria. Despite centuries of use, its metabolism is still not fully understood, and may play a role in the haemolytic disorders associated with the drug. Methods Incubations of quinine with CYPs 1A2, 2C9, 2C19, 2D6, and 3A4 were conducted, and the metabolites were characterized by accurate mass UPLC-MSE analysis. Reactive oxygen species generation was also measured in human erythrocytes inc...

  5. Metabolomics and Atherosclerosis

    OpenAIRE

    Sascha N Goonewardena; Prevette, Lisa E.; Desai, Ankit A

    2010-01-01

    Metabolites reflect the dynamic processes underlying cellular homeostasis. Recent advances in analytical chemistry and molecular biology have set the stage for metabolite profiling to help us understand complex molecular processes and physiology. Metabolomics is the comparative analysis of metabolite flux and how it relates to biological phenotypes. As an intermediate phenotype, metabolite signatures capture a unique aspect of cellular dynamics that is not typically interrogated, providing a ...

  6. CLASH-VLT: INSIGHTS ON THE MASS SUBSTRUCTURES IN THE FRONTIER FIELDS CLUSTER MACS J0416.1–2403 THROUGH ACCURATE STRONG LENS MODELING

    Energy Technology Data Exchange (ETDEWEB)

    Grillo, C. [Dark Cosmology Centre, Niels Bohr Institute, University of Copenhagen, Juliane Maries Vej 30, DK-2100 Copenhagen (Denmark); Suyu, S. H.; Umetsu, K. [Institute of Astronomy and Astrophysics, Academia Sinica, P.O. Box 23-141, Taipei 10617, Taiwan (China); Rosati, P.; Caminha, G. B. [Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Ferrara, Via Saragat 1, I-44122 Ferrara (Italy); Mercurio, A. [INAF - Osservatorio Astronomico di Capodimonte, Via Moiariello 16, I-80131 Napoli (Italy); Balestra, I.; Munari, E.; Nonino, M.; De Lucia, G.; Borgani, S.; Biviano, A.; Girardi, M. [INAF - Osservatorio Astronomico di Trieste, via G. B. Tiepolo 11, I-34143, Trieste (Italy); Lombardi, M. [Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16, I-20133 Milano (Italy); Gobat, R. [Laboratoire AIM-Paris-Saclay, CEA/DSM-CNRS-Universitè Paris Diderot, Irfu/Service d' Astrophysique, CEA Saclay, Orme des Merisiers, F-91191 Gif sur Yvette (France); Coe, D.; Koekemoer, A. M.; Postman, M. [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21208 (United States); Zitrin, A. [Cahill Center for Astronomy and Astrophysics, California Institute of Technology, MS 249-17, Pasadena, CA 91125 (United States); Halkola, A., E-mail: grillo@dark-cosmology.dk; and others

    2015-02-10

    We present a detailed mass reconstruction and a novel study on the substructure properties in the core of the Cluster Lensing And Supernova survey with Hubble (CLASH) and Frontier Fields galaxy cluster MACS J0416.1–2403. We show and employ our extensive spectroscopic data set taken with the VIsible Multi-Object Spectrograph instrument as part of our CLASH-VLT program, to confirm spectroscopically 10 strong lensing systems and to select a sample of 175 plausible cluster members to a limiting stellar mass of log (M {sub *}/M {sub ☉}) ≅ 8.6. We reproduce the measured positions of a set of 30 multiple images with a remarkable median offset of only 0.''3 by means of a comprehensive strong lensing model comprised of two cluster dark-matter halos, represented by cored elliptical pseudo-isothermal mass distributions, and the cluster member components, parameterized with dual pseudo-isothermal total mass profiles. The latter have total mass-to-light ratios increasing with the galaxy HST/WFC3 near-IR (F160W) luminosities. The measurement of the total enclosed mass within the Einstein radius is accurate to ∼5%, including the systematic uncertainties estimated from six distinct mass models. We emphasize that the use of multiple-image systems with spectroscopic redshifts and knowledge of cluster membership based on extensive spectroscopic information is key to constructing robust high-resolution mass maps. We also produce magnification maps over the central area that is covered with HST observations. We investigate the galaxy contribution, both in terms of total and stellar mass, to the total mass budget of the cluster. When compared with the outcomes of cosmological N-body simulations, our results point to a lack of massive subhalos in the inner regions of simulated clusters with total masses similar to that of MACS J0416.1–2403. Our findings of the location and shape of the cluster dark-matter halo density profiles and on the cluster substructures provide

  7. Masses of the components of SB2 binaries observed with Gaia. III. Accurate SB2 orbits for 10 binaries and masses of HIP 87895

    CERN Document Server

    Kiefer, Flavien; Arenou, Frédéric; Pourbaix, Dimitri; Famaey, Benoit; Guillout, Patrick; Lebreton, Yveline; Gómez-Morán, Ada Nebot; Mazeh, Tsevi; Salomon, Jean-Baptiste; Soubiran, Caroline; Tal-Or, Lev

    2016-01-01

    In anticipation of the Gaia astrometric mission, a large sample of spectroscopic binaries has been observed since 2010 with the SOPHIE spectrograph at the Haute--Provence Observatory. Our aim is to derive the orbital elements of double-lined spectroscopic binaries (SB2s) with an accuracy sufficient to finally obtain the masses of the components with relative errors as small as 1 % when the astrometric measurements of Gaia are taken into account. In this paper we present the results from five years of observations of 10 SB2 systems with periods ranging from 37 to 881 days. Using the TODMOR algorithm we computed radial velocities from the spectra, and then derived the orbital elements of these binary systems. The minimum masses of the components are then obtained with an accuracy better than 1.2 % for the ten binaries. Combining the radial velocities with existing interferometric measurements, we derived the masses of the primary and secondary components of HIP 87895 with an accuracy of 0.98 % and 1.2 % respect...

  8. Microbial metabolomics : Toward a platform with full metabolome coverage

    NARCIS (Netherlands)

    Werf, M.J.v.d.; Overkamp, K.M.; Muilwijk, B.; Coulier, L.; Hankemeier, T.

    2007-01-01

    Achieving metabolome data with satisfactory coverage is a formidable challenge in metabolomics because metabolites are a chemically highly diverse group of compounds. Here we present a strategy for the development of an advanced analytical platform that allows the comprehensive analysis of microbial

  9. Exploring the Process of Energy Generation in Pathophysiology by Targeted Metabolomics: Performance of a Simple and Quantitative Method

    Science.gov (United States)

    Riera-Borrull, Marta; Rodríguez-Gallego, Esther; Hernández-Aguilera, Anna; Luciano, Fedra; Ras, Rosa; Cuyàs, Elisabet; Camps, Jordi; Segura-Carretero, Antonio; Menendez, Javier A.; Joven, Jorge; Fernández-Arroyo, Salvador

    2016-01-01

    Abnormalities in mitochondrial metabolism and regulation of energy balance contribute to human diseases. The consequences of high fat and other nutrient intake, and the resulting acquired mitochondrial dysfunction, are essential to fully understand common disorders, including obesity, cancer, and atherosclerosis. To simultaneously and noninvasively measure and quantify indirect markers of mitochondrial function, we have developed a method based on gas chromatography coupled to quadrupole-time of flight mass spectrometry and an electron ionization interface, and validated the system using plasma from patients with peripheral artery disease, human cancer cells, and mouse tissues. This approach was used to increase sensibility in the measurement of a wide dynamic range and chemical diversity of multiple intermediate metabolites used in energy metabolism. We demonstrate that our targeted metabolomics method allows for quick and accurate identification and quantification of molecules, including the measurement of small yet significant biological changes in experimental samples. The apparently low process variability required for its performance in plasma, cell lysates, and tissues allowed a rapid identification of correlations between interconnected pathways. Our results suggest that delineating the process of energy generation by targeted metabolomics can be a valid surrogate for predicting mitochondrial dysfunction in biological samples. Importantly, when used in plasma, targeted metabolomics should be viewed as a robust and noninvasive source of biomarkers in specific pathophysiological scenarios.

  10. Metabolomic Profile Analysis of Human Follicular Fluid in Repeated IVF Failure Patients Using Gas Chromatography/Mass Spectrometry%反复IVF失败患者卵泡液代谢组学的检测分析

    Institute of Scientific and Technical Information of China (English)

    夏兰; 胡双纲; 赵晓明; 孙赟; 洪燕; 郑菊芬; 向祖琼; 姚宁; 赵磊文; 郭毅

    2012-01-01

    目的:探讨与卵子发育潜能相关的代谢物质.方法:运用气相色谱-质谱仪(GC-MS)回顾性分析13例反复IVF失败(RIF组)和15例同期第1次行IVF-ET成功妊娠患者(对照组)的卵泡液代谢组学.结果:用偏最小二乘法分析样本主成分,结果显示RIF组和对照组的主成分积分值集中分布于2个不同区域,且反复IVF失败组较对照组有11种氨基酸含量显著升高,而二元羧酸、胆固醇及部分有机酸含量显著降低.结论:升高的缬氨酸、苏氨酸、异亮氨酸、半胱氨酸、丝氨酸、脯氨酸、丙氨酸、苯丙氨酸、赖氨酸、甲硫氨酸、鸟氨酸,和降低的二元羧酸、胆固醇可能成为预测卵子发育潜能的代谢标志物.%Objective: To explore the metabolomic profile which can access the oocyte developmental capacity. Methods: The follicular fluid (FF) samples were collected from 13 patients with repeated IVF failure (RIF) and 15 patients who got pregnant at the first IVF-ET theropy. Gas chromatography/mass spectrometry (GC-MS) was utilized to obtain the metabolomic information. Results: The PCA-DA scores showed that the different samples were scattered into two different regions, 20 metabolites were detected differently between the two groups. Conclusion: Elevated amino acid such as valine, threonine, isoleucine, cysteine, serine, proline, alanine, phenylalanine, lysine, methionine, ornithine and the decline of dual-carboxylic acid and cholesterol may predict the oocyte developmental capacity.

  11. Hydrophilic interaction liquid chromatography coupled with mass spectrometry for metabolomic analysis of Escherichia coli%亲水作用色谱/质谱联用方法用于大肠杆菌代谢组分析

    Institute of Scientific and Technical Information of China (English)

    王希越; 高鹏; 许国旺

    2014-01-01

    The zwitterionic hydrophilic interaction liquid chromatography coupled with mass spectrometry( ZIC-HILIC/MS)method was developed and applied for studying the metabolome of Escherichia coli. In this method,the linear ranges of the 52 representative compounds were between 2-6 orders of magnitude. Moreover the lowest limits of detection of most compounds were at ng/mL levels. The analysis for six samples prepared in parallel showed that the method had good reproducibility with more than 85% metabolites with the RSDs of peak area less than 30%. The precision of the method was tested by evaluating the relative recoveries of six internal standards at the low,middle and high concentrations. The results exhibited that the intraday precisions( RSDs)of the six compounds in the same concentrations were less than 20%. The recoveries of most compounds were accepted in the range of 70%-130%. The results of metabo-lomic analysis of three Escherichia coli strains with genetic modified yfcC gene showed that some small peptides, amino acids, nucleosides, organic acids and phospholipids changed differentially after the yfcC gene modification. These results indicated that the ZIC-HILIC/MS method could detect diverse metabolites and be used for metabolomic analysis purpose with good reproducibility and stability.%建立了两性离子亲水作用色谱/质谱联用方法用于大肠杆菌胞内极性代谢物的分离分析。选取52个代表性极性物质对方法进行考察,发现此方法有较好的线性范围,且大部分物质最低检测限均在 ng/mL 数量级。平行制备6份样品进行分析,结果显示85%以上代谢物峰面积的 RSD值小于30%。6个内标物质在低、中、高3个浓度下的日内精密度( RSD)均小于20%,大部分物质的相对回收率都在可接受的范围内(70%~130%)。把此方法用于yfcC基因改造的3株大肠杆菌代谢组分析,发现一些小肽、氨基酸、核苷、有机酸

  12. Dual electrospray ionization source for confident generation of accurate mass tags using liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry.

    Science.gov (United States)

    Nepomuceno, Angelito I; Muddiman, David C; Bergen, H Robert; Craighead, James R; Burke, Michael J; Caskey, Patrick E; Allan, Jonathan A

    2003-07-15

    Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) has rapidly established a prominent role in proteomics because of its unparalleled resolving power, sensitivity and ability to achieve high mass measurement accuracy (MMA) simultaneously. However, space-charge effects must be quantitatively, routinely, and confidently corrected because they are known to profoundly influence MMA. We argue that the most effective way to account for space-charge effects is to introduce an internal mass calibrant (IMC) using a dual electrospray ionization (ESI) source where the IMC is added from a separate ESI emitter. The major disadvantage of our initial dual ESI source to achieve high MMA, and arguably the only one, was the time required to switch between the analyte emitter and IMC emitter (i.e., >300 ms). While this "switching time" was acceptable for direct infusion experiments, it did not lend itself to high-throughput applications or when conducting on-line liquid separations. In this report, we completely redesigned the dual ESI source and demonstrate several key attributes. First, the new design allows for facile alignment of ESI emitters, undetectable vibration, and the ability to extend to multiple emitters. Second, the switching time was reduced to IMC to be accumulated "simultaneously" in the external ion reservoir and injected as a single ion packet into the ion cyclotron resonance cell, eliminating the need for a separate accumulation and ion injection event for the IMC. Third, by using a high concentration of the IMC, the residence time on this emitter could be reduced to approximately 80 ms, allowing for more time spent accumulating analyte ions of significantly lower concentration. Fourth, multiplexed on-line separations can be carried out providing increased throughput. Specifically, the new dual ESI source has demonstrated its ability to produce a stable ion current over a 45-min time period at 7 T resulting in mass accuracies of 1.08 ppm +/- 0

  13. Metabolomic profiling using Orbitrap Fourier transform mass spectrometry with hydrophilic interaction chromatography : a method with wide applicability to analysis of biomolecules

    NARCIS (Netherlands)

    Kamleh, A.; Barrett, M. P.; Wildridge, D.; Burchmore, R. J. S.; Scheltema, R. A.; Watson, D. G.

    2008-01-01

    It was shown that coupling hydrophilic interaction chromatography (HILIC) to Orbitrap Fourier transform mass spectrometery (FT-MS) provided an excellent tool for metabolic profiling, principally due to rapid elution of lipids in advance of most metabolites entering the mass spectrometer. We used in

  14. Sensitivity improvement in hydrophilic interaction chromatography negative mode electrospray ionization mass spectrometry using 2-(2-methoxyethoxy)ethanol as a post-column modifier for non-targeted metabolomics.

    Science.gov (United States)

    Koch, Wendelin; Forcisi, Sara; Lehmann, Rainer; Schmitt-Kopplin, Philippe

    2014-09-26

    The application of ammonia acetate buffered liquid chromatography (LC) eluents is known to concomitantly lead to ion suppression when electrospray ionization mass spectrometry (ESI-MS) detection is used. In negative ESI mode, post column infusion of 2-(2-methoxyethoxy)ethanol (2-MEE) was shown in the literature to help to compensate this adverse effect occurring in reversed phase liquid chromatography mass spectrometry (RP-LC-MS) analyses. Here a setup of direct infusion and hydrophilic interaction chromatography (HILIC) post-column infusion experiments was established in order to investigate systematically the beneficial effects of 2-MEE. We demonstrate that, 2-MEE can help to improve ESI-MS sensitivity in HILIC too and reveal analyte structure specific behaviors. Our study indicates that 2-MEE especially improves ESI response for small and polar molecules. The ESI response of stable isotope labeled amino acids spiked into biological matrices increases up to 50-fold (i.e. D5-l-glutamic acid) when post column infusion of 2-MEE is applied. A non-targeted analysis of a pooled urine sample via HILIC-ESI-QTOF-MS supports this hypothesis. In direct infusion, the combined application of an ammonia acetate buffered solution together with 2-MEE results in an improved ESI response compared to a non-buffered solution. We observed up to 60-fold increased ESI response of l-lysine. We propose this effect is putatively caused by the formation of smaller ESI droplets and stripping of positive charge from ESI droplets due to evaporation of acetic acid anions. In summary, post-column infusion of 2-MEE especially enhances ESI response of small and polar molecules. Therefore it can be regarded as a valuable add-on in targeted or non-targeted metabolomic HILIC-MS studies since this method sets a focus on this molecule category.

  15. Metabolomics reveals mycoplasma contamination interferes with the metabolism of PANC-1 cells.

    Science.gov (United States)

    Yu, Tao; Wang, Yongtao; Zhang, Huizhen; Johnson, Caroline H; Jiang, Yiming; Li, Xiangjun; Wu, Zeming; Liu, Tian; Krausz, Kristopher W; Yu, Aiming; Gonzalez, Frank J; Huang, Min; Bi, Huichang

    2016-06-01

    Mycoplasma contamination is a common problem in cell culture and can alter cellular functions. Since cell metabolism is either directly or indirectly involved in every aspect of cell function, it is important to detect changes to the cellular metabolome after mycoplasma infection. In this study, liquid chromatography mass spectrometry (LC/MS)-based metabolomics was used to investigate the effect of mycoplasma contamination on the cellular metabolism of human pancreatic carcinoma cells (PANC-1). Multivariate analysis demonstrated that mycoplasma contamination induced significant metabolic changes in PANC-1 cells. Twenty-three metabolites were identified and found to be involved in arginine and purine metabolism and energy supply. This study demonstrates that mycoplasma contamination significantly alters cellular metabolite levels, confirming the compelling need for routine checking of cell cultures for mycoplasma contamination, particularly when used for metabolomics studies. Graphical abstract Metabolomics reveals mycoplasma contamination changes the metabolome of PANC-1 cells.

  16. Metabolomics reveals mycoplasma contamination interferes with the metabolism of PANC-1 cells.

    Science.gov (United States)

    Yu, Tao; Wang, Yongtao; Zhang, Huizhen; Johnson, Caroline H; Jiang, Yiming; Li, Xiangjun; Wu, Zeming; Liu, Tian; Krausz, Kristopher W; Yu, Aiming; Gonzalez, Frank J; Huang, Min; Bi, Huichang

    2016-06-01

    Mycoplasma contamination is a common problem in cell culture and can alter cellular functions. Since cell metabolism is either directly or indirectly involved in every aspect of cell function, it is important to detect changes to the cellular metabolome after mycoplasma infection. In this study, liquid chromatography mass spectrometry (LC/MS)-based metabolomics was used to investigate the effect of mycoplasma contamination on the cellular metabolism of human pancreatic carcinoma cells (PANC-1). Multivariate analysis demonstrated that mycoplasma contamination induced significant metabolic changes in PANC-1 cells. Twenty-three metabolites were identified and found to be involved in arginine and purine metabolism and energy supply. This study demonstrates that mycoplasma contamination significantly alters cellular metabolite levels, confirming the compelling need for routine checking of cell cultures for mycoplasma contamination, particularly when used for metabolomics studies. Graphical abstract Metabolomics reveals mycoplasma contamination changes the metabolome of PANC-1 cells. PMID:27074779

  17. Non-targeted screening for contaminants in paper and board food-contact materials using effect-directed analysis and accurate mass spectrometry.

    Science.gov (United States)

    Bengtström, Linda; Rosenmai, Anna Kjerstine; Trier, Xenia; Jensen, Lisbeth Krüger; Granby, Kit; Vinggaard, Anne Marie; Driffield, Malcolm; Højslev Petersen, Jens

    2016-06-01

    Due to large knowledge gaps in chemical composition and toxicological data for substances involved, paper and board food-contact materials (P&B FCM) have been emerging as a FCM type of particular concern for consumer safety. This study describes the development of a step-by-step strategy, including extraction, high-performance liquid chromatography (HPLC) fractionation, tentative identification of relevant substances and in vitro testing of selected tentatively identified substances. As a case study, we used two fractions from a recycled pizza box sample which exhibited aryl hydrocarbon receptor (AhR) activity. These fractions were analysed by gas chromatography (GC) and ultra-HPLC (UHPLC) coupled to quadrupole time-of-flight mass spectrometers (QTOF MS) in order tentatively to identify substances. The elemental composition was determined for peaks above a threshold, and compared with entries in a commercial mass spectral library for GC-MS (GC-EI-QTOF MS) analysis and an in-house built library of accurate masses for substances known to be used in P&B packaging for UHPLC-QTOF analysis. Of 75 tentatively identified substances, 15 were initially selected for further testing in vitro; however, only seven were commercially available and subsequently tested in vitro and quantified. Of these seven, the identities of three pigments found in printing inks were confirmed by UHPLC tandem mass spectrometry (QqQ MS/MS). Two pigments had entries in the database, meaning that a material relevant accurate mass database can provide a fast tentative identification. Pure standards of the seven tentatively identified substances were tested in vitro but could not explain a significant proportion of the AhR-response in the extract. Targeted analyses of dioxins and PCBs, both well-known AhR agonists, was performed. However, the dioxins could explain approximately 3% of the activity observed in the pizza box extract indicating that some very AhR active substance(s) still remain to be

  18. Improved batch correction in untargeted MS-based metabolomics

    NARCIS (Netherlands)

    Wehrens, Ron; Hageman, Jos A.; Eeuwijk, van Fred; Kooke, Rik; Flood, Pádraic J.; Wijnker, Erik; Keurentjes, Joost J.B.; Lommen, Arjen; Eekelen, van Henriëtte D.L.M.; Hall, Robert D.; Mumm, Roland; Vos, de Ric C.H.

    2016-01-01

    Introduction: Batch effects in large untargeted metabolomics experiments are almost unavoidable, especially when sensitive detection techniques like mass spectrometry (MS) are employed. In order to obtain peak intensities that are comparable across all batches, corrections need to be performed. S

  19. MetaboLights: towards a new COSMOS of metabolomics data management.

    Science.gov (United States)

    Steinbeck, Christoph; Conesa, Pablo; Haug, Kenneth; Mahendraker, Tejasvi; Williams, Mark; Maguire, Eamonn; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Salek, Reza M; Griffin, Julian L

    2012-10-01

    Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination and analysis. This is based on a rich ecosystem of resources around the world, which has been build during the past ten years, including but not limited to resources such as MassBank in Japan and the Human Metabolome Database in Canada. Now, the European Bioinformatics Institute has launched MetaboLights, a database for metabolomics experiments and the associated metadata (http://www.ebi.ac.uk/metabolights). It is the first comprehensive, cross-species, cross-platform metabolomics database maintained by one of the major open access data providers in molecular biology. In October, the European COSMOS consortium will start its work on Metabolomics data standardization, publication and dissemination workflows. The NIH in the US is establishing 6-8 metabolomics services cores as well as a national metabolomics repository. This communication reports about MetaboLights as a new resource for Metabolomics research, summarises the related developments and outlines how they may consolidate the knowledge management in this third large omics field next to proteomics and genomics.

  20. Biomarker Identification and Pathway Analysis by Serum Metabolomics of Lung Cancer

    OpenAIRE

    2015-01-01

    Lung cancer is one of the most common causes of cancer death, for which no validated tumor biomarker is sufficiently accurate to be useful for diagnosis. Additionally, the metabolic alterations associated with the disease are unclear. In this study, we investigated the construction, interaction, and pathways of potential lung cancer biomarkers using metabolomics pathway analysis based on the Kyoto Encyclopedia of Genes and Genomes database and the Human Metabolome Database to identify the top...

  1. Metabolomic analysis of platelets during storage

    DEFF Research Database (Denmark)

    Paglia, Giuseppe; Sigurjónsson, Ólafur E; Rolfsson, Óttar;

    2015-01-01

    BACKGROUND: Platelet concentrates (PCs) can be prepared using three methods: platelet (PLT)-rich plasma, apheresis, and buffy coat. The aim of this study was to obtain a comprehensive data set that describes metabolism of buffy coat-derived PLTs during storage and to compare it with a previously...... measurements. This data set was obtained by combining a series of standard quality control assays to monitor the quality of stored PLTs and a deep coverage metabolomics study using liquid chromatography coupled with mass spectrometry. RESULTS: Stored PLTs showed a distinct metabolic transition occurring 4 days...

  2. Metabolomics of genetically modified crops.

    Science.gov (United States)

    Simó, Carolina; Ibáñez, Clara; Valdés, Alberto; Cifuentes, Alejandro; García-Cañas, Virginia

    2014-10-20

    Metabolomic-based approaches are increasingly applied to analyse genetically modified organisms (GMOs) making it possible to obtain broader and deeper information on the composition of GMOs compared to that obtained from traditional analytical approaches. The combination in metabolomics of advanced analytical methods and bioinformatics tools provides wide chemical compositional data that contributes to corroborate (or not) the substantial equivalence and occurrence of unintended changes resulting from genetic transformation. This review provides insight into recent progress in metabolomics studies on transgenic crops focusing mainly in papers published in the last decade.

  3. Metabolomics in diabetic complications.

    Science.gov (United States)

    Filla, Laura A; Edwards, James L

    2016-04-01

    With a global prevalence of 9%, diabetes is the direct cause of millions of deaths each year and is quickly becoming a health crisis. Major long-term complications of diabetes arise from persistent oxidative stress and dysfunction in multiple metabolic pathways. The most serious complications involve vascular damage and include cardiovascular disease as well as microvascular disorders such as nephropathy, neuropathy, and retinopathy. Current clinical analyses like glycated hemoglobin and plasma glucose measurements hold some value as prognostic indicators of the severity of complications, but investigations into the underlying pathophysiology are still lacking. Advancements in biotechnology hold the key to uncovering new pathways and establishing therapeutic targets. Metabolomics, the study of small endogenous molecules, is a powerful toolset for studying pathophysiological processes and has been used to elucidate metabolic signatures of diabetes in various biological systems. Current challenges in the field involve correlating these biomarkers to specific complications to provide a better prediction of future risk and disease progression. This review will highlight the progress that has been made in the field of metabolomics including technological advancements, the identification of potential biomarkers, and metabolic pathways relevant to macro- and microvascular diabetic complications.

  4. Mono-colonization with Lactobacillus acidophilus NCFM affects the intestinal metabolome as compared to germ-free mice

    DEFF Research Database (Denmark)

    Roager, Henrik Munch; Sulek, Karolina; Skov, Kasper;

    of colonizing bacteria. In this study the effect of the Lactobacillus acidophilus NCFM strain was investigated by comparing the metabolome of mono-colonized and germ-free mice in several compartments. By liquid-chromatography coupled to mass spectrometry, we were able to show that the metabolome differed...

  5. Ultrahigh-Performance Liquid Chromatography-High-Resolution Quadrupole Time-of-Flight Mass Spectrometry Based Metabolomics Reveals Key Differences between Brachiaria decumbens and B. brizantha, Two Similar Pastures with Different Toxicities.

    Science.gov (United States)

    Pérez, Andy J; Hussain, Syeda M; Pecio, Łukasz; Kowalczyk, Mariusz; Herling, Valdo R; Stochmal, Anna

    2016-06-01

    Several species of Brachiaria (Poaceae) currently cover extensive grazing areas in Brazil, providing valuable source of feed for a large cattle population. However, numerous cases of toxicity outbreaks in livestock have raised concerns on safety of using these plants, especially B. decumbens. In this study, chemometric analysis of ultrahigh-performance liquid chromatography-high-resolution quadrupole time-of-flight mass spectrometry (UHPLC-HR-QTOF-MS) data has for the first time uncovered qualitative and quantitative differences between metabolomes of toxic B. decumbens and nontoxic B. brizantha. The steroidal saponin protoneodioscin was established as the main biomarker for B. decumbens when compared to B. brizantha, and therefore the key explanation for their phytochemical differentiation. Quantification of protodioscin in both plants showed no significant differences; consequently, the idea that this compound is solely responsible for toxicity outbreaks must be discarded. Instead, we propose that the added occurrence of its stereoisomer, protoneodioscin, in B. decumbens, can be considered as the probable cause of these events. Interestingly, the greatest concentrations of saponins for both species were reached during winter (B. decumbens = 53.6 ± 5.1 mg·g(-1) dry weight (D.W.); B. brizantha = 25.0 ± 1.9 mg·g(-1) D.W.) and spring (B. decumbens = 49.4 ± 5.0 mg·g(-1) D.W.; B. brizantha = 27.9 ± 1.4 mg·g(-1) D.W.), although in the case of B. decumbens these values do not vary significantly among seasons. PMID:27192362

  6. Selenium metabolomics in yeast using complementary reversed-phase/hydrophilic ion interaction (HILIC) liquid chromatography–electrospray hybrid quadrupole trap/Orbitrap mass spectrometry

    International Nuclear Information System (INIS)

    Highlights: ► The use of bimodal chromatographic separation enlarged amount of compounds identified. ► The method allowed the largest scale ever (>60 compounds) speciation analysis of selenium metabolites in Se-rich yeast. ► The estimated concentration of compounds was given. - Abstract: A high efficiency chromatographic separation on a porous graphitic carbon stationary phase was developed for a large-scale separation of selenium metabolites in Se-rich yeast prior to their identification by electrospray hybrid quadrupole trap/Orbitrap mass spectrometry (Orbitrap MSn). The reversed-phase (RP) separation mode offered distinctly higher separation efficiency than the hydrophilic ion interaction (HILIC) mode. The latter was nevertheless complementary and useful to validate the detection of several compounds. The method allowed the detection of 64 metabolites including 30 Se-Se or Se-S conjugates (3 triple S/Se/S ones) and 14 selenoethers. 21 previously unreported metabolites were detected on the basis of the selenium isotopic pattern usually matched with the sub-ppm mass accuracy. 9 of these metabolites were subsequently identified using the multi-stage high mass accuracy (<5 ppm) mass spectrometry. The identified metabolites (and their groups) were quantified on-line by ICP-MS fitted with a frequency-matching generator allowing a quasi-uniform response over the large (20–90%) acetonitrile mobile phase concentration range. The morphology of HPLC–ICP-MS chromatograms was remarkably similar to that of HPLC multi-ion extracted ESI-MS chromatograms. The detection limits obtained by ICP MS and ESI MS were 1 and 2 ppb, respectively.

  7. NMR/MS Translator for the Enhanced Simultaneous Analysis of Metabolomics Mixtures by NMR Spectroscopy and Mass Spectrometry: Application to Human Urine.

    Science.gov (United States)

    Bingol, Kerem; Brüschweiler, Rafael

    2015-06-01

    A novel metabolite identification strategy is presented for the combined NMR/MS analysis of complex metabolite mixtures. The approach first identifies metabolite candidates from 1D or 2D NMR spectra by NMR database query, which is followed by the determination of the masses (m/z) of their possible ions, adducts, fragments, and characteristic isotope distributions. The expected m/z ratios are then compared with the MS(1) spectrum for the direct assignment of those signals of the mass spectrum that contain information about the same metabolites as the NMR spectra. In this way, the mass spectrum can be assigned with very high confidence, and it provides at the same time validation of the NMR-derived metabolites. The method was first demonstrated on a model mixture, and it was then applied to human urine collected from a pool of healthy individuals. A number of metabolites could be detected that had not been reported previously, further extending the list of known urine metabolites. The new analysis approach, which is termed NMR/MS Translator, is fully automated and takes only a few seconds on a computer workstation. NMR/MS Translator synergistically uses the power of NMR and MS, enhancing the accuracy and efficiency of the identification of those metabolites compiled in databases. PMID:25881480

  8. The biology of plant metabolomics

    NARCIS (Netherlands)

    Hall, R.D.

    2011-01-01

    Following a general introduction, this book includes details of metabolomics of model species including Arabidopsis and tomato. Further chapters provide in-depth coverage of abiotic stress, data integration, systems biology, genetics, genomics, chemometrics and biostatisitcs. Applications of plant m

  9. Computational approaches for systems metabolomics.

    Science.gov (United States)

    Krumsiek, Jan; Bartel, Jörg; Theis, Fabian J

    2016-06-01

    Systems genetics is defined as the simultaneous assessment and analysis of multi-omics datasets. In the past few years, metabolomics has been established as a robust tool describing an important functional layer in this approach. The metabolome of a biological system represents an integrated state of genetic and environmental factors and has been referred to as a 'link between genotype and phenotype'. In this review, we summarize recent progresses in statistical analysis methods for metabolomics data in combination with other omics layers. We put a special focus on complex, multivariate statistical approaches as well as pathway-based and network-based analysis methods. Moreover, we outline current challenges and pitfalls of metabolomics-focused multi-omics analyses and discuss future steps for the field.

  10. Metabolomics Workbench (MetWB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Metabolomics Program's Data Repository and Coordinating Center (DRCC), housed at the San Diego Supercomputer Center (SDSC), University of California, San Diego,...

  11. Spatially-resolved in vivo plant metabolomics by laser ablation-based mass spectrometry imaging (MSI techniques: LDI-MSI and LAESI

    Directory of Open Access Journals (Sweden)

    Aleš eSvatoš

    2015-07-01

    Full Text Available This short review aims to summarize the current developments and applications of mass spectrometry-based methods for in situ profiling and imaging of plants with minimal or no sample pre-treatment or manipulation. Infrared-laser ablation electrospray ionization (LAESI and UV-laser desorption/ionization (LDI methods are reviewed. The underlying mechanisms of the ionization techniques - namely, laser ablation of biological samples and electrospray ionization - as well as variations of the LAESI ion source for specific targets of interest are described.

  12. Metabolomics of Genetically Modified Crops

    OpenAIRE

    Carolina Simó; Clara Ibáez; Alberto Valdés; Alejandro Cifuentes; Virginia García-Cañas

    2014-01-01

    Metabolomic-based approaches are increasingly applied to analyse genetically modified organisms (GMOs) making it possible to obtain broader and deeper information on the composition of GMOs compared to that obtained from traditional analytical approaches. The combination in metabolomics of advanced analytical methods and bioinformatics tools provides wide chemical compositional data that contributes to corroborate (or not) the substantial equivalence and occurrence of unintended changes resul...

  13. Novel quantitative metabolomic approach for the study of stress responses of plant root metabolism.

    Science.gov (United States)

    Li, Kefeng; Wang, Xu; Pidatala, Venkataramana R; Chang, Chi-Peng; Cao, Xiaohong

    2014-12-01

    Quantitative metabolomics (qMetabolomics) is a powerful tool for understanding the intricate metabolic processes involved in plant abiotic stress responses. qMetabolomics is hindered by the limited coverage and high cost of isotopically labeled standards. In this study, we first selected 271 metabolites which might play important roles in abiotic stress responses as the targets and established a comprehensive LC-MS/MS based qMetabolomic method. We then developed a novel metabolic labeling method using E. coli-Saccharomyces cerevisiae two-step cultivation for the production of uniformly (13)C-labeled metabolites as internal standards. Finally, we applied the developed qMetabolomic method to investigate the influence of Pb stress on maize root metabolism. The absolute concentration of 226 metabolites in maize roots was accurately quantified in a single run within 30 min. Our study also revealed that glycolysis, purine, pyrimidine, and phospholipids were the main metabolic pathways in maize roots involved in Pb stress response. To our knowledge, this is the most comprehensive qMetabolomic method for plant metabolomics thus far. We developed a simple and inexpensive metabolic labeling method which dramatically expanded the availability of uniformly (13)C labeled metabolites. Our findings also provided new insights of maize metabolic responses to Pb stress.

  14. Obesity-Related Metabolomic Analysis of Human Subjects in Black Soybean Peptide Intervention Study by Ultraperformance Liquid Chromatography and Quadrupole-Time-of-Flight Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Min Jung Kim

    2013-01-01

    Full Text Available The present study aimed to identify key metabolites related to weight reduction in humans by studying the metabolic profiles of sera obtained from 34 participants who underwent dietary intervention with black soybean peptides (BSP for 12 weeks. This research is a sequel to our previous work in which the effects of BSP on BMI and blood composition of lipid were investigated. Sera of the study were subjected to ultra performance liquid chromatography and quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS, and the data were analyzed using partial least-squares discriminate analysis (PLS-DA score plots. Body mass index and percent body fat of the test group were reduced. Levels of betaine, benzoic acid, pyroglutamic acid, pipecolic acid, N-phenylacetamide, uric acid, l-aspartyl-l-phenylalanine, and lysophosphatidyl cholines (lysoPCs (C18:1, C18:2, C20:1, and C20:4 showed significant increases. Levels of l-proline, valine, l-leucine/isoleucine, hypoxanthine, glutamine, l-methionine, phenylpyruvic acid, several carnitine derivatives, and lysoPCs (C14:0, PC16:0, C15:0, C16:0, C17:1, C18:0, and C22:0 were significantly decreased. In particular, lysoPC 16:0 with a VIP value of 12.02 is esteemed to be the most important metabolite for evaluating the differences between the 2 serum samples. Our result confirmed weight-lowering effects of BSP, accompanied by favorable changes in metabolites in the subjects’ blood. Therefore, this research enables us to better understand obesity and increases the predictability of the obesity-related risk by studying metabolites present in the blood.

  15. Untargeted Metabolomics To Ascertain Antibiotic Modes of Action.

    Science.gov (United States)

    Vincent, Isabel M; Ehmann, David E; Mills, Scott D; Perros, Manos; Barrett, Michael P

    2016-04-01

    Deciphering the mode of action (MOA) of new antibiotics discovered through phenotypic screening is of increasing importance. Metabolomics offers a potentially rapid and cost-effective means of identifying modes of action of drugs whose effects are mediated through changes in metabolism. Metabolomics techniques also collect data on off-target effects and drug modifications. Here, we present data from an untargeted liquid chromatography-mass spectrometry approach to identify the modes of action of eight compounds: 1-[3-fluoro-4-(5-methyl-2,4-dioxo-pyrimidin-1-yl)phenyl]-3-[2-(trifluoromethyl)phenyl]urea (AZ1), 2-(cyclobutylmethoxy)-5'-deoxyadenosine, triclosan, fosmidomycin, CHIR-090, carbonyl cyanidem-chlorophenylhydrazone (CCCP), 5-chloro-2-(methylsulfonyl)-N-(1,3-thiazol-2-yl)-4-pyrimidinecarboxamide (AZ7), and ceftazidime. Data analysts were blind to the compound identities but managed to identify the target as thymidylate kinase for AZ1, isoprenoid biosynthesis for fosmidomycin, acyl-transferase for CHIR-090, and DNA metabolism for 2-(cyclobutylmethoxy)-5'-deoxyadenosine. Changes to cell wall metabolites were seen in ceftazidime treatments, although other changes, presumably relating to off-target effects, dominated spectral outputs in the untargeted approach. Drugs which do not work through metabolic pathways, such as the proton carrier CCCP, have no discernible impact on the metabolome. The untargeted metabolomics approach also revealed modifications to two compounds, namely, fosmidomycin and AZ7. An untreated control was also analyzed, and changes to the metabolome were seen over 4 h, highlighting the necessity for careful controls in these types of studies. Metabolomics is a useful tool in the analysis of drug modes of action and can complement other technologies already in use. PMID:26833150

  16. 基于核磁和质谱分析技术的代谢组学在癌症诊断中的应用%Nuclear Magnetic Resonance Spectroscopy and Mass Spectrometry-based Metabolomics for Cancer Diagnosis

    Institute of Scientific and Technical Information of China (English)

    顾海巍; 亓云鹏; 许柠; 丁健桦; 安艳波; 陈焕文

    2012-01-01

    In this review, we aim to introduce a relatively new approach, metabolomics, and explore its potential for cancer diagnosis. We will briefly introduce the concept of metabolomics and its rela?tionship with other omics studies in systems biology for cancer detection. The field of metabolomics focuses on the parallel measurement of hundreds of small molecule metabolites in biological samples such as blood, urine, and biopsied tissue. Since metabolite levels are sensitive to subtle changes in the pathological status, metabolomics promises novel avenues for early cancer detection and a better understanding of cancer processes. In fact, many previous metabolomics studies have clearly demons?trated the promises of metabolomics not only for the diagnosis of various kinds of cancer, but also for therapeutic monitoring as well as for drug development. In addition, in this review we will discuss the challenges and future directions for developing metabolomics methods towards clinical applications for cancer diagnosis.%本文对近年来用于癌症诊断的新方法——代谢组学及其在该领域内的应用进行了简要介绍.代谢组学通过定性与定量测量生物样本(血液、尿液、组织等)中数以千计的小分子代谢物,可灵敏地反映代谢组中与病理状态有关的细微变化,从而可为癌症的早期诊断及更好地理解癌变过程提供一种新颖的思路.本文还讨论了代谢组学与系统生物学中其它一些组学在癌症检测上的关联,介绍了一些用代谢组学进行不同癌症的诊断、治疗监测以及药物开发的前期研究工作,并探讨了用于临床癌症诊断的代谢组学方法所面临的机遇、挑战与未来发展方向.

  17. Tandem Mass Spectrometry Measurement of the Collision Products of Carbamate Anions Derived from CO2 Capture Sorbents: Paving the Way for Accurate Quantitation

    Science.gov (United States)

    Jackson, Phil; Fisher, Keith J.; Attalla, Moetaz Ibrahim

    2011-08-01

    The reaction between CO2 and aqueous amines to produce a charged carbamate product plays a crucial role in post-combustion capture chemistry when primary and secondary amines are used. In this paper, we report the low energy negative-ion CID results for several anionic carbamates derived from primary and secondary amines commonly used as post-combustion capture solvents. The study was performed using the modern equivalent of a triple quadrupole instrument equipped with a T-wave collision cell. Deuterium labeling of 2-aminoethanol (1,1,2,2,-d4-2-aminoethanol) and computations at the M06-2X/6-311++G(d,p) level were used to confirm the identity of the fragmentation products for 2-hydroxyethylcarbamate (derived from 2-aminoethanol), in particular the ions CN-, NCO- and facile neutral losses of CO2 and water; there is precedent for the latter in condensed phase isocyanate chemistry. The fragmentations of 2-hydroxyethylcarbamate were generalized for carbamate anions derived from other capture amines, including ethylenediamine, diethanolamine, and piperazine. We also report unequivocal evidence for the existence of carbamate anions derived from sterically hindered amines ( Tris(2-hydroxymethyl)aminomethane and 2-methyl-2-aminopropanol). For the suite of carbamates investigated, diagnostic losses include the decarboxylation product (-CO2, 44 mass units), loss of 46 mass units and the fragments NCO- ( m/z 42) and CN- ( m/z 26). We also report low energy CID results for the dicarbamate dianion (-O2CNHC2H4NHCO{2/-}) commonly encountered in CO2 capture solution utilizing ethylenediamine. Finally, we demonstrate a promising ion chromatography-MS based procedure for the separation and quantitation of aqueous anionic carbamates, which is based on the reported CID findings. The availability of accurate quantitation methods for ionic CO2 capture products could lead to dynamic operational tuning of CO2 capture-plants and, thus, cost-savings via real-time manipulation of solvent

  18. A Metabolomic Approach to Clarifying the Effect of AST-120 on 5/6 Nephrectomized Rats by Capillary Electrophoresis with Mass Spectrometry (CE-MS)

    Science.gov (United States)

    Akiyama, Yasutoshi; Takeuchi, Yoichi; Kikuchi, Koichi; Mishima, Eikan; Yamamoto, Yasuaki; Suzuki, Chitose; Toyohara, Takafumi; Suzuki, Takehiro; Hozawa, Atsushi; Ito, Sadayoshi; Soga, Tomoyoshi; Abe, Takaaki

    2012-01-01

    The oral adsorbent AST-120 is composed of spherical carbon particles and has an adsorption ability for certain small-molecular-weight compounds that accumulate in patients with chronic kidney disease (CKD). So far, very few compounds are known to be adsorbed by AST-120 in vivo. To examine the effect of AST-120 in vivo, we comprehensively evaluated the plasma concentrations of 146 compounds (61 anions and 85 cations) in CKD model rats, with or without four weeks of treatment with AST-120. By capillary electrophoresis with mass spectrometry, we identified 6 anions and 17 cations that were significantly decreased by AST-120 treatment. In contrast, we also identified 2 cations that were significantly increased by AST-120. Among them, 4 anions, apart from indoxyl sulfate and hippurate, and 19 cations were newly identified in this study. The plasma levels of N-acetyl-neuraminate, 4-pyridoxate, 4-oxopentanoate, glycine, γ-guanidinobutyrate, N-γ-ethylglutamine, allantoin, cytosine, 5-methylcytosine and imidazole-4-acetate were significantly increased in the CKD model compared with the sham-operated group, and were significantly decreased by AST-120 treatment. Therefore, these 10 compounds could be added as uremic compounds that indicate the effect of AST-120 treatment. This study provides useful information not only for identifying the indicators of AST-120, but also for clarifying changes in the metabolic profile by AST-120 treatment in the clinical setting. PMID:23202318

  19. Selection of Taste Markers Related to Lactic Acid Bacteria Microflora Metabolism for Chinese Traditional Paocai: A Gas Chromatography-Mass Spectrometry-Based Metabolomics Approach.

    Science.gov (United States)

    Zhao, Nan; Zhang, Chuchu; Yang, Qin; Guo, Zhuang; Yang, Bo; Lu, Wenwei; Li, Dongyao; Tian, Fengwei; Liu, Xiaoming; Zhang, Hao; Chen, Wei

    2016-03-23

    Traditional paocai brine (PB) is continuously propagated by back-slopping and contains numerous lactic acid bacteria (LAB) strains. Although PB is important for the quality of paocai (Chinese sauerkraut), the taste features, taste-related compounds of PB-paocai and the effects of LAB communities from PB on the taste compounds remain unclear. An electronic tongue was used to evaluate the taste features of 13 PB-paocai samples. Umami, saltiness, bitterness, sweetness, and aftertaste astringency were the main taste features of PB-paocai. A total of 14 compounds were identified as discriminant taste markers for PB-paocai via gas chromatography-mass spectrometry (GC-MS)-based multimarker profiling. A LAB co-culture (Lactobacillus plantarum, Lactobacillus buchneri, and Pediococcus ethanoliduran) from PB could significantly increase glutamic acid (umami), sucrose (sweetness), glycine (sweetness), lactic acid (sourness), and γ-aminobutyric acid in PB-paocai, which would endow it with important flavor features. Such features could then facilitate starter screening and fermentation optimization to produce paocai-related foods with better nutritional and sensory qualities. PMID:26915389

  20. Multi-platform mass spectrometry analysis of the CSF and plasma metabolomes of rigorously matched amyotrophic lateral sclerosis, Parkinson's disease and control subjects.

    Science.gov (United States)

    Wuolikainen, Anna; Jonsson, Pär; Ahnlund, Maria; Antti, Henrik; Marklund, Stefan L; Moritz, Thomas; Forsgren, Lars; Andersen, Peter M; Trupp, Miles

    2016-04-01

    Amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD) are protein-aggregation diseases that lack clear molecular etiologies. Biomarkers could aid in diagnosis, prognosis, planning of care, drug target identification and stratification of patients into clinical trials. We sought to characterize shared and unique metabolite perturbations between ALS and PD and matched controls selected from patients with other diagnoses, including differential diagnoses to ALS or PD that visited our clinic for a lumbar puncture. Cerebrospinal fluid (CSF) and plasma from rigorously age-, sex- and sampling-date matched patients were analyzed on multiple platforms using gas chromatography (GC) and liquid chromatography (LC)-mass spectrometry (MS). We applied constrained randomization of run orders and orthogonal partial least squares projection to latent structure-effect projections (OPLS-EP) to capitalize upon the study design. The combined platforms identified 144 CSF and 196 plasma metabolites with diverse molecular properties. Creatine was found to be increased and creatinine decreased in CSF of ALS patients compared to matched controls. Glucose was increased in CSF of ALS patients and α-hydroxybutyrate was increased in CSF and plasma of ALS patients compared to matched controls. Leucine, isoleucine and ketoleucine were increased in CSF of both ALS and PD. Together, these studies, in conjunction with earlier studies, suggest alterations in energy utilization pathways and have identified and further validated perturbed metabolites to be used in panels of biomarkers for the diagnosis of ALS and PD. PMID:26883206

  1. Metabolomic Analysis in Brain Research: Opportunities and Challenges.

    Science.gov (United States)

    Vasilopoulou, Catherine G; Margarity, Marigoula; Klapa, Maria I

    2016-01-01

    Metabolism being a fundamental part of molecular physiology, elucidating the structure and regulation of metabolic pathways is crucial for obtaining a comprehensive perspective of cellular function and understanding the underlying mechanisms of its dysfunction(s). Therefore, quantifying an accurate metabolic network activity map under various physiological conditions is among the major objectives of systems biology in the context of many biological applications. Especially for CNS, metabolic network activity analysis can substantially enhance our knowledge about the complex structure of the mammalian brain and the mechanisms of neurological disorders, leading to the design of effective therapeutic treatments. Metabolomics has emerged as the high-throughput quantitative analysis of the concentration profile of small molecular weight metabolites, which act as reactants and products in metabolic reactions and as regulatory molecules of proteins participating in many biological processes. Thus, the metabolic profile provides a metabolic activity fingerprint, through the simultaneous analysis of tens to hundreds of molecules of pathophysiological and pharmacological interest. The application of metabolomics is at its standardization phase in general, and the challenges for paving a standardized procedure are even more pronounced in brain studies. In this review, we support the value of metabolomics in brain research. Moreover, we demonstrate the challenges of designing and setting up a reliable brain metabolomic study, which, among other parameters, has to take into consideration the sex differentiation and the complexity of brain physiology manifested in its regional variation. We finally propose ways to overcome these challenges and design a study that produces reproducible and consistent results. PMID:27252656

  2. Identification of specific metabolites in culture supernatant of Mycobacterium tuberculosis using metabolomics: exploration of potential biomarkers

    OpenAIRE

    Lau, Susanna KP; Lam, Ching-Wan; Curreem, Shirly OT; Lee, Kim-Chung; Lau, Candy CY; Chow, Wang-Ngai; Ngan, Antonio HY; To, Kelvin KW; Chan, Jasper FW; Hung, Ivan FN; Yam, Wing-Cheong; Yuen, Kwok-Yung; Woo, Patrick CY

    2015-01-01

    Although previous studies have reported the use of metabolomics for Mycobacterium species differentiation, little is known about the potential of extracellular metabolites of Mycobacterium tuberculosis (MTB) as specific biomarkers. Using an optimized ultrahigh performance liquid chromatography–electrospray ionization–quadruple time of flight–mass spectrometry (UHPLC–ESI–Q–TOF–MS) platform, we characterized the extracellular metabolomes of culture supernatant of nine MTB strains and nine non-t...

  3. DEVELOPMENT OF ANALYTICAL METHODS IN METABOLOMICS FOR THE STUDY OF HEREDITARY AND ACQUIRED GENETIC DISEASE

    OpenAIRE

    Arvonio, Raffaele

    2011-01-01

    METABOLOMICS AND MASS SPECTROMETRY The research project take place in the branch of metabolomics, which involves the systematic study of the metabolites present in a cell and in this area MS, thanks to its potential to carry out controlled experiments of fragmentation, plays a role as a key methodology for identification of various metabolites. The work of thesis project is focused on the analytical methods development for the diagnosis of metabolic diseases and is divided as follows: ...

  4. Accurate determination of Curium and Californium isotopic ratios by inductively coupled plasma quadrupole mass spectrometry (ICP-QMS) in 248Cm samples for transmutation studies

    International Nuclear Information System (INIS)

    The French Atomic Energy Commission has carried out several experiments including the mini-INCA (INcineration of Actinides) project for the study of minor-actinide transmutation processes in high intensity thermal neutron fluxes, in view of proposing solutions to reduce the radiotoxicity of long-lived nuclear wastes. In this context, a Cm sample enriched in 248Cm (∼97 %) was irradiated in thermal neutron flux at the High Flux Reactor (HFR) of the Laue-Langevin Institute (ILL). This work describes a quadrupole ICP-MS (ICP-QMS) analytical procedure for precise and accurate isotopic composition determination of Cm before sample irradiation and of Cm and Cf after sample irradiation. The factors that affect the accuracy and reproducibility of isotopic ratio measurements by ICP-QMS, such as peak centre correction, detector dead time, mass bias, abundance sensitivity and hydrides formation, instrumental background, and memory blank were carefully evaluated and corrected. Uncertainties of the isotopic ratios, taking into account internal precision of isotope ratio measurements, peak tailing, and hydrides formations ranged from 0.3% to 1.3%. This uncertainties range is quite acceptable for the nuclear data to be used in transmutation studies.

  5. Detection and quantitation of trace phenolphthalein (in pharmaceutical preparations and in forensic exhibits) by liquid chromatography-tandem mass spectrometry, a sensitive and accurate method.

    Science.gov (United States)

    Sharma, Kakali; Sharma, Shiba P; Lahiri, Sujit C

    2013-01-01

    Phenolphthalein, an acid-base indicator and laxative, is important as a constituent of widely used weight-reducing multicomponent food formulations. Phenolphthalein is an useful reagent in forensic science for the identification of blood stains of suspected victims and for apprehending erring officials accepting bribes in graft or trap cases. The pink-colored alkaline hand washes originating from the phenolphthalein-smeared notes can easily be determined spectrophotometrically. But in many cases, colored solution turns colorless with time, which renders the genuineness of bribe cases doubtful to the judiciary. No method is known till now for the detection and identification of phenolphthalein in colorless forensic exhibits with positive proof. Liquid chromatography-tandem mass spectrometry had been found to be most sensitive, accurate method capable of detection and quantitation of trace phenolphthalein in commercial formulations and colorless forensic exhibits with positive proof. The detection limit of phenolphthalein was found to be 1.66 pg/L or ng/mL, and the calibration curve shows good linearity (r(2) = 0.9974). PMID:23106487

  6. Identification of Plasma Metabolomic Profiling for Diagnosis of Esophageal Squamous-Cell Carcinoma Using an UPLC/TOF/MS Platform

    Directory of Open Access Journals (Sweden)

    Lihong Yin

    2013-04-01

    Full Text Available Epidemiological studies indicated that esophageal squamous-cell carcinoma (ESCC is still one of the most common causes of cancer incidence in the world. Searching for valuable markers including circulating endogenous metabolites associated with the risk of esophageal cancer, is extremely important A comparative metabolomics study was performed by using ultraperformance liquid chromatography-electrospray ionization-accurate mass time-of-flight mass spectrometry to analyze 53 pairs of plasma samples from ESCC patients and healthy controls recruited in Huaian, China. The result identified a metabolomic profiling of plasma including 25 upregulated metabolites and five downregulated metabolites, for early diagnosis of ESCC. With a database-based verification protocol, 11 molecules were identified, and six upregulated molecules of interest in ESCC were found to belong to phospholipids as follows: phosphatidylserine, phosphatidic acid, phosphatidyl choline, phosphatidylinositol, phosphatidyl ethanolamine, and sphinganine 1-phosphate. Clinical estimation of metabolic biomarkers through hierarchical cluster analysis in plasma samples from 17 ESCC patients and 29 healthy volunteers indicated that the present metabolite profile could distinguish ESCC patients from healthy individuals. The cluster of aberrant expression of these metabolites in ESCC indicates the critical role of phospholipid metabolism in the oncogenesis of ESCC and suggests its potential ability to assess the risk of ESCC development in addition to currently used risk factors.

  7. Food metabolomics: from farm to human.

    Science.gov (United States)

    Kim, Sooah; Kim, Jungyeon; Yun, Eun Ju; Kim, Kyoung Heon

    2016-02-01

    Metabolomics, one of the latest components in the suite of systems biology, has been used to understand the metabolism and physiology of living systems, including microorganisms, plants, animals and humans. Food metabolomics can be defined as the application of metabolomics in food systems, including food resources, food processing and diet for humans. The study of food metabolomics has increased gradually in the recent years, because food systems are directly related to nutrition and human health. This review describes the recent trends and applications of metabolomics to food systems, from farm to human, including food resource production, industrial food processing and food intake by humans.

  8. Metabolomic approach for improving ethanol stress tolerance in Saccharomyces cerevisiae.

    Science.gov (United States)

    Ohta, Erika; Nakayama, Yasumune; Mukai, Yukio; Bamba, Takeshi; Fukusaki, Eiichiro

    2016-04-01

    The budding yeast Saccharomyces cerevisiae is widely used for brewing and ethanol production. The ethanol sensitivity of yeast cells is still a serious problem during ethanol fermentation, and a variety of genetic approaches (e.g., random mutant screening under selective pressure of ethanol) have been developed to improve ethanol tolerance. In this study, we developed a strategy for improving ethanol tolerance of yeast cells based on metabolomics as a high-resolution quantitative phenotypic analysis. We performed gas chromatography-mass spectrometry analysis to identify and quantify 36 compounds on 14 mutant strains including knockout strains for transcription factor and metabolic enzyme genes. A strong relation between metabolome of these mutants and their ethanol tolerance was observed. Data mining of the metabolomic analysis showed that several compounds (such as trehalose, valine, inositol and proline) contributed highly to ethanol tolerance. Our approach successfully detected well-known ethanol stress related metabolites such as trehalose and proline thus, to further prove our strategy, we focused on valine and inositol as the most promising target metabolites in our study. Our results show that simultaneous deletion of LEU4 and LEU9 (leading to accumulation of valine) or INM1 and INM2 (leading to reduction of inositol) significantly enhanced ethanol tolerance. This study shows the potential of the metabolomic approach to identify target genes for strain improvement of S. cerevisiae with higher ethanol tolerance.

  9. Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies.

    Science.gov (United States)

    Treutler, Hendrik; Tsugawa, Hiroshi; Porzel, Andrea; Gorzolka, Karin; Tissier, Alain; Neumann, Steffen; Balcke, Gerd Ulrich

    2016-08-16

    The identification of metabolites by mass spectrometry constitutes a major bottleneck which considerably limits the throughput of metabolomics studies in biomedical or plant research. Here, we present a novel approach to analyze metabolomics data from untargeted, data-independent LC-MS/MS measurements. By integrated analysis of MS(1) abundances and MS/MS spectra, the identification of regulated metabolite families is achieved. This approach offers a global view on metabolic regulation in comparative metabolomics. We implemented our approach in the web application "MetFamily", which is freely available at http://msbi.ipb-halle.de/MetFamily/ . MetFamily provides a dynamic link between the patterns based on MS(1)-signal intensity and the corresponding structural similarity at the MS/MS level. Structurally related metabolites are annotated as metabolite families based on a hierarchical cluster analysis of measured MS/MS spectra. Joint examination with principal component analysis of MS(1) patterns, where this annotation is preserved in the loadings, facilitates the interpretation of comparative metabolomics data at the level of metabolite families. As a proof of concept, we identified two trichome-specific metabolite families from wild-type tomato Solanum habrochaites LA1777 in a fully unsupervised manner and validated our findings based on earlier publications and with NMR. PMID:27452369

  10. Metabolomics techniques in nanotoxicology studies.

    Science.gov (United States)

    Schnackenberg, Laura K; Sun, Jinchun; Beger, Richard D

    2012-01-01

    The rapid growth in the development of nanoparticles for uses in a variety of applications including targeted drug delivery, cancer therapy, imaging, and as biological sensors has led to questions about potential toxicity of such particles to humans. High-throughput methods are necessary to evaluate the potential toxicity of nanoparticles. The omics technologies are particularly well suited to evaluate toxicity in both in vitro and in vivo systems. Metabolomics, specifically, can rapidly screen for biomarkers related to predefined pathways or processes in biofluids and tissues. Specifically, oxidative stress has been implicated as a potential mechanism of toxicity in nanoparticles and is generally difficult to measure by conventional methods. Furthermore, metabolomics can provide mechanistic insight into nanotoxicity. This chapter focuses on the application of both LC/MS and NMR-based metabolomics approaches to study the potential toxicity of nanoparticles.

  11. Preprocessing of NMR metabolomics data.

    Science.gov (United States)

    Euceda, Leslie R; Giskeødegård, Guro F; Bathen, Tone F

    2015-05-01

    Metabolomics involves the large scale analysis of metabolites and thus, provides information regarding cellular processes in a biological sample. Independently of the analytical technique used, a vast amount of data is always acquired when carrying out metabolomics studies; this results in complex datasets with large amounts of variables. This type of data requires multivariate statistical analysis for its proper biological interpretation. Prior to multivariate analysis, preprocessing of the data must be carried out to remove unwanted variation such as instrumental or experimental artifacts. This review aims to outline the steps in the preprocessing of NMR metabolomics data and describe some of the methods to perform these. Since using different preprocessing methods may produce different results, it is important that an appropriate pipeline exists for the selection of the optimal combination of methods in the preprocessing workflow.

  12. iMet-Q: A User-Friendly Tool for Label-Free Metabolomics Quantitation Using Dynamic Peak-Width Determination.

    Science.gov (United States)

    Chang, Hui-Yin; Chen, Ching-Tai; Lih, T Mamie; Lynn, Ke-Shiuan; Juo, Chiun-Gung; Hsu, Wen-Lian; Sung, Ting-Yi

    2016-01-01

    Efficient and accurate quantitation of metabolites from LC-MS data has become an important topic. Here we present an automated tool, called iMet-Q (intelligent Metabolomic Quantitation), for label-free metabolomics quantitation from high-throughput MS1 data. By performing peak detection and peak alignment, iMet-Q provides a summary of quantitation results and reports ion abundance at both replicate level and sample level. Furthermore, it gives the charge states and isotope ratios of detected metabolite peaks to facilitate metabolite identification. An in-house standard mixture and a public Arabidopsis metabolome data set were analyzed by iMet-Q. Three public quantitation tools, including XCMS, MetAlign, and MZmine 2, were used for performance comparison. From the mixture data set, seven standard metabolites were detected by the four quantitation tools, for which iMet-Q had a smaller quantitation error of 12% in both profile and centroid data sets. Our tool also correctly determined the charge states of seven standard metabolites. By searching the mass values for those standard metabolites against Human Metabolome Database, we obtained a total of 183 metabolite candidates. With the isotope ratios calculated by iMet-Q, 49% (89 out of 183) metabolite candidates were filtered out. From the public Arabidopsis data set reported with two internal standards and 167 elucidated metabolites, iMet-Q detected all of the peaks corresponding to the internal standards and 167 metabolites. Meanwhile, our tool had small abundance variation (≤ 0.19) when quantifying the two internal standards and had higher abundance correlation (≥ 0.92) when quantifying the 167 metabolites. iMet-Q provides user-friendly interfaces and is publicly available for download at http://ms.iis.sinica.edu.tw/comics/Software_iMet-Q.html.

  13. iMet-Q: A User-Friendly Tool for Label-Free Metabolomics Quantitation Using Dynamic Peak-Width Determination.

    Directory of Open Access Journals (Sweden)

    Hui-Yin Chang

    Full Text Available Efficient and accurate quantitation of metabolites from LC-MS data has become an important topic. Here we present an automated tool, called iMet-Q (intelligent Metabolomic Quantitation, for label-free metabolomics quantitation from high-throughput MS1 data. By performing peak detection and peak alignment, iMet-Q provides a summary of quantitation results and reports ion abundance at both replicate level and sample level. Furthermore, it gives the charge states and isotope ratios of detected metabolite peaks to facilitate metabolite identification. An in-house standard mixture and a public Arabidopsis metabolome data set were analyzed by iMet-Q. Three public quantitation tools, including XCMS, MetAlign, and MZmine 2, were used for performance comparison. From the mixture data set, seven standard metabolites were detected by the four quantitation tools, for which iMet-Q had a smaller quantitation error of 12% in both profile and centroid data sets. Our tool also correctly determined the charge states of seven standard metabolites. By searching the mass values for those standard metabolites against Human Metabolome Database, we obtained a total of 183 metabolite candidates. With the isotope ratios calculated by iMet-Q, 49% (89 out of 183 metabolite candidates were filtered out. From the public Arabidopsis data set reported with two internal standards and 167 elucidated metabolites, iMet-Q detected all of the peaks corresponding to the internal standards and 167 metabolites. Meanwhile, our tool had small abundance variation (≤ 0.19 when quantifying the two internal standards and had higher abundance correlation (≥ 0.92 when quantifying the 167 metabolites. iMet-Q provides user-friendly interfaces and is publicly available for download at http://ms.iis.sinica.edu.tw/comics/Software_iMet-Q.html.

  14. NMR-based milk metabolomics

    DEFF Research Database (Denmark)

    Sundekilde, Ulrik; Larsen, Lotte Bach; Bertram, Hanne Christine S.

    2013-01-01

    Milk is a key component in infant nutrition worldwide and, in the Western parts of the world, also in adult nutrition. Milk of bovine origin is both consumed fresh and processed into a variety of dairy products including cheese, fermented milk products, and infant formula. The nutritional quality...... compounds. Furthermore, metabolomics applications elucidating how the differential regulated genes affects milk composition are also reported. This review will highlight the recent advances in NMR-based metabolomics on milk, as well as give a brief summary of when NMR spectroscopy can be useful for gaining...

  15. Metabolomic profiles of colostrum and milk from lactating sows

    DEFF Research Database (Denmark)

    Curtasu, Mihai Victor; Theil, Peter Kappel; Hedemann, Mette Skou

    2016-01-01

    -acetylcarnitine, 2-metylbutyroylcarnitine), glycerophosphocholine, and betaine. l-Acetylcarnitine and 2-metylbutyroylcarnitine, involved in the metabolism and transport of fatty acids, decreased in milk compared to colostrum, whereas l-carnitine presented an opposite trend (P ..., glycerophosphocholine and choline decreased from colostrum to milk, whereas betaine showed higher values in milk compared to colostrum. The use of liquid chromatography–mass spectrometry metabolomics as a hypothesis generator tool opens up new questions with regard to the origin and function of mammary gland...

  16. Biomarkers of Whale Shark Health: A Metabolomic Approach

    OpenAIRE

    Alistair D M Dove; Johannes Leisen; Manshui Zhou; Byrne, Jonathan J; Krista Lim-Hing; Webb, Harry D.; Leslie Gelbaum; Viant, Mark R.; Julia Kubanek; Facundo M Fernández

    2012-01-01

    In a search for biomarkers of health in whale sharks and as exploration of metabolomics as a modern tool for understanding animal physiology, the metabolite composition of serum in six whale sharks (Rhincodon typus) from an aquarium collection was explored using (1)H nuclear magnetic resonance (NMR) spectroscopy and direct analysis in real time (DART) mass spectrometry (MS). Principal components analysis (PCA) of spectral data showed that individual animals could be resolved based on the meta...

  17. 基于核磁及质谱分析技术的代谢组学在卵巢癌中的研究%NMR and mass spectrometry techniques based metabolomics in ovarian cancer research

    Institute of Scientific and Technical Information of China (English)

    葛婷婷; 娄阁

    2013-01-01

    卵巢癌是女性生殖器官恶性肿瘤中死亡率最高的疾病,早期无明显症状,70%的患者发现时已为晚期,所以卵巢癌的早发现、早治疗及个性化诊疗方案是肿瘤治疗的发展方向.代谢组学(Metabolomics)作为一种新兴技术为卵巢癌的早期诊断、疗效评价及预后判断打开了新窗口.在卵巢癌的发生发展过程中,机体产生不同的代谢产物,代谢组学能对机体代谢变化作出整体评价,筛选出有价值的生物标志物,用于肿瘤的早期诊断、治疗及预后评估.本文就代谢组学的概念和方法,代谢组学在卵巢癌的早期诊断、病理分型及靶向治疗的应用做一综述.%Ovarian cancer is the highest mortality in the female genital malignancies. Because no obvious symptoms of early ovarian cancer,it is found 70% of patients with advanced. Therefore, early detection of ovarian cancer, early treatment and personalized treatment programs is the development direction of cancer treatment. Metabolomics as an emerging technology for the early diagnosis of ovarian cancer,the efficacy evaluation and prognosis has opened up a new window. Metabolomics can make a comprehensive e-valuation of changes in metabolism, screened valuable biomarker for early diagnosis and treatment of tumors, treatment and prognosis. In this paper,we reviewed the concepts and methods of metabolomics as well as metabolomics in the early diagnosis of ovarian cancer, pathological type and targeted therapy applications.

  18. Software and Database Usage on Metabolomic Studies: Using XCMS on LC-MS Data Analysis

    Directory of Open Access Journals (Sweden)

    Mustafa Celebier

    2014-04-01

    Full Text Available Metabolome is the complete set of small-molecule metabolites to be found in a cell or a single organism. Metabolomics is the scientific study to determine and identify the chemicals in metabolome with advanced analytical techniques. Nowadays, the elucidation of the molecular mechanism of any disease with genome analysis and proteome analysis is not sufficient. Instead of these, a holistic assessment including metabolomic studies provides rational and accurate results. Metabolite levels in an organism are associated with the cellular functions. Thus, determination of the metabolite amounts identifies the phenotype of a cell or tissue related with the genetic and some other variations. Even though, the analysis of metabolites for medical diagnosis and therapy have been performed for a long time, the studies to improve the analysis methods for metabolite profiling are recently increased. The application of metabolomics includes the identification of biomarkers, enzyme-substract interactions, drug-activity studies, metabolic pathway analysis and some other studies related with the system biology. The preprocessing and computing of the data obtained from LC-MS, GC-MS, CE-MS and NMR for metabolite profiling are helpful for preventing from time consuming manual data analysis processes and possible random errors on profiling period. In addition, such preprocesses allow us to identify low amount of metabolites which are not possible to be analyzed by manual processing. Therefore, the usage of software and databases for this purpose could not be ignored. In this study, it is briefly presented the software and database used on metabolomics and it is evaluated the capability of these software on metabolite profiling. Particularly, the performance of one of the most popular software called XCMS on the evaluation of LC-MS results for metabolomics was overviewed. In the near future, metabolomics with software and database support is estimated to be a routine

  19. Biomarker discovery in neurological diseases: a metabolomic approach

    Directory of Open Access Journals (Sweden)

    Afaf El-Ansary

    2009-12-01

    Full Text Available Afaf El-Ansary, Nouf Al-Afaleg, Yousra Al-YafaeeBiochemistry Department, Science College, King Saud University, Riyadh, Saudi ArabiaAbstract: Biomarkers are pharmacological and physiological measurements or specific biochemicals in the body that have a particular molecular feature that makes them useful for measuring the progress of disease or the effects of treatment. Due to the complexity of neurological disorders, it is very difficult to have perfect markers. Brain diseases require plenty of markers to reflect the metabolic impairment of different brain cells. The recent introduction of the metabolomic approach helps the study of neurological diseases based on profiling a multitude of biochemical components related to brain metabolism. This review is a trial to elucidate the possibility to use this approach to identify plasma metabolic markers related to neurological disorders. Previous trials using different metabolomic analyses including nuclear magnetic resonance spectroscopy, gas chromatography combined with mass spectrometry, liquid chromatography combined with mass spectrometry, and capillary electrophoresis will be traced.Keywords: metabolic biomarkers, neurological disorders. metabolome, nuclear magnetic resonance, mass spectrometry, chromatography

  20. NMR-Based Milk Metabolomics

    Directory of Open Access Journals (Sweden)

    Hanne C. Bertram

    2013-04-01

    Full Text Available Milk is a key component in infant nutrition worldwide and, in the Western parts of the world, also in adult nutrition. Milk of bovine origin is both consumed fresh and processed into a variety of dairy products including cheese, fermented milk products, and infant formula. The nutritional quality and processing capabilities of bovine milk is closely associated to milk composition. Metabolomics is ideal in the study of the low-molecular-weight compounds in milk, and this review focuses on the recent nuclear magnetic resonance (NMR-based metabolomics trends in milk research, including applications linking the milk metabolite profiling with nutritional aspects, and applications which aim to link the milk metabolite profile to various technological qualities of milk. The metabolite profiling studies encompass the identification of novel metabolites, which potentially can be used as biomarkers or as bioactive compounds. Furthermore, metabolomics applications elucidating how the differential regulated genes affects milk composition are also reported. This review will highlight the recent advances in NMR-based metabolomics on milk, as well as give a brief summary of when NMR spectroscopy can be useful for gaining a better understanding of how milk composition is linked to nutritional or quality traits.

  1. NMR-Based Milk Metabolomics.

    Science.gov (United States)

    Sundekilde, Ulrik K; Larsen, Lotte B; Bertram, Hanne C

    2013-01-01

    Milk is a key component in infant nutrition worldwide and, in the Western parts of the world, also in adult nutrition. Milk of bovine origin is both consumed fresh and processed into a variety of dairy products including cheese, fermented milk products, and infant formula. The nutritional quality and processing capabilities of bovine milk is closely associated to milk composition. Metabolomics is ideal in the study of the low-molecular-weight compounds in milk, and this review focuses on the recent nuclear magnetic resonance (NMR)-based metabolomics trends in milk research, including applications linking the milk metabolite profiling with nutritional aspects, and applications which aim to link the milk metabolite profile to various technological qualities of milk. The metabolite profiling studies encompass the identification of novel metabolites, which potentially can be used as biomarkers or as bioactive compounds. Furthermore, metabolomics applications elucidating how the differential regulated genes affects milk composition are also reported. This review will highlight the recent advances in NMR-based metabolomics on milk, as well as give a brief summary of when NMR spectroscopy can be useful for gaining a better understanding of how milk composition is linked to nutritional or quality traits. PMID:24957988

  2. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health.

    Science.gov (United States)

    Vernocchi, Pamela; Del Chierico, Federica; Putignani, Lorenza

    2016-01-01

    The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies. PMID:27507964

  3. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health

    Science.gov (United States)

    Vernocchi, Pamela; Del Chierico, Federica; Putignani, Lorenza

    2016-01-01

    The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies. PMID:27507964

  4. COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

    OpenAIRE

    Salek, RM; Neumann, S. (Stefan); Schober, D.; Hummel, J; Billiau, K.; Kopka, J.; E. Correa; Reijmers, T; Rosato, A.; Tenori, L.; P.Turano; Marin, S. (Sara); Deborde, C.; Jacob, D.; Rolin, D

    2015-01-01

    International audience Metabolomics has become a crucial phenotyping technique in a range of research fields including medicine, the life sciences, biotechnology and the environmental sciences. This necessitates the transfer of experimental information between research groups, as well as potentially to publishers and funders. After the initial efforts of the metabolomics standards initiative, minimum reporting standards were proposed which included the concepts for metabolomics databases. ...

  5. Comprehensive metabolomics to evaluate the impact of industrial processing on the phytochemical composition of vegetable purees

    NARCIS (Netherlands)

    Lopez-Sanchez, P.; Vos, de R.C.H.; Jonker, H.H.; Mumm, R.; Hall, R.D.; Bialek, L.; Leenman, R.; Strassburg, K.; Vreeken, R.; Hankemeier, T.; Schumm, S.; Duynhoven, van J.P.M.

    2015-01-01

    The effects of conventional industrial processing steps on global phytochemical composition of broccoli, tomato and carrot purees were investigated by using a range of complementary targeted and untargeted metabolomics approaches including LC–PDA for vitamins, 1H NMR for polar metabolites, accurate

  6. Proteomics and Metabolomics: two emerging areas for legume improvement

    Directory of Open Access Journals (Sweden)

    Abirami eRamalingam

    2015-12-01

    this review, several studies on proteomics and metabolomics in model and crop legumes have been discussed. Additionally, applications of advanced proteomics and metabolomics approaches have also been included in this review for future applications in legume research. The integration of these ‘omic’ approaches will greatly support the identification of accurate biomarkers in legume smart breeding programs.

  7. Control of Strobilurin Fungicides in Wheat Using Direct Analysis in Real Time Accurate Time-of-Flight and Desorption Electrospray Ionization Linear Ion Trap Mass Spectrometry

    NARCIS (Netherlands)

    Schurek, J.; Vaclavik, L.; Hooijerink, H.; Lacina, O.; Poustka, J.; Sharman, M.; Caldow, M.; Nielen, M.W.F.; Hajslova, J.

    2008-01-01

    Ambient mass spectrometry has been used for the analysis of strobilurin residues in wheat. The use of this novel, challenging technique, employing a direct analysis in a real time (DART) ion-source coupled with a time-of-flight mass spectrometer (TOF MS) and a desorption electrospray ionization (DES

  8. Metabolomics in toxicology and preclinical research.

    Science.gov (United States)

    Ramirez, Tzutzuy; Daneshian, Mardas; Kamp, Hennicke; Bois, Frederic Y; Clench, Malcolm R; Coen, Muireann; Donley, Beth; Fischer, Steven M; Ekman, Drew R; Fabian, Eric; Guillou, Claude; Heuer, Joachim; Hogberg, Helena T; Jungnickel, Harald; Keun, Hector C; Krennrich, Gerhard; Krupp, Eckart; Luch, Andreas; Noor, Fozia; Peter, Erik; Riefke, Bjoern; Seymour, Mark; Skinner, Nigel; Smirnova, Lena; Verheij, Elwin; Wagner, Silvia; Hartung, Thomas; van Ravenzwaay, Bennard; Leist, Marcel

    2013-01-01

    Metabolomics, the comprehensive analysis of metabolites in a biological system, provides detailed information about the biochemical/physiological status of a biological system, and about the changes caused by chemicals. Metabolomics analysis is used in many fields, ranging from the analysis of the physiological status of genetically modified organisms in safety science to the evaluation of human health conditions. In toxicology, metabolomics is the -omics discipline that is most closely related to classical knowledge of disturbed biochemical pathways. It allows rapid identification of the potential targets of a hazardous compound. It can give information on target organs and often can help to improve our understanding regarding the mode-of-action of a given compound. Such insights aid the discovery of biomarkers that either indicate pathophysiological conditions or help the monitoring of the efficacy of drug therapies. The first toxicological applications of metabolomics were for mechanistic research, but different ways to use the technology in a regulatory context are being explored. Ideally, further progress in that direction will position the metabolomics approach to address the challenges of toxicology of the 21st century. To address these issues, scientists from academia, industry, and regulatory bodies came together in a workshop to discuss the current status of applied metabolomics and its potential in the safety assessment of compounds. We report here on the conclusions of three working groups addressing questions regarding 1) metabolomics for in vitro studies 2) the appropriate use of metabolomics in systems toxicology, and 3) use of metabolomics in a regulatory context. PMID:23665807

  9. Visualization of Multivariate Metabolomic Data

    Institute of Scientific and Technical Information of China (English)

    ZHOU Jun; CAO Bei; ZHENG Tian; LIU Lin-sheng; GUO Sheng; DUAN Jin-ao; AA Ji-ye; WANG Guang-ji; ZHANG Feng-yi; GU Rong-rong; WANG Xin-wen; ZHAO Chun-yan; LI Meng-jie; SHI Jian

    2011-01-01

    Objective Although principal components analysis profiles greatly facilitate the visualization and interpretation of the multivariate data,the quantitative concepts in both scores plot and loading plot are rather obscure.This article introduced three profiles that assisted the better understanding of metabolomic data.Methods The discriminatory profile,heat map,and statistic profile were developed to visualize the multivariate data obtained from high-throughput GC-TOF-MS analysis.Results The discriminatory profile and heat map obviously showed the discriminatory metabolites between the two groups,while the statistic profile showed the potential markers of statistic significance.Conclusion The three types of profiles greatly facilitate our understanding of the metabolomic data and the identification of the potential markers.

  10. NMR-Based Milk Metabolomics

    OpenAIRE

    Bertram, Hanne C.; Larsen, Lotte B; Sundekilde, Ulrik K

    2013-01-01

    Milk is a key component in infant nutrition worldwide and, in the Western parts of the world, also in adult nutrition. Milk of bovine origin is both consumed fresh and processed into a variety of dairy products including cheese, fermented milk products, and infant formula. The nutritional quality and processing capabilities of bovine milk is closely associated to milk composition. Metabolomics is ideal in the study of the low-molecular-weight compounds in milk, and this review focuses on the ...

  11. Feature Selection Methods for Early Predictive Biomarker Discovery Using Untargeted Metabolomic Data.

    Science.gov (United States)

    Grissa, Dhouha; Pétéra, Mélanie; Brandolini, Marion; Napoli, Amedeo; Comte, Blandine; Pujos-Guillot, Estelle

    2016-01-01

    Untargeted metabolomics is a powerful phenotyping tool for better understanding biological mechanisms involved in human pathology development and identifying early predictive biomarkers. This approach, based on multiple analytical platforms, such as mass spectrometry (MS), chemometrics and bioinformatics, generates massive and complex data that need appropriate analyses to extract the biologically meaningful information. Despite various tools available, it is still a challenge to handle such large and noisy datasets with limited number of individuals without risking overfitting. Moreover, when the objective is focused on the identification of early predictive markers of clinical outcome, few years before occurrence, it becomes essential to use the appropriate algorithms and workflow to be able to discover subtle effects among this large amount of data. In this context, this work consists in studying a workflow describing the general feature selection process, using knowledge discovery and data mining methodologies to propose advanced solutions for predictive biomarker discovery. The strategy was focused on evaluating a combination of numeric-symbolic approaches for feature selection with the objective of obtaining the best combination of metabolites producing an effective and accurate predictive model. Relying first on numerical approaches, and especially on machine learning methods (SVM-RFE, RF, RF-RFE) and on univariate statistical analyses (ANOVA), a comparative study was performed on an original metabolomic dataset and reduced subsets. As resampling method, LOOCV was applied to minimize the risk of overfitting. The best k-features obtained with different scores of importance from the combination of these different approaches were compared and allowed determining the variable stabilities using Formal Concept Analysis. The results revealed the interest of RF-Gini combined with ANOVA for feature selection as these two complementary methods allowed selecting the 48

  12. Accurate prediction of H3O+ and D3O+ sensitivity coefficients to probe a variable proton-to-electron mass ratio

    OpenAIRE

    Owens, A.; Yurchenko, S. N.; Polyansky, O. L.; Ovsyannikov, R. I.; Thiel, W.; Spirko, V.

    2015-01-01

    The mass sensitivity of the vibration–rotation–inversion transitions of H316O+, H318O+, and D316O+ is investigated variationally using the nuclear motion program TROVE (Yurchenko, Thiel & Jensen). The calculations utilize new high-level ab initio potential energy and dipole moment surfaces. Along with the mass dependence, frequency data and Einstein A coefficients are computed for all transitions probed. Particular attention is paid to the Δ|k| = 3 and Δ|k − l| = 3 transitions comprising the ...

  13. Metabolomics Society’s International Affiliations

    NARCIS (Netherlands)

    Roessner, U.; Rolin, D.; Rijswijk, van M.E.C.; Hall, R.D.; Hankemeier, T.

    2015-01-01

    In 2012 the Metabolomics Society established a more formal system for national and regional metabolomics initiatives, interest groups, societies and networks to become an International Affiliate of the Society. A number of groups (http://metabolomicssociety.org/international-affilia tions/benefits-o

  14. Symbiosis of chemometrics and metabolomics: Past, present, and future

    NARCIS (Netherlands)

    Greef, J. van der; Smilde, A.K.

    2005-01-01

    Metabolomics is a growing area in the field of systems biology. Metabolomics has already a long history and also the connection of metabolomics with chemometrics goes back some time. This review discusses the symbiosis of metabolomics and chemometrics with emphasis on the medical domain, puts the co

  15. Recent advances in plant metabolomics and greener pastures.

    Science.gov (United States)

    Sumner, Lloyd W

    2010-01-27

    Metabolomics is an extension of the omics concept and experimental approaches. However, is metabolomics just another trendy omics fashion perturbation or is metabolomics actually delivering novel content and value? This article highlights some recent advances that definitely support the role of plant metabolomics in the movement toward greener pastures.

  16. A Combined Metabolomic and Proteomic Analysis of Gestational Diabetes Mellitus

    Directory of Open Access Journals (Sweden)

    Joanna Hajduk

    2015-12-01

    Full Text Available The aim of this pilot study was to apply a novel combined metabolomic and proteomic approach in analysis of gestational diabetes mellitus. The investigation was performed with plasma samples derived from pregnant women with diagnosed gestational diabetes mellitus (n = 18 and a matched control group (n = 13. The mass spectrometry-based analyses allowed to determine 42 free amino acids and low molecular-weight peptide profiles. Different expressions of several peptides and altered amino acid profiles were observed in the analyzed groups. The combination of proteomic and metabolomic data allowed obtaining the model with a high discriminatory power, where amino acids ethanolamine, l-citrulline, l-asparagine, and peptide ions with m/z 1488.59; 4111.89 and 2913.15 had the highest contribution to the model. The sensitivity (94.44% and specificity (84.62%, as well as the total group membership classification value (90.32% calculated from the post hoc classification matrix of a joint model were the highest when compared with a single analysis of either amino acid levels or peptide ion intensities. The obtained results indicated a high potential of integration of proteomic and metabolomics analysis regardless the sample size. This promising approach together with clinical evaluation of the subjects can also be used in the study of other diseases.

  17. A Combined Metabolomic and Proteomic Analysis of Gestational Diabetes Mellitus.

    Science.gov (United States)

    Hajduk, Joanna; Klupczynska, Agnieszka; Dereziński, Paweł; Matysiak, Jan; Kokot, Piotr; Nowak, Dorota M; Gajęcka, Marzena; Nowak-Markwitz, Ewa; Kokot, Zenon J

    2015-12-16

    The aim of this pilot study was to apply a novel combined metabolomic and proteomic approach in analysis of gestational diabetes mellitus. The investigation was performed with plasma samples derived from pregnant women with diagnosed gestational diabetes mellitus (n = 18) and a matched control group (n = 13). The mass spectrometry-based analyses allowed to determine 42 free amino acids and low molecular-weight peptide profiles. Different expressions of several peptides and altered amino acid profiles were observed in the analyzed groups. The combination of proteomic and metabolomic data allowed obtaining the model with a high discriminatory power, where amino acids ethanolamine, L-citrulline, L-asparagine, and peptide ions with m/z 1488.59; 4111.89 and 2913.15 had the highest contribution to the model. The sensitivity (94.44%) and specificity (84.62%), as well as the total group membership classification value (90.32%) calculated from the post hoc classification matrix of a joint model were the highest when compared with a single analysis of either amino acid levels or peptide ion intensities. The obtained results indicated a high potential of integration of proteomic and metabolomics analysis regardless the sample size. This promising approach together with clinical evaluation of the subjects can also be used in the study of other diseases.

  18. A Comprehensive Review of School-Based Body Mass Index Screening Programs and Their Implications for School Health: Do the Controversies Accurately Reflect the Research?

    Science.gov (United States)

    Ruggieri, Dominique G.; Bass, Sarah B.

    2015-01-01

    Background: Whereas legislation for body mass index (BMI) surveillance and screening programs has passed in 25 states, the programs are often subject to ethical debates about confidentiality and privacy, school-to-parent communication, and safety and self-esteem issues for students. Despite this debate, no comprehensive analysis has been completed…

  19. Ultrafast Polyphenol Metabolomics of Red Wines Using MicroLC-MS/MS.

    Science.gov (United States)

    Ma, Yan; Tanaka, Nobuo; Vaniya, Arpana; Kind, Tobias; Fiehn, Oliver

    2016-01-20

    The taste and quality of red wine are determined by its highly complex mixture of polyphenols and many other metabolites. No single method can fully cover the full metabolome, but even for polyphenols and related compounds, current methods proved inadequate. We optimized liquid chromatography resolution and sensitivity using 1 mm i.d. columns with microLC pumps and compared data-dependent to data-independent (SWATH) MS/MS acquisitions. A high-throughput microLC-MS method was developed with a 4 min gradient at 0.05 mL/min flow rate on a Kinetex C18 column and Sciex TripleTOF mass spectrometry. Using the novel software MS-DIAL, we structurally annotated 264 compounds including 165 polyphenols in six commercial red wines by accurate mass MS/MS matching. As proof of concept, multivariate statistics revealed the difference in the metabolite profiles of the six red wines, and regression analysis linked the polyphenol contents to the taste of the red wines.

  20. Metabolomics to unveil and understand phenotypic diversity between pathogen populations.

    Directory of Open Access Journals (Sweden)

    Ruben t'Kindt

    Full Text Available Leishmaniasis is a debilitating disease caused by the parasite Leishmania. There is extensive clinical polymorphism, including variable responsiveness to treatment. We study Leishmania donovani parasites isolated from visceral leishmaniasis patients in Nepal that responded differently to antimonial treatment due to differing intrinsic drug sensitivity of the parasites. Here, we present a proof-of-principle study in which we applied a metabolomics pipeline specifically developed for L. donovani to characterize the global metabolic differences between antimonial-sensitive and antimonial-resistant L. donovani isolates. Clones of drug-sensitive and drug-resistant parasite isolates from clinical samples were cultured in vitro and harvested for metabolomics analysis. The relative abundance of 340 metabolites was determined by ZIC-HILIC chromatography coupled to LTQ-Orbitrap mass spectrometry. Our measurements cover approximately 20% of the predicted core metabolome of Leishmania and additionally detected a large number of lipids. Drug-sensitive and drug-resistant parasites showed distinct metabolic profiles, and unsupervised clustering and principal component analysis clearly distinguished the two phenotypes. For 100 metabolites, the detected intensity differed more than three-fold between the 2 phenotypes. Many of these were in specific areas of lipid metabolism, suggesting that the membrane composition of the drug-resistant parasites is extensively modified. Untargeted metabolomics has been applied on clinical Leishmania isolates to uncover major metabolic differences between drug-sensitive and drug-resistant isolates. The identified major differences provide novel insights into the mechanisms involved in resistance to antimonial drugs, and facilitate investigations using targeted approaches to unravel the key changes mediating drug resistance.

  1. Accurate prediction of H3O+ and D3O+ sensitivity coefficients to probe a variable proton-to-electron mass ratio

    Science.gov (United States)

    Owens, A.; Yurchenko, S. N.; Polyansky, O. L.; Ovsyannikov, R. I.; Thiel, W.; Špirko, V.

    2015-12-01

    The mass sensitivity of the vibration-rotation-inversion transitions of H316O+, H318O+, and D316O+ is investigated variationally using the nuclear motion program TROVE (Yurchenko, Thiel & Jensen). The calculations utilize new high-level ab initio potential energy and dipole moment surfaces. Along with the mass dependence, frequency data and Einstein A coefficients are computed for all transitions probed. Particular attention is paid to the Δ|k| = 3 and Δ|k - l| = 3 transitions comprising the accidentally coinciding |J, K = 0, v2 = 0+> and |J, K = 3, v2 = 0-> rotation-inversion energy levels. The newly computed probes exhibit sensitivities comparable to their ammonia and methanol counterparts, thus demonstrating their potential for testing the cosmological stability of the proton-to-electron mass ratio. The theoretical TROVE results are in close agreement with sensitivities obtained using the non-rigid and rigid inverter approximate models, confirming that the ab initio theory used in the present study is adequate.

  2. Rumen fluid metabolomics analysis associated with feed efficiency on crossbred steers

    Science.gov (United States)

    The rumen plays a central role in the efficiency of digestion in ruminants. To identify potential differences in rumen function that lead to differences in feed efficiency, rumen metabolomic analysis by ultra-performance liquid chromatography/ time-of-flight mass spectrometry (MS) and multivariate/u...

  3. An untargeted metabolomics approach to contaminant analysis. Pinpointing potential unknown compounds

    NARCIS (Netherlands)

    Lommen, A.; Weg, van der G.; Engelen, M.C.; Bor, G.; Hoogenboom, L.A.P.; Nielen, M.W.F.

    2007-01-01

    This study deals with an automated data analysis strategy to pinpoint potential unknown compounds in full scan mass spectrometry (MS) experiments. Three examples of an untargeted metabolomics approach to contaminant analysis are given. By comparing a plant-oil based hormone cocktail to 90 plant oil

  4. (1)H NMR studies distinguish the water soluble metabolomic profiles of untransformed and RAS-transformed cells.

    Science.gov (United States)

    Marks, Vered; Munoz, Anisleidys; Rai, Priyamvada; Walls, Jamie D

    2016-01-01

    Metabolomic profiling is an increasingly important method for identifying potential biomarkers in cancer cells with a view towards improved diagnosis and treatment. Nuclear magnetic resonance (NMR) provides a potentially noninvasive means to accurately characterize differences in the metabolomic profiles of cells. In this work, we use (1)H NMR to measure the metabolomic profiles of water soluble metabolites extracted from isogenic control and oncogenic HRAS-, KRAS-, and NRAS-transduced BEAS2B lung epithelial cells to determine the robustness of NMR metabolomic profiling in detecting differences between the transformed cells and their untransformed counterparts as well as differences among the RAS-transformed cells. Unique metabolomic signatures between control and RAS-transformed cell lines as well as among the three RAS isoform-transformed lines were found by applying principal component analysis to the NMR data. This study provides a proof of principle demonstration that NMR-based metabolomic profiling can robustly distinguish untransformed and RAS-transformed cells as well as cells transformed with different RAS oncogenic isoforms. Thus, our data may potentially provide new diagnostic signatures for RAS-transformed cells. PMID:27330862

  5. Probabilistic Principal Component Analysis for Metabolomic Data.

    LENUS (Irish Health Repository)

    Nyamundanda, Gift

    2010-11-23

    Abstract Background Data from metabolomic studies are typically complex and high-dimensional. Principal component analysis (PCA) is currently the most widely used statistical technique for analyzing metabolomic data. However, PCA is limited by the fact that it is not based on a statistical model. Results Here, probabilistic principal component analysis (PPCA) which addresses some of the limitations of PCA, is reviewed and extended. A novel extension of PPCA, called probabilistic principal component and covariates analysis (PPCCA), is introduced which provides a flexible approach to jointly model metabolomic data and additional covariate information. The use of a mixture of PPCA models for discovering the number of inherent groups in metabolomic data is demonstrated. The jackknife technique is employed to construct confidence intervals for estimated model parameters throughout. The optimal number of principal components is determined through the use of the Bayesian Information Criterion model selection tool, which is modified to address the high dimensionality of the data. Conclusions The methods presented are illustrated through an application to metabolomic data sets. Jointly modeling metabolomic data and covariates was successfully achieved and has the potential to provide deeper insight to the underlying data structure. Examination of confidence intervals for the model parameters, such as loadings, allows for principled and clear interpretation of the underlying data structure. A software package called MetabolAnalyze, freely available through the R statistical software, has been developed to facilitate implementation of the presented methods in the metabolomics field.

  6. New biomarkers of coffee consumption identified by the non-targeted metabolomic profiling of cohort study subjects.

    Directory of Open Access Journals (Sweden)

    Joseph A Rothwell

    Full Text Available Coffee contains various bioactives implicated with human health and disease risk. To accurately assess the effects of overall consumption upon health and disease, individual intake must be measured in large epidemiological studies. Metabolomics has emerged as a powerful approach to discover biomarkers of intake for a large range of foods. Here we report the profiling of the urinary metabolome of cohort study subjects to search for new biomarkers of coffee intake. Using repeated 24-hour dietary records and a food frequency questionnaire, 20 high coffee consumers (183-540 mL/d and 19 low consumers were selected from the French SU.VI.MAX2 cohort. Morning spot urine samples from each subject were profiled by high-resolution mass spectrometry. Partial least-square discriminant analysis of multidimensional liquid chromatography-mass spectrometry data clearly distinguished high consumers from low via 132 significant (p-value<0.05 discriminating features. Ion clusters whose intensities were most elevated in the high consumers were annotated using online and in-house databases and their identities checked using commercial standards and MS-MS fragmentation. The best discriminants, and thus potential markers of coffee consumption, were the glucuronide of the diterpenoid atractyligenin, the diketopiperazine cyclo(isoleucyl-prolyl, and the alkaloid trigonelline. Some caffeine metabolites, such as 1-methylxanthine, were also among the discriminants, however caffeine may be consumed from other sources and its metabolism is subject to inter-individual variation. Receiver operating characteristics curve analysis showed that the biomarkers identified could be used effectively in combination for increased sensitivity and specificity. Once validated in other cohorts or intervention studies, these specific single or combined biomarkers will become a valuable alternative to assessment of coffee intake by dietary survey and finally lead to a better understanding of

  7. Tools and databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data.

    Science.gov (United States)

    Sakurai, Nozomu; Ara, Takeshi; Enomoto, Mitsuo; Motegi, Takeshi; Morishita, Yoshihiko; Kurabayashi, Atsushi; Iijima, Yoko; Ogata, Yoshiyuki; Nakajima, Daisuke; Suzuki, Hideyuki; Shibata, Daisuke

    2014-01-01

    A metabolome--the collection of comprehensive quantitative data on metabolites in an organism--has been increasingly utilized for applications such as data-intensive systems biology, disease diagnostics, biomarker discovery, and assessment of food quality. A considerable number of tools and databases have been developed to date for the analysis of data generated by various combinations of chromatography and mass spectrometry. We report here a web portal named KOMICS (The Kazusa Metabolomics Portal), where the tools and databases that we developed are available for free to academic users. KOMICS includes the tools and databases for preprocessing, mining, visualization, and publication of metabolomics data. Improvements in the annotation of unknown metabolites and dissemination of comprehensive metabolomic data are the primary aims behind the development of this portal. For this purpose, PowerGet and FragmentAlign include a manual curation function for the results of metabolite feature alignments. A metadata-specific wiki-based database, Metabolonote, functions as a hub of web resources related to the submitters' work. This feature is expected to increase citation of the submitters' work, thereby promoting data publication. As an example of the practical use of KOMICS, a workflow for a study on Jatropha curcas is presented. The tools and databases available at KOMICS should contribute to enhanced production, interpretation, and utilization of metabolomic Big Data.

  8. Tools and databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data.

    Science.gov (United States)

    Sakurai, Nozomu; Ara, Takeshi; Enomoto, Mitsuo; Motegi, Takeshi; Morishita, Yoshihiko; Kurabayashi, Atsushi; Iijima, Yoko; Ogata, Yoshiyuki; Nakajima, Daisuke; Suzuki, Hideyuki; Shibata, Daisuke

    2014-01-01

    A metabolome--the collection of comprehensive quantitative data on metabolites in an organism--has been increasingly utilized for applications such as data-intensive systems biology, disease diagnostics, biomarker discovery, and assessment of food quality. A considerable number of tools and databases have been developed to date for the analysis of data generated by various combinations of chromatography and mass spectrometry. We report here a web portal named KOMICS (The Kazusa Metabolomics Portal), where the tools and databases that we developed are available for free to academic users. KOMICS includes the tools and databases for preprocessing, mining, visualization, and publication of metabolomics data. Improvements in the annotation of unknown metabolites and dissemination of comprehensive metabolomic data are the primary aims behind the development of this portal. For this purpose, PowerGet and FragmentAlign include a manual curation function for the results of metabolite feature alignments. A metadata-specific wiki-based database, Metabolonote, functions as a hub of web resources related to the submitters' work. This feature is expected to increase citation of the submitters' work, thereby promoting data publication. As an example of the practical use of KOMICS, a workflow for a study on Jatropha curcas is presented. The tools and databases available at KOMICS should contribute to enhanced production, interpretation, and utilization of metabolomic Big Data. PMID:24949426

  9. An Integrated Outlook on the Metagenome and Metabolome of Intestinal Diseases

    Directory of Open Access Journals (Sweden)

    Wanping Aw

    2015-11-01

    Full Text Available Recently, metagenomics and metabolomics are the two most rapidly advancing “omics” technologies. Metagenomics seeks to characterize the composition of microbial communities, their operations, and their dynamically co-evolving relationships with the habitats they occupy, whereas metabolomics studies unique chemical endpoints (metabolites that specific cellular processes leave behind. Remarkable progress in DNA sequencing and mass spectrometry technologies has enabled the comprehensive collection of information on the gut microbiome and its metabolome in order to assess the influence of the gut microbiota on host physiology on a whole-systems level. Our gut microbiota, which consists of prokaryotic cells together with its metabolites, creates a unique gut ecosystem together with the host eukaryotic cells. In this review, we will highlight the detailed relationships between gut microbiota and its metabolites on host health and the pathogenesis of various intestinal diseases such as inflammatory bowel disease and colorectal cancer. Therapeutic interventions such as probiotic and prebiotic administrations and fecal microbiota transplantations will also be discussed. We would like to promote this unique biology-wide approach of incorporating metagenome and metabolome information as we believe that this can help us understand the intricate interplay between gut microbiota and host metabolism to a greater extent. This novel integration of microbiome, metatranscriptome, and metabolome information will help us have an improved holistic understanding of the complex mammalian superorganism, thereby allowing us to gain new and unprecedented insights to providing exciting novel therapeutic approaches for optimal intestinal health.

  10. Unexpected similarities between the Schizosaccharomyces and human blood metabolomes, and novel human metabolites.

    Science.gov (United States)

    Chaleckis, Romanas; Ebe, Masahiro; Pluskal, Tomáš; Murakami, Itsuo; Kondoh, Hiroshi; Yanagida, Mitsuhiro

    2014-10-01

    Metabolomics, a modern branch of chemical biology, provides qualitative and quantitative information about the metabolic states of organisms or cells at the molecular level. Here we report non-targeted, metabolomic analyses of human blood, using liquid chromatography-mass spectrometry (LC-MS). We compared the blood metabolome to the previously reported metabolome of the fission yeast, Schizosaccharomyces pombe. The two metabolomic datasets were highly similar: 101 of 133 compounds identified in human blood (75%) were also present in S. pombe, and 45 of 57 compounds enriched in red blood cells (RBCs) (78%) were also present in yeast. The most abundant metabolites were ATP, glutathione, and glutamine. Apart from these three, the next most abundant metabolites were also involved in energy metabolism, anti-oxidation, and amino acid metabolism. We identified fourteen new blood compounds, eight of which were enriched in RBCs: citramalate, GDP-glucose, trimethyl-histidine, trimethyl-phenylalanine, trimethyl-tryptophan, trimethyl-tyrosine, UDP-acetyl-glucosamine, UDP-glucuronate, dimethyl-lysine, glutamate methyl ester, N-acetyl-(iso)leucine, N-acetyl-glutamate, N2-acetyl-lysine, and N6-acetyl-lysine. Ten of the newly identified blood metabolites were also detected in S. pombe, and ten of the 14 newly identified blood metabolites were methylated or acetylated amino acids. Trimethylated or acetylated free amino acids were also abundant in white blood cells. It may be possible to investigate their physiological roles using yeast genetics.

  11. Development of a Rapid and Accurate Identification Method for Citrobacter Species Isolated from Pork Products Using a Matrix-Assisted Laser-Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS).

    Science.gov (United States)

    Kwak, Hye-Lim; Han, Sun-Kyung; Park, Sunghoon; Park, Si Hong; Shim, Jae-Yong; Oh, Mihwa; Ricke, Steven C; Kim, Hae-Yeong

    2015-09-01

    Previous detection methods for Citrobacter are considered time consuming and laborious. In this study, we have developed a rapid and accurate detection method for Citrobacter species in pork products, using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). A total of 35 Citrobacter strains were isolated from 30 pork products and identified by both MALDI-TOF MS and 16S rRNA gene sequencing approaches. All isolates were identified to the species level by the MALDI-TOF MS, while 16S rRNA gene sequencing results could not discriminate them clearly. These results confirmed that MALDI-TOF MS is a more accurate and rapid detection method for the identification of Citrobacter species.

  12. Circadian variation of the human metabolome captured by real-time breath analysis.

    Directory of Open Access Journals (Sweden)

    Pablo Martinez-Lozano Sinues

    Full Text Available Circadian clocks play a significant role in the correct timing of physiological metabolism, and clock disruption might lead to pathological changes of metabolism. One interesting method to assess the current state of metabolism is metabolomics. Metabolomics tries to capture the entirety of small molecules, i.e. the building blocks of metabolism, in a given matrix, such as blood, saliva or urine. Using mass spectrometric approaches we and others have shown that a significant portion of the human metabolome in saliva and blood exhibits circadian modulation; independent of food intake or sleep/wake rhythms. Recent advances in mass spectrometry techniques have introduced completely non-invasive breathprinting; a method to instantaneously assess small metabolites in human breath. In this proof-of-principle study, we extend these findings about the impact of circadian clocks on metabolomics to exhaled breath. As previously established, our method allows for real-time analysis of a rich matrix during frequent non-invasive sampling. We sampled the breath of three healthy, non-smoking human volunteers in hourly intervals for 24 hours during total sleep deprivation, and found 111 features in the breath of all individuals, 36-49% of which showed significant circadian variation in at least one individual. Our data suggest that real-time mass spectrometric "breathprinting" has high potential to become a useful tool to understand circadian metabolism, and develop new biomarkers to easily and in real-time assess circadian clock phase and function in experimental and clinical settings.

  13. An Automated High-Throughput Metabolic Stability Assay Using an Integrated High-Resolution Accurate Mass Method and Automated Data Analysis Software

    Science.gov (United States)

    Shah, Pranav; Kerns, Edward; Nguyen, Dac-Trung; Obach, R. Scott; Wang, Amy Q.; Zakharov, Alexey; McKew, John; Simeonov, Anton; Hop, Cornelis E. C. A.

    2016-01-01

    Advancement of in silico tools would be enabled by the availability of data for metabolic reaction rates and intrinsic clearance (CLint) of a diverse compound structure data set by specific metabolic enzymes. Our goal is to measure CLint for a large set of compounds with each major human cytochrome P450 (P450) isozyme. To achieve our goal, it is of utmost importance to develop an automated, robust, sensitive, high-throughput metabolic stability assay that can efficiently handle a large volume of compound sets. The substrate depletion method [in vitro half-life (t1/2) method] was chosen to determine CLint. The assay (384-well format) consisted of three parts: 1) a robotic system for incubation and sample cleanup; 2) two different integrated, ultraperformance liquid chromatography/mass spectrometry (UPLC/MS) platforms to determine the percent remaining of parent compound, and 3) an automated data analysis system. The CYP3A4 assay was evaluated using two long t1/2 compounds, carbamazepine and antipyrine (t1/2 > 30 minutes); one moderate t1/2 compound, ketoconazole (10 < t1/2 < 30 minutes); and two short t1/2 compounds, loperamide and buspirone (t½ < 10 minutes). Interday and intraday precision and accuracy of the assay were within acceptable range (∼12%) for the linear range observed. Using this assay, CYP3A4 CLint and t1/2 values for more than 3000 compounds were measured. This high-throughput, automated, and robust assay allows for rapid metabolic stability screening of large compound sets and enables advanced computational modeling for individual human P450 isozymes. PMID:27417180

  14. Metabolomics in Population-Based Research

    Science.gov (United States)

    Metabolomics is the study of small molecules of both endogenous and exogenous origin, such as metabolic substrates and their products, lipids, small peptides, vitamins and other protein cofactors generated by metabolism, which are downstream from genes.

  15. Recent advances in thermal desorption-gas chromatography-mass spectrometery method to eliminate the matrix effect between air and water samples: application to the accurate determination of Henry's law constant.

    Science.gov (United States)

    Kim, Yong-Hyun; Kim, Ki-Hyun

    2014-05-16

    Accurate values for the Henry's law constants are essential to describe the environmental dynamics of a solute, but substantial errors are recognized in many reported data due to practical difficulties in measuring solubility and/or vapor pressure. Despite such awareness, validation of experimental approaches has scarcely been made. An experimental approach based on thermal desorption-gas chromatography-mass spectrometery (TD-GC-MS) method was developed to concurrently allow the accurate determination of target compounds from the headspace and aqueous samples in closed equilibrated system. The analysis of six aromatics and eight non-aromatic oxygenates was then carried out in a static headspace mode. An estimation of the potential bias and mass balance (i.e., sum of mass measured individually from gas and liquid phases vs. the mass initially added to the system) demonstrates compound-specific phase dependency so that the best results are obtained by aqueous (less soluble aromatics) and headspace analysis (more soluble non-aromatics). Accordingly, we were able to point to the possible sources of biases in previous studies and provide the best estimates for the Henry's constants (Matm(-1)): benzene (0.17), toluene (0.15), p-xylene (0.13), m-xylene (0.13), o-xylene (0.19), styrene (0.27); propionaldehyde (9.26), butyraldehyde (6.19), isovaleraldehyde (2.14), n-valeraldehyde (3.98), methyl ethyl ketone (10.5), methyl isobutyl ketone (3.93), n-butyl acetate (2.41), and isobutyl alcohol (22.2). PMID:24704185

  16. Plasma metabolomics combined with lipidomics profiling reveals the potential antipyretic mechanisms of Qingkailing injection in a rat model.

    Science.gov (United States)

    Qin, Lingling; Zhang, Zhixin; Guo, Mingxing; Zhang, Qingqing; Wang, Qing; Lu, Zhiwei; Zhao, Huizhen; Liu, Yuehong; Fu, Shuang; Wang, Meiling; Gao, Xiaoyan

    2016-07-25

    Qingkailing injection (QKLI) has a notable antipyretic effect and is widely used in China as a clinical emergency medicine. To elucidate the pharmacological action thoroughly, following the investigation of the urine metabolome and hypothalamus metabolome, plasma metabolomics combined with lipidomics profiling of the QKLI antipyretic effect in a rat model is described in this paper. Compared with pure metabolomics profiling, this non-targeted plasma metabolomics combined with lipidomics profiling based on ultra-performance liquid chromatography-coupled with quadrupole time-of-flight mass spectrometry (UPLC Q-TOF/MS) could be used for a large-scale detection of features in plasma samples. The results showed that 15 metabolites at the 1 h time point and 19 metabolites at the 2 h time point after QKLI administration were associated with the antipyretic effect of QKLI, including amino acid, phosphatidylcholine and lysophosphatidylcholine. The metabolism pathway analysis revealed that the potential biomarkers, which were important for the antipyretic mechanism of QKLI, were closely responsible for correcting the perturbed pathways of amino acid metabolism and lipid metabolism. In conclusion, the use of complementary UPLC Q-TOF/MS based metabolomics and lipidomics allows for the discovery of new potential plasma biomarkers in the QKLI antipyretic process and the associated pathways, and aided in advancing the understanding of the holism and synergism of the Chinese drug. PMID:27208622

  17. Clinical impact of human breast milk metabolomics.

    Science.gov (United States)

    Cesare Marincola, Flaminia; Dessì, Angelica; Corbu, Sara; Reali, Alessandra; Fanos, Vassilios

    2015-12-01

    Metabolomics is a research field concerned with the analysis of metabolome, the complete set of metabolites in a given cell, tissue, or biological sample. Being able to provide a molecular snapshot of biological systems, metabolomics has emerged as a functional methodology in a wide range of research areas such as toxicology, pharmacology, food technology, nutrition, microbial biotechnology, systems biology, and plant biotechnology. In this review, we emphasize the applications of metabolomics in investigating the human breast milk (HBM) metabolome. HBM is the recommended source of nutrition for infants since it contains the optimal balance of nutrients for developing babies, and it provides a range of benefits for growth, immunity, and development. The molecular mechanisms beyond the inter- and intra-variability of HBM that make its composition unique are yet to be well-characterized. Although still in its infancy, the study of HBM metabolome has already proven itself to be of great value in providing insights into this biochemical variability in relation to mother phenotype, diet, disease, and lifestyle. The results of these investigations lay the foundation for further developments useful to identify normal and aberrant biochemical changes as well as to develop strategies to promote healthy infant feeding practices.

  18. Metabolomics continues to flourish: highlights from the 2014 Metabolomics Society Conference

    NARCIS (Netherlands)

    Roessner, U.; Hall, R.D.

    2014-01-01

    The Metabolomics Society has now been organising its annual meetings for 10 years! The 10th annual conference returned, in June, to Tsuruoka, Japan where the very first meeting was also held in 2005—just shortly after our society had been formally established and our journal Metabolomics had brought

  19. Metabolomics of pulmonary exacerbations reveals the personalized nature of cystic fibrosis disease.

    Science.gov (United States)

    Quinn, Robert A; Lim, Yan Wei; Mak, Tytus D; Whiteson, Katrine; Furlan, Mike; Conrad, Douglas; Rohwer, Forest; Dorrestein, Pieter

    2016-01-01

    Background. Cystic fibrosis (CF) is a genetic disease that results in chronic infections of the lungs. CF patients experience intermittent pulmonary exacerbations (CFPE) that are associated with poor clinical outcomes. CFPE involves an increase in disease symptoms requiring more aggressive therapy. Methods. Longitudinal sputum samples were collected from 11 patients (n = 44 samples) to assess the effect of exacerbations on the sputum metabolome using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The data was analyzed with MS/MS molecular networking and multivariate statistics. Results. The individual patient source had a larger influence on the metabolome of sputum than the clinical state (exacerbation, treatment, post-treatment, or stable). Of the 4,369 metabolites detected, 12% were unique to CFPE samples; however, the only known metabolites significantly elevated at exacerbation across the dataset were platelet activating factor (PAF) and a related monacylglycerophosphocholine lipid. Due to the personalized nature of the sputum metabolome, a single patient was followed for 4.2 years (capturing four separate exacerbation events) as a case study for the detection of personalized biomarkers with metabolomics. PAF and related lipids were significantly elevated during CFPEs of this patient and ceramide was elevated during CFPE treatment. Correlating the abundance of bacterial 16S rRNA gene amplicons to metabolomics data from the same samples during a CFPE demonstrated that antibiotics were positively correlated to Stenotrophomonas and Pseudomonas, while ceramides and other lipids were correlated with Streptococcus, Rothia, and anaerobes. Conclusions. This study identified PAF and other inflammatory lipids as potential biomarkers of CFPE, but overall, the metabolome of CF sputum was patient specific, supporting a personalized approach to molecular detection of CFPE onset. PMID:27602256

  20. NMR and pattern recognition methods in metabolomics: From data acquisition to biomarker discovery: A review

    Energy Technology Data Exchange (ETDEWEB)

    Smolinska, Agnieszka, E-mail: A.Smolinska@science.ru.nl [Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen (Netherlands); Blanchet, Lionel [Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen (Netherlands); Department of Biochemistry, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen (Netherlands); Buydens, Lutgarde M.C.; Wijmenga, Sybren S. [Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen (Netherlands)

    2012-10-31

    Highlights: Black-Right-Pointing-Pointer Procedures for acquisition of different biofluids by NMR. Black-Right-Pointing-Pointer Recent developments in metabolic profiling of different biofluids by NMR are presented. Black-Right-Pointing-Pointer The crucial steps involved in data preprocessing and multivariate chemometric analysis are reviewed. Black-Right-Pointing-Pointer Emphasis is given on recent findings on Multiple Sclerosis via NMR and pattern recognition methods. - Abstract: Metabolomics is the discipline where endogenous and exogenous metabolites are assessed, identified and quantified in different biological samples. Metabolites are crucial components of biological system and highly informative about its functional state, due to their closeness to functional endpoints and to the organism's phenotypes. Nuclear Magnetic Resonance (NMR) spectroscopy, next to Mass Spectrometry (MS), is one of the main metabolomics analytical platforms. The technological developments in the field of NMR spectroscopy have enabled the identification and quantitative measurement of the many metabolites in a single sample of biofluids in a non-targeted and non-destructive manner. Combination of NMR spectra of biofluids and pattern recognition methods has driven forward the application of metabolomics in the field of biomarker discovery. The importance of metabolomics in diagnostics, e.g. in identifying biomarkers or defining pathological status, has been growing exponentially as evidenced by the number of published papers. In this review, we describe the developments in data acquisition and multivariate analysis of NMR-based metabolomics data, with particular emphasis on the metabolomics of Cerebrospinal Fluid (CSF) and biomarker discovery in Multiple Sclerosis (MScl).

  1. Non-targeted metabolomics study for the analysis of chemical compositions in three types of tea by using gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry%基于气相色谱-质谱联用与液相色谱-质谱联用的非靶向代谢组学用于3类茶叶中化学成分分析

    Institute of Scientific and Technical Information of China (English)

    张磊; 曾仲大; 叶国注; 赵春霞; 路鑫; 许国旺

    2014-01-01

    茶叶中的化学成分是构成其风味特征的物质基础。本研究建立了基于气相色谱-质谱联用和液相色谱-质谱联用的非靶向代谢组学方法。完成预处理及分析条件优化后,使用标准样品考察方法的线性、回收率及重复性,结果表明方法整体稳定且结果可靠。将该方法用于绿茶、乌龙茶和红茶中化学成分的分析。通过超声辅助溶剂提取及气相色谱-质谱联用分析共获得1812个特征峰,而使用加热溶剂提取及液相色谱-质谱联用分析可获得2608个特征峰。结合保留规律及质谱数据库,共定性173种化合物(109种随后经标准样品验证),其中只有9种化合物在上述两类分析中被同时检出,表明方法互补性良好。3类茶叶数据的偏最小二乘判别分析结果表明,三者间存在显著差异。结合模型的变量重要因子( VIP)与非参数检验共筛选出90种化合物,其中包含儿茶素、氨基酸、糖、有机酸和黄酮苷类等众多与茶叶滋味密切相关的化学成分。%Tea is one of the most widely consumed beverages in the world for its benefits to daily life and health. To discover the difference and correlation of chemical compositions in the three typical types of tea,a non-targeted metabolomics method was developed. After the optimization of extraction methods,gas chroma-tography-time-of-flight mass spectrometry and liquid chromatography-quadrupole time-of-flight mass spectrome-try were applied for metabolomics analysis,1 812 and 2 608 features were obtained,respectively. By comparing with the known compounds in public and/or commercial databases,173 compounds were tentatively identified, and 109 of them were experimentally confirmed by standards. Totally,33 tea samples including 12,12 and 9 samples of green,oolong and black tea,respectively,were analyzed by using the above two methods. Multiva-riate analysis,Mann-Whitney U test and hierarchical cluster

  2. NMR-based Metabolomics Applications in Biological and Environmental Science

    Science.gov (United States)

    As a complimentary tool to other omics platforms, metabolomics is increasingly being used bybiologists to study the dynamic response of biological systems (cells, tissues, or wholeorganisms) under diverse physiological or pathological conditions. Metabolomics deals with the quali...

  3. Plant Metabolomics : the missiong link in functional genomics strategies

    NARCIS (Netherlands)

    Hall, R.D.; Beale, M.; Fiehn, O.; Hardy, N.; Summer, L.; Bino, R.

    2002-01-01

    After the establishment of technologies for high-throughput DNA sequencing (genomics), gene expression analysis (transcriptomics), and protein analysis (proteomics), the remaining functional genomics challenge is that of metabolomics. Metabolomics is the term coined for essentially comprehensive, no

  4. Top-down Targeted Metabolomics Reveals a Sulfur-Containing Metabolite with Inhibitory Activity against Angiotensin-Converting Enzyme in Asparagus officinalis.

    Science.gov (United States)

    Nakabayashi, Ryo; Yang, Zhigang; Nishizawa, Tomoko; Mori, Tetsuya; Saito, Kazuki

    2015-05-22

    The discovery of bioactive natural compounds containing sulfur, which is crucial for inhibitory activity against angiotensin-converting enzyme (ACE), is a challenging task in metabolomics. Herein, a new S-containing metabolite, asparaptine (1), was discovered in the spears of Asparagus officinalis by targeted metabolomics using mass spectrometry for S-containing metabolites. The contribution ratio (2.2%) to the IC50 value in the crude extract showed that asparaptine (1) is a new ACE inhibitor.

  5. Top-down Targeted Metabolomics Reveals a Sulfur-Containing Metabolite with Inhibitory Activity against Angiotensin-Converting Enzyme in Asparagus officinalis.

    Science.gov (United States)

    Nakabayashi, Ryo; Yang, Zhigang; Nishizawa, Tomoko; Mori, Tetsuya; Saito, Kazuki

    2015-05-22

    The discovery of bioactive natural compounds containing sulfur, which is crucial for inhibitory activity against angiotensin-converting enzyme (ACE), is a challenging task in metabolomics. Herein, a new S-containing metabolite, asparaptine (1), was discovered in the spears of Asparagus officinalis by targeted metabolomics using mass spectrometry for S-containing metabolites. The contribution ratio (2.2%) to the IC50 value in the crude extract showed that asparaptine (1) is a new ACE inhibitor. PMID:25922884

  6. Role of Metabolomics in Traumatic Brain Injury Research.

    Science.gov (United States)

    Wolahan, Stephanie M; Hirt, Daniel; Braas, Daniel; Glenn, Thomas C

    2016-10-01

    Metabolomics is an important member of the omics community in that it defines which small molecules may be responsible for disease states. This article reviews the essential principles of metabolomics from specimen preparation, chemical analysis, to advanced statistical methods. Metabolomics in traumatic brain injury has so far been underutilized. Future metabolomics-based studies focused on the diagnoses, prognoses, and treatment effects need to be conducted across all types of traumatic brain injury. PMID:27637396

  7. Ways for accurate analysis of high purity materials using the glow discharge mass spectrometry (GD-MS); Wege zur genauen Charakterisierung hochreiner Materialien mit der Glimmentladungs-Massenspektrometrie (GD-MS)

    Energy Technology Data Exchange (ETDEWEB)

    Gusarova, Tamara

    2010-04-14

    The main aim of this work consists in the investigation, development and application of improved possibilities of accurate analysis of high purity materials using the solid sample technique of Glow Discharge Mass Spectrometry (GD-MS), as well as in the sensitivity enhancement of GD Optical Emission Spectrometry (GD-OES) by implicating the hollow cathode effect. The emphasis of the PhD thesis consists in the accurate quantification for GD-MS. As appropriate certified reference materials (CRMs) for calibration are lacking in most cases an accurate quantification especially for trace elements mass fractions at {mu}g kg{sup -1} level can often not be achieved. To overcome this problem and to expand the possibilities of modern GD-MS hereby, synthetic standards were applied for calibration of both high resolution GD-MS instruments ''VG 9000'' and ''Element GD''. The standards were prepared by doping of matrix powder with trace element standard solutions followed by drying and pressing the doped powder to compact pellets. With the quantification approach worked out and described here accurate analysis results with small uncertainties can be achieved for most elements of periodic table in almost every matrix composition. Furthermore direct traceability of the analytical results to the International System of Units (SI) is provided ensuring their higher metrological quality. Numerous additional systematic investigations concerning the preparation of the synthetic standards and their properties were carried out. The results of calibration of GD-MS instruments with synthetic standards for Co (Co-C), Cu, In, Fe and Zn matrices were checked by measuring CRMs. These results were also contrasted with those of other quantification approaches, as usually used in GD-MS routine. The results achieved with synthetic standards had the highest accuracy. The successful participation in the round robin test CCQM-P107 between international

  8. Accurate Measurement of the in vivo Ammonium Concentration in Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Hugo F. Cueto-Rojas

    2016-04-01

    Full Text Available Ammonium (NH4+ is the most common N-source for yeast fermentations, and N-limitation is frequently applied to reduce growth and increase product yields. While there is significant molecular knowledge on NH4+ transport and assimilation, there have been few attempts to measure the in vivo concentration of this metabolite. In this article, we present a sensitive and accurate analytical method to quantify the in vivo intracellular ammonium concentration in Saccharomyces cerevisiae based on standard rapid sampling and metabolomics techniques. The method validation experiments required the development of a proper sample processing protocol to minimize ammonium production/consumption during biomass extraction by assessing the impact of amino acid degradation—an element that is often overlooked. The resulting cold chloroform metabolite extraction method, together with quantification using ultra high performance liquid chromatography-isotope dilution mass spectrometry (UHPLC-IDMS, was not only more sensitive than most of the existing methods but also more accurate than methods that use electrodes, enzymatic reactions, or boiling water or boiling ethanol biomass extraction because it minimized ammonium consumption/production during sampling processing and interference from other metabolites in the quantification of intracellular ammonium. Finally, our validation experiments showed that other metabolites such as pyruvate or 2-oxoglutarate (αKG need to be extracted with cold chloroform to avoid measurements being biased by the degradation of other metabolites (e.g., amino acids.

  9. Training in metabolomics research. I. Designing the experiment, collecting and extracting samples and generating metabolomics data.

    Science.gov (United States)

    Barnes, Stephen; Benton, H Paul; Casazza, Krista; Cooper, Sara J; Cui, Xiangqin; Du, Xiuxia; Engler, Jeffrey; Kabarowski, Janusz H; Li, Shuzhao; Pathmasiri, Wimal; Prasain, Jeevan K; Renfrow, Matthew B; Tiwari, Hemant K

    2016-07-01

    The study of metabolism has had a long history. Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes. The National Institutes of Health Common Fund Metabolomics Program was established in 2012 to stimulate interest in the approaches and technologies of metabolomics. To deliver one of the program's goals, the University of Alabama at Birmingham has hosted an annual 4-day short course in metabolomics for faculty, postdoctoral fellows and graduate students from national and international institutions. This paper is the first part of a summary of the training materials presented in the course to be used as a resource for all those embarking on metabolomics research. The complete set of training materials including slide sets and videos can be viewed at http://www.uab.edu/proteomics/metabolomics/workshop/workshop_june_2015.php. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27434804

  10. Systematic Applications of Metabolomics in Metabolic Engineering

    Directory of Open Access Journals (Sweden)

    Robert A. Dromms

    2012-12-01

    Full Text Available The goals of metabolic engineering are well-served by the biological information provided by metabolomics: information on how the cell is currently using its biochemical resources is perhaps one of the best ways to inform strategies to engineer a cell to produce a target compound. Using the analysis of extracellular or intracellular levels of the target compound (or a few closely related molecules to drive metabolic engineering is quite common. However, there is surprisingly little systematic use of metabolomics datasets, which simultaneously measure hundreds of metabolites rather than just a few, for that same purpose. Here, we review the most common systematic approaches to integrating metabolite data with metabolic engineering, with emphasis on existing efforts to use whole-metabolome datasets. We then review some of the most common approaches for computational modeling of cell-wide metabolism, including constraint-based models, and discuss current computational approaches that explicitly use metabolomics data. We conclude with discussion of the broader potential of computational approaches that systematically use metabolomics data to drive metabolic engineering.

  11. Use of Rhizosphere Metabolomics to Investigate Exudation of Phenolics by Arabidopsis Roots

    Science.gov (United States)

    Lee, Yong Jian; Rai, Amit; Reuben, Sheela; Nesati, Victor; Almeida, Reinaldo; Swarup, Sanjay

    2013-04-01

    and anthocyanin metabolites. We describe here the metabolites present in the root exudates using high resolution accurate mass (HRAM) metabolomics approach. Using this approach, biased rhizosphere for another class of PGPR strains can now be created. In this case, lignin- and anthocyanin- utilizing strains will be selectively preferred. We have set up a platform to perform metabolomics of exudates at the root surface. This has allowed us to use the liquid extraction surface analysis (LESA) system using a Thermo Velos Pro Orbitrap-MS to identify differences in exudate profiles along the root system of Arabidopsis. This platform enables direct sampling and measurement from plant roots grown aeroponically. As the metabolites are extracted from root surface and directly injected into the mass spectrometer, there is minimal loss of sample in this process. This method will now allow us to further dissect rhizosphere properties from places such as young root apex, as well as from the more mature base of roots. Taken together, these resources of altered rhizosphere, nutrient utilization pathways in microbes and surface analysis technology will help in extending our understanding of the processes in the plant rhizosphere.

  12. Organization of GC/MS and LC/MS metabolomics data into chemical libraries

    Directory of Open Access Journals (Sweden)

    DeHaven Corey D

    2010-10-01

    Full Text Available Abstract Background Metabolomics experiments involve generating and comparing small molecule (metabolite profiles from complex mixture samples to identify those metabolites that are modulated in altered states (e.g., disease, drug treatment, toxin exposure. One non-targeted metabolomics approach attempts to identify and interrogate all small molecules in a sample using GC or LC separation followed by MS or MSn detection. Analysis of the resulting large, multifaceted data sets to rapidly and accurately identify the metabolites is a challenging task that relies on the availability of chemical libraries of metabolite spectral signatures. A method for analyzing spectrometry data to identify and Quantify Individual Components in a Sample, (QUICS, enables generation of chemical library entries from known standards and, importantly, from unknown metabolites present in experimental samples but without a corresponding library entry. This method accounts for all ions in a sample spectrum, performs library matches, and allows review of the data to quality check library entries. The QUICS method identifies ions related to any given metabolite by correlating ion data across the complete set of experimental samples, thus revealing subtle spectral trends that may not be evident when viewing individual samples and are likely to be indicative of the presence of one or more otherwise obscured metabolites. Results LC-MS/MS or GC-MS data from 33 liver samples were analyzed simultaneously which exploited the inherent biological diversity of the samples and the largely non-covariant chemical nature of the metabolites when viewed over multiple samples. Ions were partitioned by both retention time (RT and covariance which grouped ions from a single common underlying metabolite. This approach benefitted from using mass, time and intensity data in aggregate over the entire sample set to reject outliers and noise thereby producing higher quality chemical identities. The

  13. Application of 1H-NMR metabolomic profiling for reef-building corals.

    Directory of Open Access Journals (Sweden)

    Emilia M Sogin

    Full Text Available In light of global reef decline new methods to accurately, cheaply, and quickly evaluate coral metabolic states are needed to assess reef health. Metabolomic profiling can describe the response of individuals to disturbance (i.e., shifts in environmental conditions across biological models and is a powerful approach for characterizing and comparing coral metabolism. For the first time, we assess the utility of a proton-nuclear magnetic resonance spectroscopy (1H-NMR-based metabolomics approach in characterizing coral metabolite profiles by 1 investigating technical, intra-, and inter-sample variation, 2 evaluating the ability to recover targeted metabolite spikes, and 3 assessing the potential for this method to differentiate among coral species. Our results indicate 1H-NMR profiling of Porites compressa corals is highly reproducible and exhibits low levels of variability within and among colonies. The spiking experiments validate the sensitivity of our methods and showcase the capacity of orthogonal partial least squares discriminate analysis (OPLS-DA to distinguish between profiles spiked with varying metabolite concentrations (0 mM, 0.1 mM, and 10 mM. Finally, 1H-NMR metabolomics coupled with OPLS-DA, revealed species-specific patterns in metabolite profiles among four reef-building corals (Pocillopora damicornis, Porites lobata, Montipora aequituberculata, and Seriatopora hystrix. Collectively, these data indicate that 1H-NMR metabolomic techniques can profile reef-building coral metabolomes and have the potential to provide an integrated picture of the coral phenotype in response to environmental change.

  14. Application of 1H-NMR Metabolomic Profiling for Reef-Building Corals

    Science.gov (United States)

    Sogin, Emilia M.; Anderson, Paul; Williams, Philip; Chen, Chii-Shiarng; Gates, Ruth D.

    2014-01-01

    In light of global reef decline new methods to accurately, cheaply, and quickly evaluate coral metabolic states are needed to assess reef health. Metabolomic profiling can describe the response of individuals to disturbance (i.e., shifts in environmental conditions) across biological models and is a powerful approach for characterizing and comparing coral metabolism. For the first time, we assess the utility of a proton-nuclear magnetic resonance spectroscopy (1H-NMR)-based metabolomics approach in characterizing coral metabolite profiles by 1) investigating technical, intra-, and inter-sample variation, 2) evaluating the ability to recover targeted metabolite spikes, and 3) assessing the potential for this method to differentiate among coral species. Our results indicate 1H-NMR profiling of Porites compressa corals is highly reproducible and exhibits low levels of variability within and among colonies. The spiking experiments validate the sensitivity of our methods and showcase the capacity of orthogonal partial least squares discriminate analysis (OPLS-DA) to distinguish between profiles spiked with varying metabolite concentrations (0 mM, 0.1 mM, and 10 mM). Finally, 1H-NMR metabolomics coupled with OPLS-DA, revealed species-specific patterns in metabolite profiles among four reef-building corals (Pocillopora damicornis, Porites lobata, Montipora aequituberculata, and Seriatopora hystrix). Collectively, these data indicate that 1H-NMR metabolomic techniques can profile reef-building coral metabolomes and have the potential to provide an integrated picture of the coral phenotype in response to environmental change. PMID:25354140

  15. Biomarkers of whale shark health: a metabolomic approach.

    Science.gov (United States)

    Dove, Alistair D M; Leisen, Johannes; Zhou, Manshui; Byrne, Jonathan J; Lim-Hing, Krista; Webb, Harry D; Gelbaum, Leslie; Viant, Mark R; Kubanek, Julia; Fernández, Facundo M

    2012-01-01

    In a search for biomarkers of health in whale sharks and as exploration of metabolomics as a modern tool for understanding animal physiology, the metabolite composition of serum in six whale sharks (Rhincodon typus) from an aquarium collection was explored using (1)H nuclear magnetic resonance (NMR) spectroscopy and direct analysis in real time (DART) mass spectrometry (MS). Principal components analysis (PCA) of spectral data showed that individual animals could be resolved based on the metabolite composition of their serum and that two unhealthy individuals could be discriminated from the remaining healthy animals. The major difference between healthy and unhealthy individuals was the concentration of homarine, here reported for the first time in an elasmobranch, which was present at substantially lower concentrations in unhealthy whale sharks, suggesting that this metabolite may be a useful biomarker of health status in this species. The function(s) of homarine in sharks remain uncertain but it likely plays a significant role as an osmolyte. The presence of trimethylamine oxide (TMAO), another well-known protective osmolyte of elasmobranchs, at 0.1-0.3 mol L(-1) was also confirmed using both NMR and MS. Twenty-three additional potential biomarkers were identified based on significant differences in the frequency of their occurrence between samples from healthy and unhealthy animals, as detected by DART MS. Overall, NMR and MS provided complementary data that showed that metabolomics is a useful approach for biomarker prospecting in poorly studied species like elasmobranchs.

  16. Biomarkers of whale shark health: a metabolomic approach.

    Directory of Open Access Journals (Sweden)

    Alistair D M Dove

    Full Text Available In a search for biomarkers of health in whale sharks and as exploration of metabolomics as a modern tool for understanding animal physiology, the metabolite composition of serum in six whale sharks (Rhincodon typus from an aquarium collection was explored using (1H nuclear magnetic resonance (NMR spectroscopy and direct analysis in real time (DART mass spectrometry (MS. Principal components analysis (PCA of spectral data showed that individual animals could be resolved based on the metabolite composition of their serum and that two unhealthy individuals could be discriminated from the remaining healthy animals. The major difference between healthy and unhealthy individuals was the concentration of homarine, here reported for the first time in an elasmobranch, which was present at substantially lower concentrations in unhealthy whale sharks, suggesting that this metabolite may be a useful biomarker of health status in this species. The function(s of homarine in sharks remain uncertain but it likely plays a significant role as an osmolyte. The presence of trimethylamine oxide (TMAO, another well-known protective osmolyte of elasmobranchs, at 0.1-0.3 mol L(-1 was also confirmed using both NMR and MS. Twenty-three additional potential biomarkers were identified based on significant differences in the frequency of their occurrence between samples from healthy and unhealthy animals, as detected by DART MS. Overall, NMR and MS provided complementary data that showed that metabolomics is a useful approach for biomarker prospecting in poorly studied species like elasmobranchs.

  17. Biomarkers of whale shark health: a metabolomic approach.

    Science.gov (United States)

    Dove, Alistair D M; Leisen, Johannes; Zhou, Manshui; Byrne, Jonathan J; Lim-Hing, Krista; Webb, Harry D; Gelbaum, Leslie; Viant, Mark R; Kubanek, Julia; Fernández, Facundo M

    2012-01-01

    In a search for biomarkers of health in whale sharks and as exploration of metabolomics as a modern tool for understanding animal physiology, the metabolite composition of serum in six whale sharks (Rhincodon typus) from an aquarium collection was explored using (1)H nuclear magnetic resonance (NMR) spectroscopy and direct analysis in real time (DART) mass spectrometry (MS). Principal components analysis (PCA) of spectral data showed that individual animals could be resolved based on the metabolite composition of their serum and that two unhealthy individuals could be discriminated from the remaining healthy animals. The major difference between healthy and unhealthy individuals was the concentration of homarine, here reported for the first time in an elasmobranch, which was present at substantially lower concentrations in unhealthy whale sharks, suggesting that this metabolite may be a useful biomarker of health status in this species. The function(s) of homarine in sharks remain uncertain but it likely plays a significant role as an osmolyte. The presence of trimethylamine oxide (TMAO), another well-known protective osmolyte of elasmobranchs, at 0.1-0.3 mol L(-1) was also confirmed using both NMR and MS. Twenty-three additional potential biomarkers were identified based on significant differences in the frequency of their occurrence between samples from healthy and unhealthy animals, as detected by DART MS. Overall, NMR and MS provided complementary data that showed that metabolomics is a useful approach for biomarker prospecting in poorly studied species like elasmobranchs. PMID:23166652

  18. Metabolomic applications to decipher gut microbial metabolic influence in health and disease

    Directory of Open Access Journals (Sweden)

    Francois-Pierre eMartin

    2012-04-01

    Full Text Available Dietary preferences and nutrients composition have been shown to influence human and gut microbial metabolism, which ultimately has specific effects on health and diseases’ risk. Increasingly, results from molecular biology and microbiology demonstrate the key role of the gut microbiota metabolic interface to the overall mammalian host’s health status. There is therefore raising interest in nutrition research to characterize the molecular foundations of the gut microbial mammalian cross-talk at both physiological and biochemical pathway levels. Tackling these challenges can be achieved through systems biology approaches, such as metabolomics, to underpin the highly complex metabolic exchanges between diverse biological compartments, including organs, systemic biofluids and microbial symbionts. By the development of specific biomarkers for prediction of health and disease, metabolomics is increasingly used in clinical applications as regard to disease aetiology, diagnostic stratification and potentially mechanism of action of therapeutical and nutraceutical solutions. Surprisingly, an increasing number of metabolomics investigations in pre-clinical and clinical studies based on proton nuclear magnetic resonance (1H NMR spectroscopy and mass spectrometry (MS provided compelling evidence that system wide and organ-specific biochemical processes are under the influence of gut microbial metabolism. This review aims at describing recent applications of metabolomics in clinical fields where main objective is to discern the biochemical mechanisms under the influence of the gut microbiota, with insight into gastrointestinal health and diseases diagnostics and improvement of homeostasis metabolic regulation.

  19. Toward the comprehensive understanding of the gut ecosystem via metabolomics-based integrated omics approach.

    Science.gov (United States)

    Aw, Wanping; Fukuda, Shinji

    2015-01-01

    Recent advances in DNA sequencing and mass spectrometry technologies have allowed us to collect more data on microbiome and metabolome to assess the influence of the gut microbiota on human health at a whole-systems level. Major advances in metagenomics and metabolomics technologies have shown that the gut microbiota contributes to host overall health status to a large extent. As such, the gut microbiota is often likened to a measurable and functional organ consisting of prokaryotic cells, which creates the unique gut ecosystem together with the host eukaryotic cells. In this review, we discuss in detail the relationship between gut microbiota and its metabolites like choline, bile acids, phenols, and short-chain fatty acids in the host health and etiopathogenesis of various pathological states such as multiple sclerosis, autism, obesity, diabetes, and chronic kidney disease. By integrating metagenomic and metabolomic information on a systems biology-wide approach, we would be better able to understand this interplay between gut microbiome and host metabolism. Integration of the microbiome, metatranscriptome, and metabolome information will pave the way toward an improved holistic understanding of the complex mammalian superorganism. Through the modeling of metabolic interactions between lifestyle, diet, and microbiota, integrated omics-based understanding of the gut ecosystem is the new avenue, providing exciting novel therapeutic approaches for optimal host health. PMID:25338280

  20. Tools and Databases of the KOMICS Web Portal for Preprocessing, Mining, and Dissemination of Metabolomics Data

    Directory of Open Access Journals (Sweden)

    Nozomu Sakurai

    2014-01-01

    Full Text Available A metabolome—the collection of comprehensive quantitative data on metabolites in an organism—has been increasingly utilized for applications such as data-intensive systems biology, disease diagnostics, biomarker discovery, and assessment of food quality. A considerable number of tools and databases have been developed to date for the analysis of data generated by various combinations of chromatography and mass spectrometry. We report here a web portal named KOMICS (The Kazusa Metabolomics Portal, where the tools and databases that we developed are available for free to academic users. KOMICS includes the tools and databases for preprocessing, mining, visualization, and publication of metabolomics data. Improvements in the annotation of unknown metabolites and dissemination of comprehensive metabolomic data are the primary aims behind the development of this portal. For this purpose, PowerGet and FragmentAlign include a manual curation function for the results of metabolite feature alignments. A metadata-specific wiki-based database, Metabolonote, functions as a hub of web resources related to the submitters' work. This feature is expected to increase citation of the submitters' work, thereby promoting data publication. As an example of the practical use of KOMICS, a workflow for a study on Jatropha curcas is presented. The tools and databases available at KOMICS should contribute to enhanced production, interpretation, and utilization of metabolomic Big Data.

  1. An R package for the integrated analysis of metabolomics and spectral data.

    Science.gov (United States)

    Costa, Christopher; Maraschin, Marcelo; Rocha, Miguel

    2016-06-01

    Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as nuclear magnetic resonance, gas or liquid chromatography, mass spectrometry, infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines.

  2. Metabolomics to Explore Impact of Dairy Intake

    Directory of Open Access Journals (Sweden)

    Hong Zheng

    2015-06-01

    Full Text Available Dairy products are an important component in the Western diet and represent a valuable source of nutrients for humans. However, a reliable dairy intake assessment in nutrition research is crucial to correctly elucidate the link between dairy intake and human health. Metabolomics is considered a potential tool for assessment of dietary intake instead of traditional methods, such as food frequency questionnaires, food records, and 24-h recalls. Metabolomics has been successfully applied to discriminate between consumption of different dairy products under different experimental conditions. Moreover, potential metabolites related to dairy intake were identified, although these metabolites need to be further validated in other intervention studies before they can be used as valid biomarkers of dairy consumption. Therefore, this review provides an overview of metabolomics for assessment of dairy intake in order to better clarify the role of dairy products in human nutrition and health.

  3. Microbiome, Metabolome and Inflammatory Bowel Disease.

    Science.gov (United States)

    Ahmed, Ishfaq; Roy, Badal C; Khan, Salman A; Septer, Seth; Umar, Shahid

    2016-01-01

    Inflammatory Bowel Disease (IBD) is a multifactorial disorder that conceptually occurs as a result of altered immune responses to commensal and/or pathogenic gut microbes in individuals most susceptible to the disease. During Crohn's Disease (CD) or Ulcerative Colitis (UC), two components of the human IBD, distinct stages define the disease onset, severity, progression and remission. Epigenetic, environmental (microbiome, metabolome) and nutritional factors are important in IBD pathogenesis. While the dysbiotic microbiota has been proposed to play a role in disease pathogenesis, the data on IBD and diet are still less convincing. Nonetheless, studies are ongoing to examine the effect of pre/probiotics and/or FODMAP reduced diets on both the gut microbiome and its metabolome in an effort to define the healthy diet in patients with IBD. Knowledge of a unique metabolomic fingerprint in IBD could be useful for diagnosis, treatment and detection of disease pathogenesis. PMID:27681914

  4. Metabolomics and bioactive substances in plants

    DEFF Research Database (Denmark)

    Khakimov, Bekzod

    (Analytical and Bioanalytical Chemistry, In Press, DOI: 10.1007/s00216-013-7341-z) outlines a novel GC-MS derivatization method using TMSCN for trimethylsilylation for improved analysis of complex biological mixtures . A review paper (Journal of Cereal Science, Accepted) written for the special issue......Metabolomic analysis of plants broadens understanding of how plants may benefit humans, animals and the environment, provide sustainable food and energy, and improve current agricultural, pharmacological and medicinal practices in order to bring about healthier and longer life. The quality...... and data processing. The study mainly concerned the three most commonly applied analytical techniques in plant metabolomics, GC-MS, LC-MS and NMR. In addition, advanced chemometrics methods e.g. PARAFAC2 and ASCA have been extensively used for development of complex metabolomics data processing...

  5. [Metabolomics analysis of taxadiene producing yeasts].

    Science.gov (United States)

    Yan, Huifang; Ding, Mingzhu; Yuan, Yingjin

    2014-02-01

    In order to study the inherent difference among terpenes producing yeasts from the point of metabolomics, we selected taxadiene producing yeasts as the model system. The changes of cellular metabolites during fermentation log phase of artificial functional yeasts were determined using metabolomics methods. The results represented that compared to W303-1A as a blank control, the metabolites in glycolysis, tricarboxylic acid cycle (TCA) cycle and several amino acids were influenced. And due to the changes of metabolites, the growth of cells was inhibited to a certain extent. Among the metabolites identified, citric acid content in taxadiene producing yeasts changed the most, the decreasing amplitude reached 90% or more. Therefore, citric acid can be a marker metabolite for the future study of artificial functional yeasts. The metabolomics analysis of taxadiene producing yeasts can provide more information in further studies on optimization of terpenes production in heterologous chassis.

  6. Microbiome, Metabolome and Inflammatory Bowel Disease

    Science.gov (United States)

    Ahmed, Ishfaq; Roy, Badal C.; Khan, Salman A.; Septer, Seth; Umar, Shahid

    2016-01-01

    Inflammatory Bowel Disease (IBD) is a multifactorial disorder that conceptually occurs as a result of altered immune responses to commensal and/or pathogenic gut microbes in individuals most susceptible to the disease. During Crohn’s Disease (CD) or Ulcerative Colitis (UC), two components of the human IBD, distinct stages define the disease onset, severity, progression and remission. Epigenetic, environmental (microbiome, metabolome) and nutritional factors are important in IBD pathogenesis. While the dysbiotic microbiota has been proposed to play a role in disease pathogenesis, the data on IBD and diet are still less convincing. Nonetheless, studies are ongoing to examine the effect of pre/probiotics and/or FODMAP reduced diets on both the gut microbiome and its metabolome in an effort to define the healthy diet in patients with IBD. Knowledge of a unique metabolomic fingerprint in IBD could be useful for diagnosis, treatment and detection of disease pathogenesis. PMID:27681914

  7. Microbiome, Metabolome and Inflammatory Bowel Disease

    Directory of Open Access Journals (Sweden)

    Ishfaq Ahmed

    2016-06-01

    Full Text Available Inflammatory Bowel Disease (IBD is a multifactorial disorder that conceptually occurs as a result of altered immune responses to commensal and/or pathogenic gut microbes in individuals most susceptible to the disease. During Crohn’s Disease (CD or Ulcerative Colitis (UC, two components of the human IBD, distinct stages define the disease onset, severity, progression and remission. Epigenetic, environmental (microbiome, metabolome and nutritional factors are important in IBD pathogenesis. While the dysbiotic microbiota has been proposed to play a role in disease pathogenesis, the data on IBD and diet are still less convincing. Nonetheless, studies are ongoing to examine the effect of pre/probiotics and/or FODMAP reduced diets on both the gut microbiome and its metabolome in an effort to define the healthy diet in patients with IBD. Knowledge of a unique metabolomic fingerprint in IBD could be useful for diagnosis, treatment and detection of disease pathogenesis.

  8. mzGroupAnalyzer--predicting pathways and novel chemical structures from untargeted high-throughput metabolomics data.

    Directory of Open Access Journals (Sweden)

    Hannes Doerfler

    Full Text Available The metabolome is a highly dynamic entity and the final readout of the genotype x environment x phenotype (GxExP relationship of an organism. Monitoring metabolite dynamics over time thus theoretically encrypts the whole range of possible chemical and biochemical transformations of small molecules involved in metabolism. The bottleneck is, however, the sheer number of unidentified structures in these samples. This represents the next challenge for metabolomics technology and is comparable with genome sequencing 30 years ago. At the same time it is impossible to handle the amount of data involved in a metabolomics analysis manually. Algorithms are therefore imperative to allow for automated m/z feature extraction and subsequent structure or pathway assignment. Here we provide an automated pathway inference strategy comprising measurements of metabolome time series using LC- MS with high resolution and high mass accuracy. An algorithm was developed, called mzGroupAnalyzer, to automatically explore the metabolome for the detection of metabolite transformations caused by biochemical or chemical modifications. Pathways are extracted directly from the data and putative novel structures can be identified. The detected m/z features can be mapped on a van Krevelen diagram according to their H/C and O/C ratios for pattern recognition and to visualize oxidative processes and biochemical transformations. This method was applied to Arabidopsis thaliana treated simultaneously with cold and high light. Due to a protective antioxidant response the plants turn from green to purple color via the accumulation of flavonoid structures. The detection of potential biochemical pathways resulted in 15 putatively new compounds involved in the flavonoid-pathway. These compounds were further validated by product ion spectra from the same data. The mzGroupAnalyzer is implemented in the graphical user interface (GUI of the metabolomics toolbox COVAIN (Sun & Weckwerth, 2012

  9. Linking metabolomics data to underlying metabolic regulation

    Directory of Open Access Journals (Sweden)

    Thomas eNägele

    2014-11-01

    Full Text Available The comprehensive experimental analysis of a metabolic constitution plays a central role in approaches of organismal systems biology.Quantifying the impact of a changing environment on the homeostasis of cellular metabolism has been the focus of numerous studies applying various metabolomics techniques. It has been proven that approaches which integrate different analytical techniques, e.g. LC-MS, GC-MS, CE-MS and H-NMR, can provide a comprehensive picture of a certain metabolic homeostasis. Identification of metabolic compounds and quantification of metabolite levels represent the groundwork for the analysis of regulatory strategies in cellular metabolism. This significantly promotes our current understanding of the molecular organization and regulation of cells, tissues and whole organisms.Nevertheless, it is demanding to elicit the pertinent information which is contained in metabolomics data sets.Based on the central dogma of molecular biology, metabolite levels and their fluctuations are the result of a directed flux of information from gene activation over transcription to translation and posttranslational modification.Hence, metabolomics data represent the summed output of a metabolic system comprising various levels of molecular organization.As a consequence, the inverse assignment of metabolomics data to underlying regulatory processes should yield information which-if deciphered correctly-provides comprehensive insight into a metabolic system.Yet, the deduction of regulatory principles is complex not only due to the high number of metabolic compounds, but also because of a high level of cellular compartmentalization and differentiation.Motivated by the question how metabolomics approaches can provide a representative view on regulatory biochemical processes, this article intends to present and discuss current metabolomics applications, strategies of data analysis and their limitations with respect to the interpretability in context of

  10. GC/TOF-MS代谢组学技术研究雷公藤甲素在大鼠体内的急性毒性%Gas chromatography time-of-flight mass spectrometry based metabolomic approach to evaluate acute toxicity of triptolide in rats

    Institute of Scientific and Technical Information of China (English)

    邵凤; 刘林生; 阿基业

    2014-01-01

    采用GC/TOF-MS代谢组学技术研究雷公藤甲素对大鼠尿液中内源性小分子化合物的影响和毒性作用机制,寻找与毒性相关标志物,为雷公藤类药物临床毒性的早期预防和诊断提供依据.SD大鼠随机分为4组,分别为雷公藤甲素高(2.4 mg/kg)、中(1.2 mg/kg)、低(0.6 mg/kg)剂量组及空白对照组.单次灌胃给药后,收集第0、1、3和7天的尿液,GC/TOF-MS进行分析,对尿液中内源性小分子化合物进行鉴定并获取半定量数据,经过主成分分析发现:不同剂量给药和不同时间取样尿液中内源性小分子代谢谱有明显差异,可被清晰区分并呈明显的动态变化轨迹.代谢组学数据分析结果与常规血液生化和组织病理学检查结果基本吻合.研究结果发现,给药引起尿液中的苹果酸、枸橼酸、牛磺酸、谷氨酸、苏氨酸及软脂酸等发生明显改变,提示与雷公藤甲素毒性相关,为潜在的毒性标志物.本研究结果表明,通过测定尿液中小分子代谢物可反映雷公藤甲素对大鼠的毒性,代谢组学技术可以作为药物毒性评价方法.代谢通路分析结果提示,雷公藤甲素对肝脏的毒性机制可能与大鼠肝脏线粒体受损、影响三羧酸循环、氨基酸代谢及脂质代谢有关.%To evaluate toxicity in rats after orally giving triptolide by using the gas chromatography time-of-flight mass spectrometry (GC/TOF-MS) based metabolomics approach.Potential biomarkers identified here paved a way to new implications of clinical early prevention and diagnosis of safety.In this study,SD rats were randomly divided into four groups,that included high dose (2.4 mg/kg),medium dose (1.2 mg/kg),low dose (0.6 mg/kg) and control groups,respectively.Following by single orally dosing,urine,serum and tissue sample were collected,respectively on day 0,day 1,day 3 and day 7 for a subsequent metabolomic bioanalysis.Multivariate data analysis was then used to process the data which

  11. Authenticity assessment of beef origin by principal component analysis of matrix-assisted laser desorption/ionization mass spectrometric data.

    Science.gov (United States)

    Zaima, Nobuhiro; Goto-Inoue, Naoko; Hayasaka, Takahiro; Enomoto, Hirofumi; Setou, Mitsutoshi

    2011-06-01

    It has become necessary to assess the authenticity of beef origin because of concerns regarding human health hazards. In this study, we used a metabolomic approach involving matrix-assisted laser desorption/ionization imaging mass spectrometry to assess the authenticity of beef origin. Highly accurate data were obtained for samples of extracted lipids from beef of different origin; the samples were grouped according to their origin. The analysis of extracted lipids in this study ended within 10 min, suggesting this approach can be used as a simple authenticity assessment before a definitive identification by isotope analysis.

  12. Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosis

    DEFF Research Database (Denmark)

    Huang, Sijia; Chong, Nicole; Lewis, Nathan;

    2016-01-01

    .993. Moreover, important metabolic pathways, such as taurine and hypotaurine metabolism and the alanine, aspartate, and glutamate pathway, are revealed as critical biological pathways for early diagnosis of breast cancer. Conclusions: We have successfully developed a new type of pathway-based model to study....... Methods: We propose that higher-order functional representation of metabolomics data, such as pathway-based metabolomic features, can be used as robust biomarkers for breast cancer. Towards this, we have developed a new computational method that uses personalized pathway dysregulation scores for disease...... diagnosis. We applied this method to predict breast cancer occurrence, in combination with correlation feature selection (CFS) and classification methods. Results: The resulting all-stage and early-stage diagnosis models are highly accurate in two sets of testing blood samples, with average AUCs (Area Under...

  13. Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments

    OpenAIRE

    Yamanishi, Yoshihiro; Tabei, Yasuo; Kotera, Masaaki

    2015-01-01

    Motivation: Recent advances in mass spectrometry and related metabolomics technologies have enabled the rapid and comprehensive analysis of numerous metabolites. However, biosynthetic and biodegradation pathways are only known for a small portion of metabolites, with most metabolic pathways remaining uncharacterized. Results: In this study, we developed a novel method for supervised de novo metabolic pathway reconstruction with an improved graph alignment-based approach in the reaction-fillin...

  14. Metabolomics-Based Screening of Biofilm-Inhibitory Compounds against Pseudomonas aeruginosa from Burdock Leaf

    OpenAIRE

    Zaixiang Lou; Yuxia Tang; Xinyi Song; Hongxin Wang

    2015-01-01

    Screening of anti-biofilm compounds from the burdock leaf based on metabolomics is reported here. The crystal violet assay indicated 34% ethanol elution fraction of burdock leaf could completely inhibit biofilm formation of Pseudomonas aeruginosa at 1 mg·mL−1. Then, the chemical composition of burdock leaf fraction was analyzed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and 11 active compounds (chlorogenic acid, caffeic acid, p-coumaric acid, quercetin, ursolic aci...

  15. The Metabolome of Chlamydomonas reinhardtii following Induction of Anaerobic H2 Production by Sulfur Depletion*

    OpenAIRE

    Timmins, Matthew; Zhou, Wenxu; Rupprecht, Jens; Lim, Lysha; Thomas-Hall, Skye R.; Doebbe, Anja; Kruse, Olaf; Hankamer, Ben; Marx, Ute C.; Smith, Steven M.; Schenk, Peer M.

    2009-01-01

    The metabolome of the model species Chlamydomonas reinhardtii has been analyzed during 120 h of sulfur depletion to induce anaerobic hydrogen (H2) production, using NMR spectroscopy, gas chromatography coupled to mass spectrometry, and TLC. The results indicate that these unicellular green algae consume freshly supplied acetate in the medium to accumulate energy reserves during the first 24 h of sulfur depletion. In addition to the previously reported accumulation of starch, large amounts of ...

  16. MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics

    OpenAIRE

    Jeffryes, James G; Colastani, Ricardo L; ElBadawi-Sidhu, Mona; Kind, Tobias; Niehaus, Thomas D; Broadbelt, Linda J.; Hanson, Andrew D.; Fiehn, Oliver; Keith E J Tyo; Henry, Christopher S.

    2015-01-01

    Background In spite of its great promise, metabolomics has proven difficult to execute in an untargeted and generalizable manner. Liquid chromatography–mass spectrometry (LC–MS) has made it possible to gather data on thousands of cellular metabolites. However, matching metabolites to their spectral features continues to be a bottleneck, meaning that much of the collected information remains uninterpreted and that new metabolites are seldom discovered in untargeted studies. These challenges re...

  17. Comparative Metabolomic and Genomic Analyses of TCDD-Elicited Metabolic Disruption in Mouse and Rat Liver

    OpenAIRE

    Forgacs, Agnes L.; Kent, Michael N.; Makley, Meghan K.; Mets, Bryan; DelRaso, Nicholas; Jahns, Gary L.; Burgoon, Lyle D; Zacharewski, Timothy R.; Reo, Nicholas V.

    2011-01-01

    2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) elicits a broad spectrum of species-specific effects that have not yet been fully characterized. This study compares the temporal effects of TCDD on hepatic aqueous and lipid metabolite extracts from immature ovariectomized C57BL/6 mice and Sprague-Dawley rats using gas chromatography-mass spectrometry and nuclear magnetic resonance–based metabolomic approaches and integrates published gene expression data to identify species-specific pathways affect...

  18. Training in metabolomics research. I. Designing the experiment, collecting and extracting samples and generating metabolomics data

    Science.gov (United States)

    Barnes, Stephen; Benton, H. Paul; Casazza, Krista; Cooper, Sara J.; Cui, Xiangqin; Du, Xiuxia; Engler, Jeffrey; Kabarowski, Janusz H.; Li, Shuzhao; Pathmasiri, Wimal; Prasain, Jeevan K.; Renfrow, Matthew B.; Tiwari, Hemant K.

    2016-01-01

    The study of metabolism has had a long history. Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes. The National Institutes of Health Common Fund Metabolomics Program was established in 2012 to stimulate interest in the approaches and technologies of metabolomics. To deliver one of the program’s goals, the University of Alabama at Birmingham has hosted an annual 4-day short course in metabolomics for faculty, postdoctoral fellows and graduate students from national and international institutions. This paper is the first part of a summary of the training materials presented in the course to be used as a resource for all those embarking on metabolomics research. PMID:27434804

  19. Similar metabolic responses in pigs and humans to breads with different contents and compositions of dietary fibers: a metabolomics study

    DEFF Research Database (Denmark)

    Nielsen, Kirstine Lykke; Hartvigsen, Merete; Hedemann, Mette Skou;

    2014-01-01

    mass spectrometry metabolomics. Results: We found that the postprandial responses, as reflected in blood metabolomes, are similar in pigs and humans. Twenty-one of 26 identified metabolites that were found to be different between the species were qualitatively similar in response to the test breads, despite...... respond similarly to a nutritional intervention. Using metabolomics, we compared the acute metabolic response to 4 test breads between conventional pigs (growing) and adult human subjects (with the metabolic syndrome). Design: Six catheterized pigs and 15 human subjects were tested in a randomized...... crossover design with 4 breads: white-wheat bread low in dietary fiber, rye bread with whole-rye kernels, and 2 whitewheat breads supplemented with either wheat arabinoxylan or oat b-glucan. Blood samples drawn 215, 30, and 120 min postprandially were analyzed by untargeted liquid chromatography...

  20. LC-MS metabolomics from study design to data-analysis – using a versatile pathogen as a test case

    Directory of Open Access Journals (Sweden)

    Maya Berg

    2013-01-01

    Full Text Available Thanks to significant improvements in LC-MS technology, metabolomics is increasingly used as a tool to discriminate the responses of organisms to various stimuli or drugs. In this minireview we discuss all aspects of the LC-MS metabolomics pipeline, using a complex and versatile model organism, Leishmania donovani, as an illustrative example. The benefits of a hyphenated mass spectrometry platform and a detailed overview of the entire experimental pipeline from sampling, sample storage and sample list set-up to LC-MS measurements and the generation of meaningful results with state-of-the-art data-analysis software will be thoroughly discussed. Finally, we also highlight important pitfalls in the processing of LC-MS data and comment on the benefits of implementing metabolomics in a systems biology approach.

  1. E-Cigarette Affects the Metabolome of Primary Normal Human Bronchial Epithelial Cells.

    Directory of Open Access Journals (Sweden)

    Argo Aug

    Full Text Available E-cigarettes are widely believed to be safer than conventional cigarettes and have been even suggested as aids for smoking cessation. However, while reasonable with some regards, this judgment is not yet supported by adequate biomedical research data. Since bronchial epithelial cells are the immediate target of inhaled toxicants, we hypothesized that exposure to e-cigarettes may affect the metabolome of human bronchial epithelial cells (HBEC and that the changes are, at least in part, induced by oxidant-driven mechanisms. Therefore, we evaluated the effect of e-cigarette liquid (ECL on the metabolome of HBEC and examined the potency of antioxidants to protect the cells. We assessed the changes of the intracellular metabolome upon treatment with ECL in comparison of the effect of cigarette smoke condensate (CSC with mass spectrometry and principal component analysis on air-liquid interface model of normal HBEC. Thereafter, we evaluated the capability of the novel antioxidant tetrapeptide O-methyl-l-tyrosinyl-γ-l-glutamyl-l-cysteinylglycine (UPF1 to attenuate the effect of ECL. ECL caused a significant shift in the metabolome that gradually gained its maximum by the 5th hour and receded by the 7th hour. A second alteration followed at the 13th hour. Treatment with CSC caused a significant initial shift already by the 1st hour. ECL, but not CSC, significantly increased the concentrations of arginine, histidine, and xanthine. ECL, in parallel with CSC, increased the content of adenosine diphosphate and decreased that of three lipid species from the phosphatidylcholine family. UPF1 partially counteracted the ECL-induced deviations, UPF1's maximum effect occurred at the 5th hour. The data support our hypothesis that ECL profoundly alters the metabolome of HBEC in a manner, which is comparable and partially overlapping with the effect of CSC. Hence, our results do not support the concept of harmlessness of e-cigarettes.

  2. Establishment of Protocols for Global Metabolomics by LC-MS for Biomarker Discovery.

    Science.gov (United States)

    Saigusa, Daisuke; Okamura, Yasunobu; Motoike, Ikuko N; Katoh, Yasutake; Kurosawa, Yasuhiro; Saijyo, Reina; Koshiba, Seizo; Yasuda, Jun; Motohashi, Hozumi; Sugawara, Junichi; Tanabe, Osamu; Kinoshita, Kengo; Yamamoto, Masayuki

    2016-01-01

    Metabolomics is a promising avenue for biomarker discovery. Although the quality of metabolomic analyses, especially global metabolomics (G-Met) using mass spectrometry (MS), largely depends on the instrumentation, potential bottlenecks still exist at several basic levels in the metabolomics workflow. Therefore, we established a precise protocol initially for the G-Met analyses of human blood plasma to overcome some these difficulties. In our protocol, samples are deproteinized in a 96-well plate using an automated liquid-handling system, and conducted either using a UHPLC-QTOF/MS system equipped with a reverse phase column or a LC-FTMS system equipped with a normal phase column. A normalization protocol of G-Met data was also developed to compensate for intra- and inter-batch differences, and the variations were significantly reduced along with our normalization, especially for the UHPLC-QTOF/MS data with a C18 reverse-phase column for positive ions. Secondly, we examined the changes in metabolomic profiles caused by the storage of EDTA-blood specimens to identify quality markers for the evaluation of the specimens' pre-analytical conditions. Forty quality markers, including lysophospholipids, dipeptides, fatty acids, succinic acid, amino acids, glucose, and uric acid were identified by G-Met for the evaluation of plasma sample quality and established the equation of calculating the quality score. We applied our quality markers to a small-scale study to evaluate the quality of clinical samples. The G-Met protocols and quality markers established here should prove useful for the discovery and development of biomarkers for a wider range of diseases. PMID:27579980

  3. Establishment of Protocols for Global Metabolomics by LC-MS for Biomarker Discovery

    Science.gov (United States)

    Okamura, Yasunobu; Motoike, Ikuko N.; Katoh, Yasutake; Kurosawa, Yasuhiro; Saijyo, Reina; Koshiba, Seizo; Yasuda, Jun; Motohashi, Hozumi; Sugawara, Junichi; Tanabe, Osamu; Kinoshita, Kengo; Yamamoto, Masayuki

    2016-01-01

    Metabolomics is a promising avenue for biomarker discovery. Although the quality of metabolomic analyses, especially global metabolomics (G-Met) using mass spectrometry (MS), largely depends on the instrumentation, potential bottlenecks still exist at several basic levels in the metabolomics workflow. Therefore, we established a precise protocol initially for the G-Met analyses of human blood plasma to overcome some these difficulties. In our protocol, samples are deproteinized in a 96-well plate using an automated liquid-handling system, and conducted either using a UHPLC-QTOF/MS system equipped with a reverse phase column or a LC-FTMS system equipped with a normal phase column. A normalization protocol of G-Met data was also developed to compensate for intra- and inter-batch differences, and the variations were significantly reduced along with our normalization, especially for the UHPLC-QTOF/MS data with a C18 reverse-phase column for positive ions. Secondly, we examined the changes in metabolomic profiles caused by the storage of EDTA-blood specimens to identify quality markers for the evaluation of the specimens’ pre-analytical conditions. Forty quality markers, including lysophospholipids, dipeptides, fatty acids, succinic acid, amino acids, glucose, and uric acid were identified by G-Met for the evaluation of plasma sample quality and established the equation of calculating the quality score. We applied our quality markers to a small-scale study to evaluate the quality of clinical samples. The G-Met protocols and quality markers established here should prove useful for the discovery and development of biomarkers for a wider range of diseases. PMID:27579980

  4. NMR-based Metabolomics for Cancer Research

    Science.gov (United States)

    Metabolomics is considered as a complementary tool to other omics platforms to provide a snapshot of the cellular biochemistry and physiology taking place at any instant. Metabolmics approaches have been widely used to provide comprehensive and quantitative analyses of the metabo...

  5. Data analysis strategies in nutritional metabolomics

    NARCIS (Netherlands)

    J. Westerhuis; E. van Velzen; H. Hoefsloot; A. Smilde

    2009-01-01

    In the expanding field of nutritional metabolomics the use of optimized and robust strategies are essential to find meaningful and significant results. Data from nutritional studies can be extremely large, multidimensional and complex. Moreover the data may hide just a subtle biological variation du

  6. Data fusion in metabolomic cancer diagnostics

    DEFF Research Database (Denmark)

    Bro, Rasmus; Nielsen, Hans Jørgen; Savorani, Francesco;

    2013-01-01

    We have recently shown that fluorescence spectroscopy of plasma samples has promising abilities regarding early detection of colorectal cancer. In the present paper, these results were further developed by combining fluorescence with the biomarkers, CEA and TIMP-1 and traditional metabolomic meas...

  7. Metabolomics Analyses of Cancer Cells in Controlled Microenvironments.

    Science.gov (United States)

    Gravel, Simon-Pierre; Avizonis, Daina; St-Pierre, Julie

    2016-01-01

    The tumor microenvironment is a complex and heterogeneous milieu in which cancer cells undergo metabolic reprogramming to fuel their growth. Cancer cell lines grown in vitro using traditional culture methods represent key experimental models to gain a mechanistic understanding of tumor biology. This protocol describes the use of gas chromatography-mass spectrometry (GC-MS) to assess metabolic changes in cancer cells grown under varied levels of oxygen and nutrients that may better mimic the tumor microenvironment. Intracellular metabolite changes, metabolite uptake and release, as well as stable isotope ((13)C) tracer analyses are done in a single experimental setup to provide an integrated understanding of metabolic adaptation. Overall, this chapter describes some essential tools and methods to perform comprehensive metabolomics analyses. PMID:27581029

  8. Multi-platform metabolomics assays for human lung lavage fluids in an air pollution exposure study.

    Science.gov (United States)

    Surowiec, Izabella; Karimpour, Masoumeh; Gouveia-Figueira, Sandra; Wu, Junfang; Unosson, Jon; Bosson, Jenny A; Blomberg, Anders; Pourazar, Jamshid; Sandström, Thomas; Behndig, Annelie F; Trygg, Johan; Nording, Malin L

    2016-07-01

    Metabolomics protocols are used to comprehensively characterize the metabolite content of biological samples by exploiting cutting-edge analytical platforms, such as gas chromatography (GC) or liquid chromatography (LC) coupled to mass spectrometry (MS) assays, as well as nuclear magnetic resonance (NMR) assays. We have developed novel sample preparation procedures combined with GC-MS, LC-MS, and NMR metabolomics profiling for analyzing bronchial wash (BW) and bronchoalveolar lavage (BAL) fluid from 15 healthy volunteers following exposure to biodiesel exhaust and filtered air. Our aim was to investigate the responsiveness of metabolite profiles in the human lung to air pollution exposure derived from combustion of biofuels, such as rapeseed methyl ester biodiesel, which are increasingly being promoted as alternatives to conventional fossil fuels. Our multi-platform approach enabled us to detect the greatest number of unique metabolites yet reported in BW and BAL fluid (82 in total). All of the metabolomics assays indicated that the metabolite profiles of the BW and BAL fluids differed appreciably, with 46 metabolites showing significantly different levels in the corresponding lung compartments. Furthermore, the GC-MS assay revealed an effect of biodiesel exhaust exposure on the levels of 1-monostearylglycerol, sucrose, inosine, nonanoic acid, and ethanolamine (in BAL) and pentadecanoic acid (in BW), whereas the LC-MS assay indicated a shift in the levels of niacinamide (in BAL). The NMR assay only identified lactic acid (in BW) as being responsive to biodiesel exhaust exposure. Our findings demonstrate that the proposed multi-platform approach is useful for wide metabolomics screening of BW and BAL fluids and can facilitate elucidation of metabolites responsive to biodiesel exhaust exposure. Graphical Abstract Graphical abstract illustrating the study workflow. NMR Nuclear Magnetic Resonance, LC-TOFMS Liquid chromatography-Time Of Flight Mass Spectrometry, GC Gas

  9. Metabolomics of Clostridial Biofuel Production

    Energy Technology Data Exchange (ETDEWEB)

    Rabinowitz, Joshua D [Princeton Univ., NJ (United States); Aristilde, Ludmilla [Cornell Univ., Ithaca, NY (United States); Amador-Noguez, Daniel [Univ. of Wisconsin, Madison, WI (United States)

    2015-09-08

    Members of the genus Clostridium collectively have the ideal set of the metabolic capabilities for fermentative biofuel production: cellulose degradation, hydrogen production, and solvent excretion. No single organism, however, can effectively convert cellulose into biofuels. Here we developed, using metabolomics and isotope tracers, basic science knowledge of Clostridial metabolism of utility for future efforts to engineer such an organism. In glucose fermentation carried out by the biofuel producer Clostridium acetobutylicum, we observed a remarkably ordered series of metabolite concentration changes as the fermentation progressed from acidogenesis to solventogenesis. In general, high-energy compounds decreased while low-energy species increased during solventogenesis. These changes in metabolite concentrations were accompanied by large changes in intracellular metabolic fluxes, with pyruvate directed towards acetyl-CoA and solvents instead of oxaloacetate and amino acids. Thus, the solventogenic transition involves global remodeling of metabolism to redirect resources from biomass production into solvent production. In contrast to C. acetobutylicum, which is an avid fermenter, C. cellulolyticum metabolizes glucose only slowly. We find that glycolytic intermediate concentrations are radically different from fast fermenting organisms. Associated thermodynamic and isotope tracer analysis revealed that the full glycolytic pathway in C. cellulolyticum is reversible. This arises from changes in cofactor utilization for phosphofructokinase and an alternative pathway from phosphoenolpyruvate to pyruvate. The net effect is to increase the high-energy phosphate bond yield of glycolysis by 150% (from 2 to 5) at the expense of lower net flux. Thus, C. cellulolyticum prioritizes glycolytic energy efficiency over speed. Degradation of cellulose results in other sugars in addition to glucose. Simultaneous feeding of stable isotope-labeled glucose and unlabeled pentose sugars

  10. Present and foreseeable future of metabolomics in forensic analysis.

    Science.gov (United States)

    Castillo-Peinado, L S; Luque de Castro, M D

    2016-06-21

    The revulsive publications during the last years on the precariousness of forensic sciences worldwide have promoted the move of major steps towards improvement of this science. One of the steps (viz. a higher involvement of metabolomics in the new era of forensic analysis) deserves to be discussed under different angles. Thus, the characteristics of metabolomics that make it a useful tool in forensic analysis, the aspects in which this omics is so far implicit, but not mentioned in forensic analyses, and how typical forensic parameters such as the post-mortem interval or fingerprints take benefits from metabolomics are critically discussed in this review. The way in which the metabolomics-forensic binomial succeeds when either conventional or less frequent samples are used is highlighted here. Finally, the pillars that should support future developments involving metabolomics and forensic analysis, and the research required for a fruitful in-depth involvement of metabolomics in forensic analysis are critically discussed.

  11. Metabolomics and its application to studying metal toxicity.

    Science.gov (United States)

    Booth, Sean C; Workentine, Matthew L; Weljie, Aalim M; Turner, Raymond J

    2011-11-01

    Here we explain the omics approach of metabolomics and how it can be applied to study a physiological response to toxic metal exposure. This review aims to educate the metallomics field to the tool of metabolomics. Metabolomics is becoming an increasingly used tool to compare natural and challenged states of various organisms, from disease states in humans to toxin exposure to environmental systems. This approach is key to understanding and identifying the cellular or biochemical targets of metals and the underlying physiological response. Metabolomics steps are described and overviews of its application to metal toxicity to organisms are given. As this approach is very new there are yet only a small number of total studies and therefore only a brief overview of some metal metabolomics studies is described. A frank critical evaluation of the approach is given to provide newcomers to the method a clear idea of the challenges and the rewards of applying metabolomics to their research.

  12. Review: Microfluidic Applications in Metabolomics and Metabolic Profiling

    OpenAIRE

    Kraly, James R.; Holcomb, Ryan E.; Guan, Qian; Charles S. Henry

    2009-01-01

    Metabolomics is an emerging area of research focused on measuring small molecules in biological samples. There are a number of different types of metabolomics, ranging from global profiling of all metabolites in a single sample to measurement of a selected group of analytes. Microfluidics and related technologies have been used in this research area with good success. The aim of this review article is to summarize the use of microfluidics in metabolomics. Direct application of microfluidics t...

  13. {alpha}{sub v}{beta}{sub 3} imaging can accurately distinguish between mature teratoma and necrosis in {sup 18}F-FDG-negative residual masses after treatment of non-seminomatous testicular cancer: a preclinical study

    Energy Technology Data Exchange (ETDEWEB)

    Aide, Nicolas [Francois Baclesse Cancer Centre and Caen University, Bioticla Team, EA1772, IFR 146 ICORE, GRECAN, Caen (France); Caen University Hospital and Francois Baclesse Cancer Centre, PET Unit, Caen (France); Centre Francois Baclesse, Service de Medecine Nucleaire, Caen (France); Briand, Melanie; Dutoit, Soizic; Deslandes, Edwiges; Poulain, Laurent [Francois Baclesse Cancer Centre and Caen University, Bioticla Team, EA1772, IFR 146 ICORE, GRECAN, Caen (France); Bohn, Pierre; Rouvet, Jean; Modzelewski, Romain; Vera, Pierre [Henri Becquerel Cancer Center and Rouen University Hospital and QuantIF- LITIS (EA4108), Department of Nuclear Medicine, Rouen (France); Lasnon, Charline [Caen University Hospital and Francois Baclesse Cancer Centre, PET Unit, Caen (France); Chasle, Jacques [Francois Baclesse Cancer Centre and Caen University, Pathology Department, Caen (France); Vela, Antony [Francois Baclesse Cancer Centre and Caen University, Radiophysics Unit, Caen (France); Carreiras, Franck [Universite de Cergy Pontoise, UFR Sciences et Techniques, ERRMECe, EA 1391, Institut des materiaux, Cergy-Pontoise (France)

    2011-02-15

    We assessed whether imaging {alpha}{sub v}{beta}{sub 3} integrin could distinguish mature teratoma from necrosis in human non-seminomatous germ cell tumour (NSGCT) post-chemotherapy residual masses. Human embryonal carcinoma xenografts (six/rat) were untreated (controls) or treated to form mature teratomas with low-dose cisplatin and all-trans retinoic acid (ATRA) over a period of 8 weeks. In another group, necrosis was induced in xenografts with high-dose cisplatin plus etoposide (two cycles).{sup 18}F-Fluorodeoxyglucose ({sup 18}F-FDG) small animal positron emission tomography (SA PET) imaging was performed in three rats (one control and two treated for 4 and 8 weeks with cisplatin+ATRA). Imaging of {alpha}{sub v}{beta}{sub 3} expression was performed in six rats bearing mature teratomas and two rats with necrotic lesions on a microSPECT/CT device after injection of the tracer [{sup 99m}Tc]HYNIC-RGD [6-hydrazinonicotinic acid conjugated to cyclo(Arg-Gly-Asp-D-Phe-Lys)]. Correlative immunohistochemistry studies of human and mouse {alpha}{sub v}{beta}{sub 3} expression were performed. Cisplatin+ATRA induced differentiation of the xenografts. After 8 weeks, some glandular structures and mesenchymal cells were visible; in contrast, control tumours showed undifferentiated tissues. SA PET imaging showed that mature teratoma had very low avidity for {sup 18}F-FDG [mean standardised uptake value (SUV{sub mean}) = 0.48 {+-} 0.05] compared to untreated embryonal carcinoma (SUV{sub mean} = 0.92 {+-} 0.13) (p = 0.005). {alpha}{sub v}{beta}{sub 3} imaging accurately distinguished mature teratoma (tumour to muscle ratio = 4.29 {+-} 1.57) from necrosis (tumour to muscle ratio = 1.3 {+-} 0.26) (p = 0.0002). Immunohistochemistry studies showed that {alpha}{sub v}{beta}{sub 3} integrin expression was strong in the glandular structures of mature teratoma lesions and negative in host stroma. Imaging {alpha}{sub v}{beta}{sub 3} integrin accurately distinguished mature teratoma from

  14. HILIC-MS for metabolomics: An attractive and complementary approach to RPLC-MS.

    Science.gov (United States)

    Tang, Dao-Quan; Zou, Ll; Yin, Xiao-Xing; Ong, Choon Nam

    2016-09-01

    Hydrophilic interaction chromatography (HILIC) is an emerging separation mode of liquid chromatography (LC). Using highly hydrophilic stationary phases capable of retaining polar/ionic metabolites, and accompany with high organic content mobile phase that offer readily compatibility with mass spectrometry (MS) has made HILIC an attractive complementary tool to the widely used reverse-phase (RP) chromatographic separations in metabolomic studies. The combination of HILIC and RPLC coupled with an MS detector expands the number of detected analytes and provides more comprehensive metabolite coverage than use of only RP chromatography. This review describes the recent applications of HILIC-MS/MS in metabolomic studies, ranging from amino acids, lipids, nucleotides, organic acids, pharmaceuticals, and metabolites of specific nature. The biological systems investigated include microbials, cultured cell line, plants, herbal medicine, urine, and serum as well as tissues from animals and humans. Owing to its unique capability to measure more-polar biomolecules, the HILIC separation technique would no doubt enhance the comprehensiveness of metabolite detection, and add significant value for metabolomic investigations. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 35:574-600, 2016. PMID:25284160

  15. An integrated strategy for in vivo metabolite profiling using high-resolution mass spectrometry based data processing techniques

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Jian, E-mail: jian.guo@astrazeneca.com [DMPK of Infection Innovative Medicine, AstraZeneca Pharmaceuticals, 35 Gatehouse Drive, Waltham, MA 02451 (United States); Zhang, Minli [DMPK of Infection Innovative Medicine, AstraZeneca Pharmaceuticals, 35 Gatehouse Drive, Waltham, MA 02451 (United States); Elmore, Charles S. [DMPK of Innovative Medicine, Isotope Chemistry, AstraZeneca Pharmaceuticals, Mölndal SE 431 83 (Sweden); Vishwanathan, Karthick [DMPK of Infection Innovative Medicine, AstraZeneca Pharmaceuticals, 35 Gatehouse Drive, Waltham, MA 02451 (United States)

    2013-05-30

    Graphical abstract: -- Highlights: •Profiling the metabolites of model compounds in rats using high resolution mass spectrometry based data processing techniques. •Demonstrating an integrated strategy in vivo metabolite profiling using data mining tools. •Unusual metabolites generated via thiazole-ring opening were characterized based on processed LC–MS.data. -- Abstract: An ongoing challenge of drug metabolite profiling is to detect and identify unknown or low-level metabolites in complex biological matrices. Here we present a generic strategy for metabolite detection using multiple accurate-mass-based data processing tools via the analysis of rat samples of two model drug candidates, AZD6280 and AZ12488024. First, the function of isotopic pattern recognition was proved to be highly effective in the detection of metabolites derived from [{sup 14}C]-AZD6280 that possesses a distinct isotopic pattern. The metabolites revealed using this approach were in excellent qualitative correlation to those observed in radiochromatograms. Second, the effectiveness of accurate mass based untargeted data mining tools such as background subtraction, mass defect filtering, or a data mining package (MZmine) used for metabolomic analysis in detection of metabolites of [{sup 14}C]-AZ12488024 in rat urine, feces, bile and plasma samples was examined and a total of 33 metabolites of AZ12488024 were detected. Among them, at least 16 metabolites were only detected by the aid of the data mining packages and not via radiochromatograms. New metabolic pathways such as S-oxidation and thiomethylation reactions occurring on the thiazole ring were proposed based on the processed data. The results of these experiments also demonstrated that accurate mass-based mass defect filtering (MDF) and data mining techniques used in metabolomics are complementary and can be valuable tools for delineating low-level metabolites in complex matrices. Furthermore, the application of distinct multiple

  16. An integrated strategy for in vivo metabolite profiling using high-resolution mass spectrometry based data processing techniques

    International Nuclear Information System (INIS)

    Graphical abstract: -- Highlights: •Profiling the metabolites of model compounds in rats using high resolution mass spectrometry based data processing techniques. •Demonstrating an integrated strategy in vivo metabolite profiling using data mining tools. •Unusual metabolites generated via thiazole-ring opening were characterized based on processed LC–MS.data. -- Abstract: An ongoing challenge of drug metabolite profiling is to detect and identify unknown or low-level metabolites in complex biological matrices. Here we present a generic strategy for metabolite detection using multiple accurate-mass-based data processing tools via the analysis of rat samples of two model drug candidates, AZD6280 and AZ12488024. First, the function of isotopic pattern recognition was proved to be highly effective in the detection of metabolites derived from [14C]-AZD6280 that possesses a distinct isotopic pattern. The metabolites revealed using this approach were in excellent qualitative correlation to those observed in radiochromatograms. Second, the effectiveness of accurate mass based untargeted data mining tools such as background subtraction, mass defect filtering, or a data mining package (MZmine) used for metabolomic analysis in detection of metabolites of [14C]-AZ12488024 in rat urine, feces, bile and plasma samples was examined and a total of 33 metabolites of AZ12488024 were detected. Among them, at least 16 metabolites were only detected by the aid of the data mining packages and not via radiochromatograms. New metabolic pathways such as S-oxidation and thiomethylation reactions occurring on the thiazole ring were proposed based on the processed data. The results of these experiments also demonstrated that accurate mass-based mass defect filtering (MDF) and data mining techniques used in metabolomics are complementary and can be valuable tools for delineating low-level metabolites in complex matrices. Furthermore, the application of distinct multiple data

  17. Using liquid chromatography-mass spectrometry based metabolomics to discriminate between cold pressed rice bran oils produced from two different cultivars of Oryza sativa L. ssp. indica in Thailand

    Institute of Scientific and Technical Information of China (English)

    Tossaton CHAROONRATANA; Thanapat SONGSAK; Apirak SAKUNPAK; Pathamaporn PATHOMPAK; Laksana CHAROENCHAI

    2015-01-01

    A newly developed liquid chromatography⁃mass spectrometry ( LC⁃MS) method for the analysis of cold pressed rice bran oil ( RBO) was established and used to discriminate between RBOs produced from two different cultivars of major Thai fragrant rice species. The cold pressed RBO was prepared using the screw com⁃pression method. The LC⁃MS data were preprocessed with MZmine 2�10 program before evaluating with princi⁃pal component analysis using SIMCA 13 software. The LC⁃MS method was able to detect and quantify several kinds of valuable constituents such as fatty acids, vitamin E, and γ⁃oryzanol. The chromatographic condition was feasible;short time for analysis and simple method were achieved. From score plot and loading plot of principle component analysis ( PCA) , two rice cultivar samples were clearly separated, and it was revealed that Khao⁃Hom⁃Pathum was more suitable than Khao⁃Hom⁃Mali for cold pressed RBO production since it contained high total γ⁃oryzanol and less saturated free fatty acids. As with the fixed price of all the rice brans, this infor⁃mation can be used in order to, if possible, preserve the price of rice brans from different cultivars.

  18. Metabolomic profiling from formalin-fixed, paraffin-embedded tumor tissue using targeted LC/MS/MS: application in sarcoma.

    Directory of Open Access Journals (Sweden)

    Andrew D Kelly

    Full Text Available The relatively new field of onco-metabolomics attempts to identify relationships between various cancer phenotypes and global metabolite content. Previous metabolomics studies utilized either nuclear magnetic resonance spectroscopy or gas chromatography/mass spectrometry, and analyzed metabolites present in urine and serum. However, direct metabolomic assessment of tumor tissues is important for determining altered metabolism in cancers. In this respect, the ability to obtain reliable data from archival specimens is desirable and has not been reported to date. In this feasibility study, we demonstrate the analysis of polar metabolites extracted directly from ten formalin-fixed, paraffin-embedded (FFPE specimens, including five soft tissue sarcomas and five paired normal samples. Using targeted liquid chromatography-tandem mass spectrometry (LC/MS/MS via selected reaction monitoring (SRM, we detect an average of 106 metabolites across the samples with excellent reproducibility and correlation between different sections of the same specimen. Unsupervised hierarchical clustering and principal components analysis reliably recovers a priori known tumor and normal tissue phenotypes, and supervised analysis identifies candidate metabolic markers supported by the literature. In addition, we find that diverse biochemical processes are well-represented in the list of detected metabolites. Our study supports the notion that reliable and broadly informative metabolomic data may be acquired from FFPE soft tissue sarcoma specimens, a finding that is likely to be extended to other malignancies.

  19. Surrogate markers of visceral adiposity in young adults: waist circumference and body mass index are more accurate than waist hip ratio, model of adipose distribution and visceral adiposity index.

    Directory of Open Access Journals (Sweden)

    Susana Borruel

    Full Text Available Surrogate indexes of visceral adiposity, a major risk factor for metabolic and cardiovascular disorders, are routinely used in clinical practice because objective measurements of visceral adiposity are expensive, may involve exposure to radiation, and their availability is limited. We compared several surrogate indexes of visceral adiposity with ultrasound assessment of subcutaneous and visceral adipose tissue depots in 99 young Caucasian adults, including 20 women without androgen excess, 53 women with polycystic ovary syndrome, and 26 men. Obesity was present in 7, 21, and 7 subjects, respectively. We obtained body mass index (BMI, waist circumference (WC, waist-hip ratio (WHR, model of adipose distribution (MOAD, visceral adiposity index (VAI, and ultrasound measurements of subcutaneous and visceral adipose tissue depots and hepatic steatosis. WC and BMI showed the strongest correlations with ultrasound measurements of visceral adiposity. Only WHR correlated with sex hormones. Linear stepwise regression models including VAI were only slightly stronger than models including BMI or WC in explaining the variability in the insulin sensitivity index (yet BMI and WC had higher individual standardized coefficients of regression, and these models were superior to those including WHR and MOAD. WC showed 0.94 (95% confidence interval 0.88-0.99 and BMI showed 0.91 (0.85-0.98 probability of identifying the presence of hepatic steatosis according to receiver operating characteristic curve analysis. In conclusion, WC and BMI not only the simplest to obtain, but are also the most accurate surrogate markers of visceral adiposity in young adults, and are good indicators of insulin resistance and powerful predictors of the presence of hepatic steatosis.

  20. How accurate are parental responses concerning their fourth-grade children's school-meal participation, and what is the relationship between children's body mass index and school-meal participation based on parental responses?

    Directory of Open Access Journals (Sweden)

    Paxton-Aiken Amy E

    2012-03-01

    Full Text Available Abstract Background This article investigated (1 parental response accuracy of fourth-grade children's school-meal participation and whether accuracy differed by children's body mass index (BMI, sex, and race, and (2 the relationship between BMI and school-meal participation (based on parental responses. Methods Data were from four cross-sectional studies conducted from fall 1999 to spring 2003 with fourth-grade children from 13 schools total. Consent forms asked parents to report children's usual school-meal participation. As two studies' consent forms did not ask about lunch participation, complete data were available for breakfast on 1,496 children (51% Black; 49% boys and for lunch on 785 children (46% Black; 48% boys. Researchers compiled nametag records (during meal observations of meal participation on randomly selected days during children's fourth-grade school year for breakfast (average nametag days across studies: 7-35 and for lunch (average nametag days across studies: 4-10 and categorized participation as "usually" (≥ 50% of days or "not usually" ( Results Concerning breakfast participation and lunch participation, 74% and 92% of parents provided accurate responses, respectively. Parental response accuracy was better for older children for breakfast and lunch participation, and for Black than White children for lunch participation. Usual school-meal participation was significantly related to children's BMI but in opposite directions -- positively for breakfast and inversely for lunch. Conclusions Parental response accuracy of children's school-meal participation was moderately high; however, disparate effects for children's age and race warrant caution when relying on parental responses. The BMI results, which showed a relationship between school-meal participation (based on parental responses and childhood obesity, conflict with results from a recent article that used data from the same four studies and found no significant

  1. An integrated strategy for rapid and accurate determination of free and cell-bound microcystins and related peptides in natural blooms by liquid chromatography-electrospray-high resolution mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry using both positive and negative ionization modes.

    Science.gov (United States)

    Flores, Cintia; Caixach, Josep

    2015-08-14

    An integrated high resolution mass spectrometry (HRMS) strategy has been developed for rapid and accurate determination of free and cell-bound microcystins (MCs) and related peptides in water blooms. The natural samples (water and algae) were filtered for independent analysis of aqueous and sestonic fractions. These fractions were analyzed by MALDI-TOF/TOF-MS and ESI-Orbitrap-HCD-MS. MALDI, ESI and the study of fragmentation sequences have been provided crucial structural information. The potential of combined positive and negative ionization modes, full scan and fragmentation acquisition modes (TOF/TOF and HCD) by HRMS and high resolution and accurate mass was investigated in order to allow unequivocal determination of MCs. Besides, a reliable quantitation has been possible by HRMS. This composition helped to decrease the probability of false positives and negatives, as alternative to commonly used LC-ESI-MS/MS methods. The analysis was non-target, therefore covered the possibility to analyze all MC analogs concurrently without any pre-selection of target MC. Furthermore, archived data was subjected to retrospective "post-targeted" analysis and a screening of other potential toxins and related peptides as anabaenopeptins in the samples was done. Finally, the MS protocol and identification tools suggested were applied to the analysis of characteristic water blooms from Spanish reservoirs. PMID:26141269

  2. An integrated strategy for rapid and accurate determination of free and cell-bound microcystins and related peptides in natural blooms by liquid chromatography-electrospray-high resolution mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry using both positive and negative ionization modes.

    Science.gov (United States)

    Flores, Cintia; Caixach, Josep

    2015-08-14

    An integrated high resolution mass spectrometry (HRMS) strategy has been developed for rapid and accurate determination of free and cell-bound microcystins (MCs) and related peptides in water blooms. The natural samples (water and algae) were filtered for independent analysis of aqueous and sestonic fractions. These fractions were analyzed by MALDI-TOF/TOF-MS and ESI-Orbitrap-HCD-MS. MALDI, ESI and the study of fragmentation sequences have been provided crucial structural information. The potential of combined positive and negative ionization modes, full scan and fragmentation acquisition modes (TOF/TOF and HCD) by HRMS and high resolution and accurate mass was investigated in order to allow unequivocal determination of MCs. Besides, a reliable quantitation has been possible by HRMS. This composition helped to decrease the probability of false positives and negatives, as alternative to commonly used LC-ESI-MS/MS methods. The analysis was non-target, therefore covered the possibility to analyze all MC analogs concurrently without any pre-selection of target MC. Furthermore, archived data was subjected to retrospective "post-targeted" analysis and a screening of other potential toxins and related peptides as anabaenopeptins in the samples was done. Finally, the MS protocol and identification tools suggested were applied to the analysis of characteristic water blooms from Spanish reservoirs.

  3. Metabolomics analysis of shucked mussels' freshness.

    Science.gov (United States)

    Aru, Violetta; Pisano, Maria Barbara; Savorani, Francesco; Engelsen, Søren Balling; Cosentino, Sofia; Cesare Marincola, Flaminia

    2016-08-15

    In this work a NMR metabolomics approach was applied to analyze changes in the metabolic profile of the bivalve mollusk Mytilus galloprovincialis upon storage at 0°C and 4°C for 10 and 6 days, respectively. The most significant microbial groups involved in spoilage of mussels were also investigated. The time-related metabolic signature of mussels was analysed by Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) which revealed a clear discrimination between the fresh samples and those stored at 0°C and 4°C. The results evidenced a noticeable increase in acetate, lactate, succinate, alanine, branched chain amino acids, trimethylamine and a progressive decline of osmolytes like betaine, homarine and taurine during storage. Exploration of the correlations of these metabolites with microbial counts suggested their use as potential biomarkers of spoilage. The results support the use of NMR metabolomics as a valuable tool to provide information on seafood freshness.

  4. Metabolomics analysis of shucked mussels' freshness.

    Science.gov (United States)

    Aru, Violetta; Pisano, Maria Barbara; Savorani, Francesco; Engelsen, Søren Balling; Cosentino, Sofia; Cesare Marincola, Flaminia

    2016-08-15

    In this work a NMR metabolomics approach was applied to analyze changes in the metabolic profile of the bivalve mollusk Mytilus galloprovincialis upon storage at 0°C and 4°C for 10 and 6 days, respectively. The most significant microbial groups involved in spoilage of mussels were also investigated. The time-related metabolic signature of mussels was analysed by Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) which revealed a clear discrimination between the fresh samples and those stored at 0°C and 4°C. The results evidenced a noticeable increase in acetate, lactate, succinate, alanine, branched chain amino acids, trimethylamine and a progressive decline of osmolytes like betaine, homarine and taurine during storage. Exploration of the correlations of these metabolites with microbial counts suggested their use as potential biomarkers of spoilage. The results support the use of NMR metabolomics as a valuable tool to provide information on seafood freshness. PMID:27006214

  5. Time-resolved metabolomics reveals metabolic modulation in rice foliage

    Directory of Open Access Journals (Sweden)

    Arita Masanori

    2008-06-01

    Full Text Available Abstract Background To elucidate the interaction of dynamics among modules that constitute biological systems, comprehensive datasets obtained from "omics" technologies have been used. In recent plant metabolomics approaches, the reconstruction of metabolic correlation networks has been attempted using statistical techniques. However, the results were unsatisfactory and effective data-mining techniques that apply appropriate comprehensive datasets are needed. Results Using capillary electrophoresis mass spectrometry (CE-MS and capillary electrophoresis diode-array detection (CE-DAD, we analyzed the dynamic changes in the level of 56 basic metabolites in plant foliage (Oryza sativa L. ssp. japonica at hourly intervals over a 24-hr period. Unsupervised clustering of comprehensive metabolic profiles using Kohonen's self-organizing map (SOM allowed classification of the biochemical pathways activated by the light and dark cycle. The carbon and nitrogen (C/N metabolism in both periods was also visualized as a phenotypic linkage map that connects network modules on the basis of traditional metabolic pathways rather than pairwise correlations among metabolites. The regulatory networks of C/N assimilation/dissimilation at each time point were consistent with previous works on plant metabolism. In response to environmental stress, glutathione and spermidine fluctuated synchronously with their regulatory targets. Adenine nucleosides and nicotinamide coenzymes were regulated by phosphorylation and dephosphorylation. We also demonstrated that SOM analysis was applicable to the estimation of unidentifiable metabolites in metabolome analysis. Hierarchical clustering of a correlation coefficient matrix could help identify the bottleneck enzymes that regulate metabolic networks. Conclusion Our results showed that our SOM analysis with appropriate metabolic time-courses effectively revealed the synchronous dynamics among metabolic modules and elucidated the

  6. Metabolomics-based discovery of diagnostic biomarkers for onchocerciasis.

    Directory of Open Access Journals (Sweden)

    Judith R Denery

    Full Text Available BACKGROUND: Development of robust, sensitive, and reproducible diagnostic tests for understanding the epidemiology of neglected tropical diseases is an integral aspect of the success of worldwide control and elimination programs. In the treatment of onchocerciasis, clinical diagnostics that can function in an elimination scenario are non-existent and desperately needed. Due to its sensitivity and quantitative reproducibility, liquid chromatography-mass spectrometry (LC-MS based metabolomics is a powerful approach to this problem. METHODOLOGY/PRINCIPAL FINDINGS: Analysis of an African sample set comprised of 73 serum and plasma samples revealed a set of 14 biomarkers that showed excellent discrimination between Onchocerca volvulus-positive and negative individuals by multivariate statistical analysis. Application of this biomarker set to an additional sample set from onchocerciasis endemic areas where long-term ivermectin treatment has been successful revealed that the biomarker set may also distinguish individuals with worms of compromised viability from those with active infection. Machine learning extended the utility of the biomarker set from a complex multivariate analysis to a binary format applicable for adaptation to a field-based diagnostic, validating the use of complex data mining tools applied to infectious disease biomarker discovery and diagnostic development. CONCLUSIONS/SIGNIFICANCE: An LC-MS metabolomics-based diagnostic has the potential to monitor the progression of onchocerciasis in both endemic and non-endemic geographic areas, as well as provide an essential tool to multinational programs in the ongoing fight against this neglected tropical disease. Ultimately this technology can be expanded for the diagnosis of other filarial and/or neglected tropical diseases.

  7. Using metabolomics to evaluate food intake

    DEFF Research Database (Denmark)

    Manach, Claudine; Brennan, Lorraine; Dragsted, Lars Ove

    2015-01-01

    Improving dietary assessment is essential for modern nutritional epidemiology. This chapter discusses the potential of metabolomics for the identification of new biomarkers of intake and presents the first candidate biomarkers discovered using this approach. It then describes the challenges that ...... that lay ahead, including the validation of identified biomarkers, methodological improvements for accelerating biomarker identification, and the development of sharing tools for data and resources....

  8. Metabolomics as a diagnostic tool in gastroenterology

    Institute of Scientific and Technical Information of China (English)

    Vicky; De; Preter; Kristin; Verbeke

    2013-01-01

    Metabolomics has increasingly been applied in addition to other "omic" approaches in the study of the pathophysiology of different gastrointestinal diseases.Metabolites represent molecular readouts of the cell status reflecting a physiological phenotype.In addition,changes in metabolite concentrations induced by exogenous factors such as environmental and dietary factors which do not affect the genome,are taken into account.Metabolic reactions initiated by the host or gut microbiota can lead to "marker" metabolites present in different biological fluids that allow differentiation between health and disease.Several lines of evidence implicated the involvement of intestinal microbiota in the pathogenesis of inflammatory bowel disease(IBD).Also in irritable bowel syndrome(IBS),a role of an abnormal microbiota composition,so-called dysbiosis,is supported by experimental data.These compositional alterations could play a role in the aetiology of both diseases by altering the metabolic activities of the gut bacteria.Several studies have applied a metabolomic approach to identify these metabolite signatures.However,before translating a potential metabolite biomarker into clinical use,additional validation studies are required.This review summarizes contributions that metabolomics has made in IBD and IBS and presents potential future directions within the field.

  9. Environmental metabolomics: a SWOT analysis (strengths, weaknesses, opportunities, and threats).

    Science.gov (United States)

    Miller, Marion G

    2007-02-01

    Metabolomic approaches have the potential to make an exceptional contribution to understanding how chemicals and other environmental stressors can affect both human and environmental health. However, the application of metabolomics to environmental exposures, although getting underway, has not yet been extensively explored. This review will use a SWOT analysis model to discuss some of the strengths, weaknesses, opportunities, and threats that are apparent to an investigator venturing into this relatively new field. SWOT has been used extensively in business settings to uncover new outlooks and identify problems that would impede progress. The field of environmental metabolomics provides great opportunities for discovery, and this is recognized by a high level of interest in potential applications. However, understanding the biological consequence of environmental exposures can be confounded by inter- and intra-individual differences. Metabolomic profiles can yield a plethora of data, the interpretation of which is complex and still being evaluated and researched. The development of the field will depend on the availability of technologies for data handling and that permit ready access metabolomic databases. Understanding the relevance of metabolomic endpoints to organism health vs adaptation vs variation is an important step in understanding what constitutes a substantive environmental threat. Metabolomic applications in reproductive research are discussed. Overall, the development of a comprehensive mechanistic-based interpretation of metabolomic changes offers the possibility of providing information that will significantly contribute to the protection of human health and the environment.

  10. Plant metabolomics and its potential application for human nutrition

    NARCIS (Netherlands)

    Hall, R.D.; Brouwer, I.D.; Fitzgerald, M.A.

    2008-01-01

    With the growing interest in the use of metabolomic technologies for a wide range of biological targets, food applications related to nutrition and quality are rapidly emerging. Metabolomics offers us the opportunity to gain deeper insights into, and have better control of, the fundamental biochemic

  11. Metabolomics for Undergraduates: Identification and Pathway Assignment of Mitochondrial Metabolites

    Science.gov (United States)

    Marques, Ana Patrícia; Serralheiro, Maria Luisa; Ferreira, António E. N.; Freire, Ana Ponces; Cordeiro, Carlos; Silva, Marta Sousa

    2016-01-01

    Metabolomics is a key discipline in systems biology, together with genomics, transcriptomics, and proteomics. In this omics cascade, the metabolome represents the biochemical products that arise from cellular processes and is often regarded as the final response of a biological system to environmental or genetic changes. The overall screening…

  12. Environmental metabolomics: a SWOT analysis (strengths, weaknesses, opportunities, and threats).

    Science.gov (United States)

    Miller, Marion G

    2007-02-01

    Metabolomic approaches have the potential to make an exceptional contribution to understanding how chemicals and other environmental stressors can affect both human and environmental health. However, the application of metabolomics to environmental exposures, although getting underway, has not yet been extensively explored. This review will use a SWOT analysis model to discuss some of the strengths, weaknesses, opportunities, and threats that are apparent to an investigator venturing into this relatively new field. SWOT has been used extensively in business settings to uncover new outlooks and identify problems that would impede progress. The field of environmental metabolomics provides great opportunities for discovery, and this is recognized by a high level of interest in potential applications. However, understanding the biological consequence of environmental exposures can be confounded by inter- and intra-individual differences. Metabolomic profiles can yield a plethora of data, the interpretation of which is complex and still being evaluated and researched. The development of the field will depend on the availability of technologies for data handling and that permit ready access metabolomic databases. Understanding the relevance of metabolomic endpoints to organism health vs adaptation vs variation is an important step in understanding what constitutes a substantive environmental threat. Metabolomic applications in reproductive research are discussed. Overall, the development of a comprehensive mechanistic-based interpretation of metabolomic changes offers the possibility of providing information that will significantly contribute to the protection of human health and the environment. PMID:17269710

  13. Speaking Fluently And Accurately

    Institute of Scientific and Technical Information of China (English)

    JosephDeVeto

    2004-01-01

    Even after many years of study,students make frequent mistakes in English. In addition, many students still need a long time to think of what they want to say. For some reason, in spite of all the studying, students are still not quite fluent.When I teach, I use one technique that helps students not only speak more accurately, but also more fluently. That technique is dictations.

  14. Accurate Finite Difference Algorithms

    Science.gov (United States)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  15. 液相色谱-同位素稀释质谱法准确测定人血清中葡萄糖含量%Accurate Determination of Serum Glucose by Liquid Chromatography-Isotope Dilution Mass Spectrometry

    Institute of Scientific and Technical Information of China (English)

    申玉星; 全灿; 马康

    2011-01-01

    以D-[13C6]葡萄糖标记物作为内标,用高效液相色谱-串联质谱法测定血清中的葡萄糖含量.向室温平衡后的血清样品中加入葡萄糖标记物,用乙醇沉淀蛋白,低温离心去除蛋白,上清液过0.22 μm有机滤膜.采用LC/MS电喷雾离子源(ESI),正离子模式,选择离子监测模式进行检测.方法的线性相关系数R2 =0.999 5,加标回收率为100.1%~102.8%,检出限为8μg/kg,相对标准偏差0.49%.该方法的样品前处理简单,测定准确高、精密度好,可用于血清中葡萄糖含量的高准确度定值.%A high performance liquid chromatography tandem mass spectrometric method was established for the determination of glucose concentration in serum with the aid of D-[13C6] glucose internal standard. D-[13 C6 ] glucose was added to the serum sample in balance at room temperature. Then the protein was precipitated and extracted in anhydrous ethanol with centrifugation at low temperature. The supernatant was filtered through a 0. 22 μm syringe filter into HPLC vials. Identification was achieved by electro-spray ionization (ESI) in positive mode using SIM mode. The calibration curve of glucose showed good linearity with correlation coefficient of R2=0. 999 5, recoveries of spiked samples were in the range 100. 1% to 102. 8%, the detection limit of the method was 8 μg/kg (S/N = 3) , and the relative standard derivations were 0. 49%. The established method is simple, accurate and precise, is appropriate for the determination of serum glucose with great accuracy.

  16. Integration of datasets from different analytical techniques to assess the impact of nutrition on human metabolome

    Directory of Open Access Journals (Sweden)

    Pamela eVernocchi

    2012-12-01

    Full Text Available Bacteria colonizing the human intestinal tract exhibit a high phylogenetic diversity that reflects their immense metabolic potentials. The catalytic activity of gut microbes has an important impact on gastrointestinal (GI functions and host health. The microbial conversion of carbohydrates and other food components leads to the formation of a large number of compounds that affect the host metabolome and have beneficial or adverse effects on human health. Meabolomics is a metabolic-biology system approach focused on the metabolic responses understanding of living systems to physio-pathological stimuli by using multivariate statistical data on human body fluids obtained by different instrumental techniques. A metabolomic approach based on an analytical platform could be able to separate, detect, characterize and quantify a wide range of metabolites and its metabolic pathways. This approach has been recently applied to study the metabolic changes triggered in the gut microbiota by specific diet components and diet variations, specific diseases, probiotic and synbiotic food intake.This review describes the metabolomic data obtained by analyzing human fluids by using different techniques and particularly Gas Chromatography Mass Spectrometry Solid-phase Micro Extraction (GC-MS/SPME, Proton Nuclear Magnetic Resonance (1H-NMR Spectroscopy and Fourier Transform Infrared (FTIR Spectroscopy. This instrumental approach have a good potential in the identification and detection of specific food intake and diseases biomarkers.

  17. Development and Evaluation of a Parallel Reaction Monitoring Strategy for Large-Scale Targeted Metabolomics Quantification.

    Science.gov (United States)

    Zhou, Juntuo; Liu, Huiying; Liu, Yang; Liu, Jia; Zhao, Xuyang; Yin, Yuxin

    2016-04-19

    Recent advances in mass spectrometers which have yielded higher resolution and faster scanning speeds have expanded their application in metabolomics of diverse diseases. Using a quadrupole-Orbitrap LC-MS system, we developed an efficient large-scale quantitative method targeting 237 metabolites involved in various metabolic pathways using scheduled, parallel reaction monitoring (PRM). We assessed the dynamic range, linearity, reproducibility, and system suitability of the PRM assay by measuring concentration curves, biological samples, and clinical serum samples. The quantification performances of PRM and MS1-based assays in Q-Exactive were compared, and the MRM assay in QTRAP 6500 was also compared. The PRM assay monitoring 237 polar metabolites showed greater reproducibility and quantitative accuracy than MS1-based quantification and also showed greater flexibility in postacquisition assay refinement than the MRM assay in QTRAP 6500. We present a workflow for convenient PRM data processing using Skyline software which is free of charge. In this study we have established a reliable PRM methodology on a quadrupole-Orbitrap platform for evaluation of large-scale targeted metabolomics, which provides a new choice for basic and clinical metabolomics study. PMID:27002337

  18. Revealing disease-associated pathways by network integration of untargeted metabolomics.

    Science.gov (United States)

    Pirhaji, Leila; Milani, Pamela; Leidl, Mathias; Curran, Timothy; Avila-Pacheco, Julian; Clish, Clary B; White, Forest M; Saghatelian, Alan; Fraenkel, Ernest

    2016-09-01

    Uncovering the molecular context of dysregulated metabolites is crucial to understand pathogenic pathways. However, their system-level analysis has been limited owing to challenges in global metabolite identification. Most metabolite features detected by untargeted metabolomics carried out by liquid-chromatography-mass spectrometry cannot be uniquely identified without additional, time-consuming experiments. We report a network-based approach, prize-collecting Steiner forest algorithm for integrative analysis of untargeted metabolomics (PIUMet), that infers molecular pathways and components via integrative analysis of metabolite features, without requiring their identification. We demonstrated PIUMet by analyzing changes in metabolism of sphingolipids, fatty acids and steroids in a Huntington's disease model. Additionally, PIUMet enabled us to elucidate putative identities of altered metabolite features in diseased cells, and infer experimentally undetected, disease-associated metabolites and dysregulated proteins. Finally, we established PIUMet's ability for integrative analysis of untargeted metabolomics data with proteomics data, demonstrating that this approach elicits disease-associated metabolites and proteins that cannot be inferred by individual analysis of these data. PMID:27479327

  19. Metabolomic Effects of Xylitol and Fluoride on Plaque Biofilm in Vivo

    Science.gov (United States)

    Takahashi, N.; Washio, J.

    2011-01-01

    Dental caries is initiated by demineralization of the tooth surface through acid production from sugar by plaque biofilm. Fluoride and xylitol have been used worldwide as caries-preventive reagents, based on in vitro-proven inhibitory mechanisms on bacterial acid production. We attempted to confirm the inhibitory mechanisms of fluoride and xylitol in vivo by performing metabolome analysis on the central carbon metabolism in supragingival plaque using the combination of capillary electrophoresis and a time-of-flight mass spectrometer. Fluoride (225 and 900 ppm F−) inhibited lactate production from 10% glucose by 34% and 46%, respectively, along with the increase in 3-phosphoglycerate and the decrease in phosphoenolpyruvate in the EMP pathway in supragingival plaque. These results confirmed that fluoride inhibited bacterial enolase in the EMP pathway and subsequently repressed acid production in vivo. In contrast, 10% xylitol had no effect on acid production and the metabolome profile in supragingival plaque, although xylitol 5-phosphate was produced. These results suggest that xylitol is not an inhibitor of plaque acid production but rather a non-fermentative sugar alcohol. Metabolome analyses of plaque biofilm can be applied for monitoring the efficacy of dietary components and medicines for plaque biofilm, leading to the development of effective plaque control. PMID:21940519

  20. Efficacy of Fluidized Bed Bioartificial Liver in Treating Fulminant Hepatic Failure in Pigs: A Metabolomics Study.

    Science.gov (United States)

    Zhou, Pengcheng; Shao, Li; Zhao, Lifu; Lv, Guoliang; Pan, Xiaoping; Zhang, Anye; Li, Jianzhou; Zhou, Ning; Chen, Deying; Li, Lanjuan

    2016-01-01

    Bioartificial livers may act as a promising therapy for fulminant hepatic failure (FHF) with better accessibility and less injury compared to orthotopic liver transplantation. This study aims to evaluate the efficacy and safety of a fluidized bed bioartificial liver (FBBAL) and to explore its therapeutic mechanisms based on metabolomics. FHF was induced by D-galactosamine. Eighteen hours later, pigs were treated with an FBBAL containing encapsulated primary porcine hepatocytes (B group), with a sham FBBAL (containing cell-free capsules, S group) or with only intensive care (C group) for 6 h. Serum samples were assayed using ultra-performance liquid chromatography-mass spectrometry. The difference in survival time (51.6 ± 7.9 h vs. 49.3 ± 6.6 h) and serum metabolome was negligible between the S and C groups, whereas FBBAL treatment significantly prolonged survival time (70.4 ± 11.5h, P sphingomyelinase, and fatty acids and an increase in conjugated bile acids. The FBBAL exhibits some liver functions and may exert its therapeutic effect by altering the serum metabolome of FHF pigs. Moreover, alginate-chitosan capsules have less influence on serum metabolites. Nevertheless, the alterations were not universally beneficial, revealing that much should be done to improve the FBBAL. PMID:27194381

  1. Metabolomics analysis of metabolic effects of nicotinamide phosphoribosyltransferase (NAMPT inhibition on human cancer cells.

    Directory of Open Access Journals (Sweden)

    Vladimir Tolstikov

    Full Text Available Nicotinamide phosphoribosyltransferase (NAMPT plays an important role in cellular bioenergetics. It is responsible for converting nicotinamide to nicotinamide adenine dinucleotide, an essential molecule in cellular metabolism. NAMPT has been extensively studied over the past decade due to its role as a key regulator of nicotinamide adenine dinucleotide-consuming enzymes. NAMPT is also known as a potential target for therapeutic intervention due to its involvement in disease. In the current study, we used a global mass spectrometry-based metabolomic approach to investigate the effects of FK866, a small molecule inhibitor of NAMPT currently in clinical trials, on metabolic perturbations in human cancer cells. We treated A2780 (ovarian cancer and HCT-116 (colorectal cancer cell lines with FK866 in the presence and absence of nicotinic acid. Significant changes were observed in the amino acids metabolism and the purine and pyrimidine metabolism. We also observed metabolic alterations in glycolysis, the citric acid cycle (TCA, and the pentose phosphate pathway. To expand the range of the detected polar metabolites and improve data confidence, we applied a global metabolomics profiling platform by using both non-targeted and targeted hydrophilic (HILIC-LC-MS and GC-MS analysis. We used Ingenuity Knowledge Base to facilitate the projection of metabolomics data onto metabolic pathways. Several metabolic pathways showed differential responses to FK866 based on several matches to the list of annotated metabolites. This study suggests that global metabolomics can be a useful tool in pharmacological studies of the mechanism of action of drugs at a cellular level.

  2. Metabolomic characteristics of arsenic-associated diabetes in a prospective cohort in Chihuahua, Mexico.

    Science.gov (United States)

    Martin, Elizabeth; González-Horta, Carmen; Rager, Julia; Bailey, Kathryn A; Sánchez-Ramírez, Blanca; Ballinas-Casarrubias, Lourdes; Ishida, María C; Gutiérrez-Torres, Daniela S; Hernández Cerón, Roberto; Viniegra Morales, Damián; Baeza Terrazas, Francisco A; Saunders, R Jesse; Drobná, Zuzana; Mendez, Michelle A; Buse, John B; Loomis, Dana; Jia, Wei; García-Vargas, Gonzalo G; Del Razo, Luz M; Stýblo, Miroslav; Fry, Rebecca

    2015-04-01

    Chronic exposure to inorganic arsenic (iAs) has been linked to an increased risk of diabetes, yet the specific disease phenotype and underlying mechanisms are poorly understood. In the present study we set out to identify iAs exposure-associated metabolites with altered abundance in nondiabetic and diabetic individuals in an effort to understand the relationship between exposure, metabolomic response, and disease status. A nested study design was used to profile metabolomic shifts in urine and plasma collected from 90 diabetic and 86 nondiabetic individuals matched for varying iAs concentrations in drinking water, body mass index, age, and sex. Diabetes diagnosis was based on measures of fasting plasma glucose and 2-h blood glucose. Multivariable models were used to identify metabolites with altered abundance associated with iAs exposure among diabetic and nondiabetic individuals. A total of 132 metabolites were identified to shift in urine or plasma in response to iAs exposure characterized by the sum of iAs metabolites in urine (U-tAs). Although many metabolites were altered in both diabetic and nondiabetic 35 subjects, diabetic individuals displayed a unique response to iAs exposure with 59 altered metabolites including those that play a role in tricarboxylic acid cycle and amino acid metabolism. Taken together, these data highlight the broad impact of iAs exposure on the human metabolome, and demonstrate some specificity of the metabolomic response between diabetic and nondiabetic individuals. These data may provide novel insights into the mechanisms and phenotype of diabetes associated with iAs exposure.

  3. Electronic Nose and Exhaled Breath NMR-based Metabolomics Applications in Airways Disease.

    Science.gov (United States)

    Santini, Giuseppe; Mores, Nadia; Penas, Andreu; Capuano, Rosamaria; Mondino, Chiara; Trové, Andrea; Macagno, Francesco; Zini, Gina; Cattani, Paola; Martinelli, Eugenio; Motta, Andrea; Macis, Giuseppe; Ciabattoni, Giovanni; Montuschi, Paolo

    2016-01-01

    Breathomics, the multidimensional molecular analysis of exhaled breath, includes analysis of exhaled breath with gas-chromatography/mass spectrometry (GC/MS) and electronic noses (e-noses), and metabolomics of exhaled breath condensate (EBC), a non-invasive technique which provides information on the composition of airway lining fluid, generally by high-resolution nuclear magnetic resonance (NMR) spectroscopy or MS methods. Metabolomics is the identification and quantification of small molecular weight metabolites in a biofluid. Specific profiles of volatile compounds in exhaled breath and metabolites in EBC (breathprints) are potentially useful surrogate markers of inflammatory respiratory diseases. Electronic noses (e-noses) are artificial sensor systems, usually consisting of chemical cross-reactive sensor arrays for characterization of patterns of breath volatile compounds, and algorithms for breathprints classification. E-noses are handheld, portable, and provide real-time data. E-nose breathprints can reflect respiratory inflammation. E-noses and NMR-based metabolomics of EBC can distinguish patients with respiratory diseases such as asthma, COPD, and lung cancer, or diseases with a clinically relevant respiratory component including cystic fibrosis and primary ciliary dyskinesia, and healthy individuals. Breathomics has also been reported to identify patients affected by different types of respiratory diseases. Patterns of breath volatile compounds detected by e-nose and EBC metabolic profiles have been associated with asthma phenotypes. In combination with other -omics platforms, breathomics might provide a molecular approach to respiratory disease phenotyping and a molecular basis to tailored pharmacotherapeutic strategies. Breathomics might also contribute to identify new surrogate markers of respiratory inflammation, thus, facilitating drug discovery. Validation in newly recruited, prospective independent cohorts is essential for development of e

  4. Review of sample preparation strategies for MS-based metabolomic studies in industrial biotechnology.

    Science.gov (United States)

    Causon, Tim J; Hann, Stephan

    2016-09-28

    Fermentation and cell culture biotechnology in the form of so-called "cell factories" now play an increasingly significant role in production of both large (e.g. proteins, biopharmaceuticals) and small organic molecules for a wide variety of applications. However, associated metabolic engineering optimisation processes relying on genetic modification of organisms used in cell factories, or alteration of production conditions remain a challenging undertaking for improving the final yield and quality of cell factory products. In addition to genomic, transcriptomic and proteomic workflows, analytical metabolomics continues to play a critical role in studying detailed aspects of critical pathways (e.g. via targeted quantification of metabolites), identification of biosynthetic intermediates, and also for phenotype differentiation and the elucidation of previously unknown pathways (e.g. via non-targeted strategies). However, the diversity of primary and secondary metabolites and the broad concentration ranges encompassed during typical biotechnological processes means that simultaneous extraction and robust analytical determination of all parts of interest of the metabolome is effectively impossible. As the integration of metabolome data with transcriptome and proteome data is an essential goal of both targeted and non-targeted methods addressing production optimisation goals, additional sample preparation steps beyond necessary sampling, quenching and extraction protocols including clean-up, analyte enrichment, and derivatisation are important considerations for some classes of metabolites, especially those present in low concentrations or exhibiting poor stability. This contribution critically assesses the potential of current sample preparation strategies applied in metabolomic studies of industrially-relevant cell factory organisms using mass spectrometry-based platforms primarily coupled to liquid-phase sample introduction (i.e. flow injection, liquid

  5. Quantitative metabolomics of photoreceptor degeneration and the effects of stem cell-derived retinal pigment epithelium transplantation.

    Science.gov (United States)

    Wang, Junhua; Westenskow, Peter D; Fang, Mingliang; Friedlander, Martin; Siuzdak, Gary

    2016-10-28

    Photoreceptor degeneration is characteristic of vision-threatening diseases including age-related macular degeneration. Photoreceptors are metabolically demanding cells in the retina, but specific details about their metabolic behaviours are unresolved. The quantitative metabolomics of retinal degeneration could provide valuable insights and inform future therapies. Here, we determined the metabolomic 'fingerprint' of healthy and dystrophic retinas in rat models using optimized metabolite extraction techniques. A number of classes of metabolites were consistently dysregulated during degeneration: vitamin A analogues, fatty acid amides, long-chain polyunsaturated fatty acids, acyl carnitines and several phospholipid species. For the first time, a distinct temporal trend of several important metabolites including DHA (4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoic acid), all-trans-retinal and its toxic end-product N-retinyl-N-retinylidene-ethanolamine were observed between healthy and dystrophic retinas. In this study, metabolomics was further used to determine the temporal effects of the therapeutic intervention of grafting stem cell-derived retinal pigment epithelium (RPE) in dystrophic retinas, which significantly prevented photoreceptor atrophy in our previous studies. The result revealed that lipid levels such as phosphatidylethanolamine in eyes were restored in those animals receiving the RPE grafts. In conclusion, this study provides insight into the metabolomics of retinal degeneration, and further understanding of the efficacy of RPE transplantation.This article is part of the themed issue 'Quantitative mass spectrometry'. PMID:27644974

  6. Biological variation of Vanilla planifolia leaf metabolome.

    Science.gov (United States)

    Palama, Tony Lionel; Fock, Isabelle; Choi, Young Hae; Verpoorte, Robert; Kodja, Hippolyte

    2010-04-01

    The metabolomic analysis of Vanilla planifolia leaves collected at different developmental stages was carried out using (1)H-nuclear magnetic resonance (NMR) spectroscopy and multivariate data analysis in order to evaluate their variation. Ontogenic changes of the metabolome were considered since leaves of different ages were collected at two different times of the day and in two different seasons. Principal component analysis (PCA) and partial least square modeling discriminate analysis (PLS-DA) of (1)H NMR data provided a clear separation according to leaf age, time of the day and season of collection. Young leaves were found to have higher levels of glucose, bis[4-(beta-D-glucopyranosyloxy)-benzyl]-2-isopropyltartrate (glucoside A) and bis[4-(beta-D-glucopyranosyloxy)-benzyl]-2-(2-butyl)-tartrate (glucoside B), whereas older leaves had more sucrose, acetic acid, homocitric acid and malic acid. Results obtained from PLS-DA analysis showed that leaves collected in March 2008 had higher levels of glucosides A and B as compared to those collected in August 2007. However, the relative standard deviation (RSD) exhibited by the individual values of glucosides A and B showed that those compounds vary more according to their developmental stage (50%) than to the time of day or the season in which they were collected (19%). Although morphological variations of the V. planifolia accessions were observed, no clear separation of the accessions was determined from the analysis of the NMR spectra. The results obtained in this study, show that this method based on the use of (1)H NMR spectroscopy in combination with multivariate analysis has a great potential for further applications in the study of vanilla leaf metabolome.

  7. The exo-metabolome in filamentous fungi

    DEFF Research Database (Denmark)

    Thrane, Ulf; Andersen, Birgitte; Frisvad, Jens Christian;

    2007-01-01

    Filamentous fungi are a diverse group of eukaryotic microorganisms that have a significant impact on human life as spoilers of food and feed by degradation and toxin production. They are also most useful as a source of bulk and fine chemicals and pharmaceuticals. This chapter focuses on the exo......-metabolome in filamentous fungi, which comprises more than 30,000 known secondary metabolites. Profiles of this diverse range of secondary metabolites have, for more than 25 years, been central in development of fungal systematics, taxonomy, and ecology, today integrated in a multidisciplinary and polyphasic approach...

  8. LC-QTOF/MS metabolomic profiles in human plasma after a 5-week high dietary fiber intake

    DEFF Research Database (Denmark)

    Johansson-Persson, Anna; Barri, Thaer; Ulmius, Matilda;

    2013-01-01

    The objective was to investigate the alterations of plasma metabolome profiles to identify exposure and effect markers of dietary fiber intake. Subjects (n¿=¿25) aged 58.6 (1.1)¿years (mean and SD) with a body mass index of 26.6 (0.5)¿kg/m(2) were given a high fiber (HF) and a low fiber (LF) diet...

  9. A Comparative Metabolomic Evaluation of Behcet’s Disease with Arthritis and Seronegative Arthritis Using Synovial Fluid

    OpenAIRE

    Joong Kyong Ahn; Sooah Kim; Jungyeon Kim; Jiwon Hwang; Kyoung Heon Kim; Hoon-Suk Cha

    2015-01-01

    Behcet's disease (BD) with arthritis is often confused with seronegative arthritis (SNA) because of shared clinical symptoms and the lack of definitive biomarkers for BD. To investigate possible metabolic patterns and potential biomarkers of BD with arthritis, metabolomic profiling of synovial fluid (SF) from 6 patients with BD with arthritis and 18 patients with SNA was performed using gas chromatography/time-of-flight mass spectrometry in conjunction with univariate and multivariate statist...

  10. Application of a high-throughput process analytical technology metabolomics pipeline to Port wine forced ageing process

    OpenAIRE

    C.C. Castro; Martins, Rui C.; J. A. Teixeira; Ferreira, António C.

    2014-01-01

    Metabolomics aims at gathering the maximum amount of metabolic information for a total interpretation of biological systems. A process analytical technology pipeline, combining gas chromatography–mass spectrometry data preprocessing with multivariate analysis, was applied to a Port wine “forced ageing” process under different oxygen saturation regimes at 60 °C. It was found that extreme “forced ageing” conditions promote the occurrence of undesirable chemical reactions by production of di...

  11. Temporal metabolomic responses of cultured HepG2 liver cells to high fructose and high glucose exposures

    OpenAIRE

    Meissen, John K.; Hirahatake, Kristin M.; Adams, Sean H.; Fiehn, Oliver

    2014-01-01

    High fructose consumption has been implicated with deleterious effects on human health, including hyperlipidemia elicited through de novo lipogenesis. However, more global effects of fructose on cellular metabolism have not been elucidated. In order to explore the metabolic impact of fructose-containing nutrients, we applied both GC-TOF and HILIC-QTOF mass spectrometry metabolomic strategies using extracts from cultured HepG2 cells exposed to fructose, glucose, or fructose + glucose. Cellular...

  12. PLS-Based and Regularization-Based Methods for the Selection of Relevant Variables in Non-targeted Metabolomics Data.

    Science.gov (United States)

    Bujak, Renata; Daghir-Wojtkowiak, Emilia; Kaliszan, Roman; Markuszewski, Michał J

    2016-01-01

    Non-targeted metabolomics constitutes a part of the systems biology and aims at determining numerous metabolites in complex biological samples. Datasets obtained in the non-targeted metabolomics studies are high-dimensional due to sensitivity of mass spectrometry-based detection methods as well as complexity of biological matrices. Therefore, a proper selection of variables which contribute into group classification is a crucial step, especially in metabolomics studies which are focused on searching for disease biomarker candidates. In the present study, three different statistical approaches were tested using two metabolomics datasets (RH and PH study). The orthogonal projections to latent structures-discriminant analysis (OPLS-DA) without and with multiple testing correction as well as the least absolute shrinkage and selection operator (LASSO) with bootstrapping, were tested and compared. For the RH study, OPLS-DA model built without multiple testing correction selected 46 and 218 variables based on the VIP criteria using Pareto and UV scaling, respectively. For the PH study, 217 and 320 variables were selected based on the VIP criteria using Pareto and UV scaling, respectively. In the RH study, OPLS-DA model built after correcting for multiple testing, selected 4 and 19 variables as in terms of Pareto and UV scaling, respectively. For the PH study, 14 and 18 variables were selected based on the VIP criteria in terms of Pareto and UV scaling, respectively. In the RH and PH study, the LASSO selected 14 and 4 variables with reproducibility between 99.3 and 100%, respectively. In the light of PLS-based models, the larger the search space the higher the probability of developing models that fit the training data well with simultaneous poor predictive performance on the validation set. The LASSO offers potential improvements over standard linear regression due to the presence of the constrain, which promotes sparse solutions. This paper is the first one to date

  13. A metabolomics study on human dietary intervention with apples

    DEFF Research Database (Denmark)

    Dragsted, L. O.; Kristensen, M.; Ravn-Haren, Gitte;

    2009-01-01

    Metabolomics is a promising tool for searching out new biomarkers and the development of hypotheses in nutrition research. This chapter will describe the design of human dietary intervention studies where samples are collected for metabolomics analyses as well as the analytical issues and data...... interpretation. Design considerations for metabolomic studies include the overall structure of the study as well as the control group, sample collection and handling, sample storage, sample analysis, quality control measures and plans for data analyses. Suggestions for designing feasible and ethical dietary...

  14. A primer to nutritional metabolomics by NMR spectroscopy and chemometrics

    DEFF Research Database (Denmark)

    Savorani, Francesco; Rasmussen, Morten Arendt; Mikkelsen, Mette Skau;

    2013-01-01

    This paper outlines the advantages and disadvantages of using high throughput NMR metabolomics for nutritional studies with emphasis on the workflow and data analytical methods for generation of new knowledge. The paper describes one-by-one the major research activities in the interdisciplinary...... metabolomics platform and highlights the opportunities that NMR spectra can provide in future nutrition studies. Three areas are emphasized: (1) NMR as an unbiased and non-destructive platform for providing an overview of the metabolome under investigation, (2) NMR for providing versatile information and data...

  15. Metabolomics, a promising approach to translational research in cardiology

    Directory of Open Access Journals (Sweden)

    Martino Deidda

    2015-12-01

    In this article, we will provide a description of metabolomics in comparison with other, better known “omics” disciplines such as genomics and proteomics. In addition, we will review the current rationale for the implementation of metabolomics in cardiology, its basic methodology and the available data from human studies in this discipline. The topics covered will delineate the importance of being able to use the metabolomic information to understand the mechanisms of diseases from the perspective of systems biology, and as a non-invasive approach to the diagnosis, grading and treatment of cardiovascular diseases.

  16. Targeting of the hydrophobic metabolome by pathogens.

    Science.gov (United States)

    Helms, J Bernd; Kaloyanova, Dora V; Strating, Jeroen R P; van Hellemond, Jaap J; van der Schaar, Hilde M; Tielens, Aloysius G M; van Kuppeveld, Frank J M; Brouwers, Jos F

    2015-05-01

    The hydrophobic molecules of the metabolome - also named the lipidome - constitute a major part of the entire metabolome. Novel technologies show the existence of a staggering number of individual lipid species, the biological functions of which are, with the exception of only a few lipid species, unknown. Much can be learned from pathogens that have evolved to take advantage of the complexity of the lipidome to escape the immune system of the host organism and to allow their survival and replication. Different types of pathogens target different lipids as shown in interaction maps, allowing visualization of differences between different types of pathogens. Bacterial and viral pathogens target predominantly structural and signaling lipids to alter the cellular phenotype of the host cell. Fungal and parasitic pathogens have complex lipidomes themselves and target predominantly the release of polyunsaturated fatty acids from the host cell lipidome, resulting in the generation of eicosanoids by either the host cell or the pathogen. Thus, whereas viruses and bacteria induce predominantly alterations in lipid metabolites at the host cell level, eukaryotic pathogens focus on interference with lipid metabolites affecting systemic inflammatory reactions that are part of the immune system. A better understanding of the interplay between host-pathogen interactions will not only help elucidate the fundamental role of lipid species in cellular physiology, but will also aid in the generation of novel therapeutic drugs. PMID:25754025

  17. The Human Blood Metabolome-Transcriptome Interface.

    Directory of Open Access Journals (Sweden)

    Jörg Bartel

    2015-06-01

    Full Text Available Biological systems consist of multiple organizational levels all densely interacting with each other to ensure function and flexibility of the system. Simultaneous analysis of cross-sectional multi-omics data from large population studies is a powerful tool to comprehensively characterize the underlying molecular mechanisms on a physiological scale. In this study, we systematically analyzed the relationship between fasting serum metabolomics and whole blood transcriptomics data from 712 individuals of the German KORA F4 cohort. Correlation-based analysis identified 1,109 significant associations between 522 transcripts and 114 metabolites summarized in an integrated network, the 'human blood metabolome-transcriptome interface' (BMTI. Bidirectional causality analysis using Mendelian randomization did not yield any statistically significant causal associations between transcripts and metabolites. A knowledge-based interpretation and integration with a genome-scale human metabolic reconstruction revealed systematic signatures of signaling, transport and metabolic processes, i.e. metabolic reactions mainly belonging to lipid, energy and amino acid metabolism. Moreover, the construction of a network based on functional categories illustrated the cross-talk between the biological layers at a pathway level. Using a transcription factor binding site enrichment analysis, this pathway cross-talk was further confirmed at a regulatory level. Finally, we demonstrated how the constructed networks can be used to gain novel insights into molecular mechanisms associated to intermediate clinical traits. Overall, our results demonstrate the utility of a multi-omics integrative approach to understand the molecular mechanisms underlying both normal physiology and disease.

  18. MetaDB a Data Processing Workflow in Untargeted MS-Based Metabolomics Experiments

    Directory of Open Access Journals (Sweden)

    Pietro eFranceschi

    2014-12-01

    Full Text Available Due to their sensitivity and speed, mass-spectrometry based analytical technologies are widely used to in metabolomics to characterize biological phenomena. To address issues like metadata organization, quality assessment, data processing, data storage and, finally, submission to public repositories, bioinformatic pipelines of a non-interactive nature are often employed, complementing the interactive software used for initial inspection and visualization of the data. These pipelines often are created as open-source software allowing the complete and exhaustive documentation of each step, ensuring the reproducibility of the analysis of extensive and often expensive experiments.In this paper we will review the major steps which constitute such a data processing pipeline, discussing them in the context of open source software for untargeted Liquid Chromatography Mass Spectrometry (LC-MS and Gas Chromatography Mass Spectrometry (GC-MS metabolomics experiments recently developed at our institute. The software has been developed by integrating our metaMS R package with a user-friendly web based application written in Grails. MetaMS takes care of data pre-processing and annotation, while the interface deals with the creation of the sample lists, the organization of the data storage and the generation of survey plots for quality assessment. Experimental and biological metadata are stored in the ISA-Tab format making the proposed pipeline fully integrated with the Metabolights framework.

  19. Training in metabolomics research. I. Designing the experiment, collecting and extracting samples and generating metabolomics data.

    Science.gov (United States)

    Barnes, S; Benton, H P; Casazza, K; Cooper, S J; Cui, X; Du, X; Engler, J A; Kabarowski, J H; Li, S; Pathmasiri, W; Prasain, J K; Renfrow, M B; Tiwari, H K

    2016-07-01

    Metabolomics is perhaps the most challenging of the -omics fields, given the complexity of an organism's metabolome and the rapid rate at which it changes. When one sets out to study metabolism there are numerous dynamic variables that can influence metabolism that must be considered. Recognizing the experimental challenges confronting researchers who undertake metabolism studies, workshops like the one at University of Alabama at Birmingham have been established to offer instructional guidance. A summary of the UAB course training materials is being published as a two-part Special Feature Tutorial. In this month's Part I the authors discuss details of good experimental design and sample collection and handling. In an upcoming Part II, the authors discuss in detail the various aspects of data analysis. PMID:27434812

  20. Loss-of-function variants influence the human serum metabolome.

    Science.gov (United States)

    Yu, Bing; Li, Alexander H; Metcalf, Ginger A; Muzny, Donna M; Morrison, Alanna C; White, Simon; Mosley, Thomas H; Gibbs, Richard A; Boerwinkle, Eric

    2016-08-01

    The metabolome is a collection of small molecules resulting from multiple cellular and biological processes that can act as biomarkers of disease, and African-Americans exhibit high levels of genetic diversity. Exome sequencing of a sample of deeply phenotyped African-Americans allowed us to analyze the effects of annotated loss-of-function (LoF) mutations on 308 serum metabolites measured by untargeted liquid and gas chromatography coupled with mass spectrometry. In an independent sample, we identified and replicated four genes harboring six LoF mutations that significantly affected five metabolites. These sites were related to a 19 to 45% difference in geometric mean metabolite levels, with an average effect size of 25%. We show that some of the affected metabolites are risk predictors or diagnostic biomarkers of disease and, using the principle of Mendelian randomization, are in the causal pathway of disease. For example, LoF mutations in SLCO1B1 elevate the levels of hexadecanedioate, a fatty acid significantly associated with increased blood pressure levels and risk of incident heart failure in both African-Americans and an independent sample of European-Americans. We show that SLCO1B1 LoF mutations significantly increase the risk of incident heart failure, thus implicating the metabolite in the causal pathway of disease. These results reveal new avenues into gene function and the understanding of disease etiology by integrating -omic technologies into a deeply phenotyped population study. PMID:27602404

  1. Comparative Metabolomic and Lipidomic Analysis of Phenotype Stratified Prostate Cells.

    Directory of Open Access Journals (Sweden)

    Tanya C Burch

    Full Text Available Prostate cancer (PCa is the most prevalent cancer amongst men and the second most common cause of cancer related-deaths in the USA. Prostate cancer is a heterogeneous disease ranging from indolent asymptomatic cases to very aggressive life threatening forms. The goal of this study was to identify differentially expressed metabolites and lipids in prostate cells with different tumorigenic phenotypes. We have used mass spectrometry metabolomic profiling, lipidomic profiling, bioinformatic and statistical methods to identify, quantify and characterize differentially regulated molecules in five prostate derived cell lines. We have identified potentially interesting species of different lipid subclasses including phosphatidylcholines (PCs, phosphatidylethanolamines (PEs, glycerophosphoinositols (PIs and other metabolites that are significantly upregulated in prostate cancer cells derived from distant metastatic sites. Transcriptomic and biochemical analysis of key enzymes that are involved in lipid metabolism demonstrate the significant upregulation of choline kinase alpha in the metastatic cells compared to the non-malignant and non-metastatic cells. This suggests that different de novo lipogenesis and other specific signal transduction pathways are activated in aggressive metastatic cells as compared to normal and non-metastatic cells.

  2. Unraveling Biochemical Pathways Affected by Mitochondrial Dysfunctions Using Metabolomic Approaches

    Science.gov (United States)

    Demine, Stéphane; Reddy, Nagabushana; Renard, Patricia; Raes, Martine; Arnould, Thierry

    2014-01-01

    Mitochondrial dysfunction(s) (MDs) can be defined as alterations in the mitochondria, including mitochondrial uncoupling, mitochondrial depolarization, inhibition of the mitochondrial respiratory chain, mitochondrial network fragmentation, mitochondrial or nuclear DNA mutations and the mitochondrial accumulation of protein aggregates. All these MDs are known to alter the capacity of ATP production and are observed in several pathological states/diseases, including cancer, obesity, muscle and neurological disorders. The induction of MDs can also alter the secretion of several metabolites, reactive oxygen species production and modify several cell-signalling pathways to resolve the mitochondrial dysfunction or ultimately trigger cell death. Many metabolites, such as fatty acids and derived compounds, could be secreted into the blood stream by cells suffering from mitochondrial alterations. In this review, we summarize how a mitochondrial uncoupling can modify metabolites, the signalling pathways and transcription factors involved in this process. We describe how to identify the causes or consequences of mitochondrial dysfunction using metabolomics (liquid and gas chromatography associated with mass spectrometry analysis, NMR spectroscopy) in the obesity and insulin resistance thematic. PMID:25257998

  3. Unraveling Biochemical Pathways Affected by Mitochondrial Dysfunctions Using Metabolomic Approaches

    Directory of Open Access Journals (Sweden)

    Stéphane Demine

    2014-09-01

    Full Text Available Mitochondrial dysfunction(s (MDs can be defined as alterations in the mitochondria, including mitochondrial uncoupling, mitochondrial depolarization, inhibition of the mitochondrial respiratory chain, mitochondrial network fragmentation, mitochondrial or nuclear DNA mutations and the mitochondrial accumulation of protein aggregates. All these MDs are known to alter the capacity of ATP production and are observed in several pathological states/diseases, including cancer, obesity, muscle and neurological disorders. The induction of MDs can also alter the secretion of several metabolites, reactive oxygen species production and modify several cell-signalling pathways to resolve the mitochondrial dysfunction or ultimately trigger cell death. Many metabolites, such as fatty acids and derived compounds, could be secreted into the blood stream by cells suffering from mitochondrial alterations. In this review, we summarize how a mitochondrial uncoupling can modify metabolites, the signalling pathways and transcription factors involved in this process. We describe how to identify the causes or consequences of mitochondrial dysfunction using metabolomics (liquid and gas chromatography associated with mass spectrometry analysis, NMR spectroscopy in the obesity and insulin resistance thematic.

  4. Dissemination of metabolomics results: role of MetaboLights and COSMOS.

    Science.gov (United States)

    Salek, Reza M; Haug, Kenneth; Steinbeck, Christoph

    2013-05-17

    With ever-increasing amounts of metabolomics data produced each year, there is an even greater need to disseminate data and knowledge produced in a standard and reproducible way. To assist with this a general purpose, open source metabolomics repository, MetaboLights, was launched in 2012. To promote a community standard, initially culminated as metabolomics standards initiative (MSI), COordination of Standards in MetabOlomicS (COSMOS) was introduced. COSMOS aims to link life science e-infrastructures within the worldwide metabolomics community as well as develop and maintain open source exchange formats for raw and processed data, ensuring better flow of metabolomics information.

  5. Field-based Metabolomics for Assessing Contaminated Surface Waters

    Science.gov (United States)

    Metabolomics is becoming well-established for studying chemical contaminant-induced alterations to normal biological function. For example, the literature contains a wealth of laboratory-based studies involving analysis of samples from organisms exposed to individual chemical tox...

  6. Global metabolomic profiling targeting childhood obesity in the Hispanic population

    Science.gov (United States)

    Metabolomics may unravel important biological pathways involved in the pathophysiology of childhood obesity. We aimed to 1) identify metabolites that differ significantly between nonobese and obese Hispanic children; 2) collapse metabolites into principal components (PCs) associated with obesity and...

  7. Interpreting Metabolomics Data to Mode of Action of Chemicals

    Science.gov (United States)

    Metabolomics approach utilizes high-throughput identification, quantification, and characterization of low molecular weight endogenous metabolites from numerous metabolic pathways. Exposure to environmental chemicals, which act through multiple mechanisms, cause perturbation of...

  8. Applying Metabolomics to differentiate amphibian responses to multiple stressors

    Science.gov (United States)

    Introduction/Objectives/Methods One of the biggest challenges in ecological risk assessment is determining the impact of multiple stressors on individual organisms and populations in ‘real world’ scenarios. Emerging ‘omic technologies, notably, metabolomics, pr...

  9. Metabolomic determinants of necrotizing enterocolitis in preterm piglets

    Science.gov (United States)

    Studies in premature infants and animals show that carbohydrate malabsorption and gut microbiota colonisation are key elements for triggering necrotizing enterocolitis (NEC). Our aim was to determine how dietary carbohydrate composition affects the metabolomic profile and whether unique metabolite s...

  10. Human gut microbes impact host serum metabolome and insulin sensitivity

    DEFF Research Database (Denmark)

    Pedersen, Helle Krogh; Gudmundsdottir, Valborg; Nielsen, Henrik Bjørn;

    2016-01-01

    Insulin resistance is a forerunner state of ischaemic cardiovascular disease and type 2 diabetes. Here we show how the human gut microbiome impacts the serum metabolome and associates with insulin resistance in 277 non-diabetic Danish individuals. The serum metabolome of insulin-resistant individ......Insulin resistance is a forerunner state of ischaemic cardiovascular disease and type 2 diabetes. Here we show how the human gut microbiome impacts the serum metabolome and associates with insulin resistance in 277 non-diabetic Danish individuals. The serum metabolome of insulin......-resistant individuals is characterized by increased levels of branched-chain amino acids (BCAAs), which correlate with a gut microbiome that has an enriched biosynthetic potential for BCAAs and is deprived of genes encoding bacterial inward transporters for these amino acids. Prevotella copri and Bacteroides vulgatus...

  11. Identification of specific metabolites in culture supernatant of Mycobacterium tuberculosis using metabolomics: exploration of potential biomarkers.

    Science.gov (United States)

    Lau, Susanna K P; Lam, Ching-Wan; Curreem, Shirly O T; Lee, Kim-Chung; Lau, Candy C Y; Chow, Wang-Ngai; Ngan, Antonio H Y; To, Kelvin K W; Chan, Jasper F W; Hung, Ivan F N; Yam, Wing-Cheong; Yuen, Kwok-Yung; Woo, Patrick C Y

    2015-01-01

    Although previous studies have reported the use of metabolomics for Mycobacterium species differentiation, little is known about the potential of extracellular metabolites of Mycobacterium tuberculosis (MTB) as specific biomarkers. Using an optimized ultrahigh performance liquid chromatography-electrospray ionization-quadruple time of flight-mass spectrometry (UHPLC-ESI-Q-TOF-MS) platform, we characterized the extracellular metabolomes of culture supernatant of nine MTB strains and nine non-tuberculous Mycobacterium (NTM) strains (four M. avium complex, one M. bovis Bacillus Calmette-Guérin (BCG), one M. chelonae, one M. fortuitum and two M. kansasii). Principal component analysis readily distinguished the metabolomes between MTB and NTM. Using multivariate and univariate analysis, 24 metabolites with significantly higher levels in MTB were identified. While seven metabolites were identified by tandem mass spectrometry (MS/MS), the other 17 metabolites were unidentified by MS/MS against database matching, suggesting that they may be potentially novel compounds. One metabolite was identified as dexpanthenol, the alcohol analog of pantothenic acid (vitamin B5), which was not known to be produced by bacteria previously. Four metabolites were identified as 1-tuberculosinyladenosine (1-TbAd), a product of the virulence-associated enzyme Rv3378c, and three previously undescribed derivatives of 1-TbAd. Two derivatives differ from 1-TbAd by the ribose group of the nucleoside while the other likely differs by the base. The remaining two metabolites were identified as a tetrapeptide, Val-His-Glu-His, and a monoacylglycerophosphoglycerol, phosphatidylglycerol (PG) (16∶0/0∶0), respectively. Further studies on the chemical structure and biosynthetic pathway of these MTB-specific metabolites would help understand their biological functions. Studies on clinical samples from tuberculosis patients are required to explore for their potential role as diagnostic biomarkers. PMID

  12. Profiling of Altered Metabolomic States in Nicotiana tabacum Cells Induced by Priming Agents

    Science.gov (United States)

    Mhlongo, Msizi I.; Steenkamp, Paul A.; Piater, Lizelle A.; Madala, Ntakadzeni E.; Dubery, Ian A.

    2016-01-01

    Metabolomics has developed into a valuable tool for advancing our understanding of plant metabolism. Plant innate immune defenses can be activated and enhanced so that, subsequent to being pre-sensitized, plants are able to launch a stronger and faster defense response upon exposure to pathogenic microorganisms, a phenomenon known as priming. Here, three contrasting chemical activators, namely acibenzolar-S-methyl, azelaic acid and riboflavin, were used to induce a primed state in Nicotiana tabacum cells. Identified biomarkers were then compared to responses induced by three phytohormones—abscisic acid, methyljasmonate, and salicylic acid. Altered metabolomes were studied using a metabolite fingerprinting approach based on liquid chromatography and mass spectrometry. Multivariate data models indicated that these inducers cause time-dependent metabolic perturbations in the cultured cells and revealed biomarkers of which the levels are affected by these agents. A total of 34 metabolites were annotated from the mass spectral data and online databases. Venn diagrams were used to identify common biomarkers as well as those unique to a specific agent. Results implicate 20 cinnamic acid derivatives conjugated to (i) quinic acid (chlorogenic acids), (ii) tyramine, (iii) polyamines, or (iv) glucose as discriminatory biomarkers of priming in tobacco cells. Functional roles for most of these metabolites in plant defense responses could thus be proposed. Metabolites induced by the activators belong to the early phenylpropanoid pathway, which indicates that different stimuli can activate similar pathways but with different metabolite fingerprints. Possible linkages to phytohormone-dependent pathways at a metabolomic level were indicated in the case of cells treated with salicylic acid and methyljasmonate. The results contribute to a better understanding of the priming phenomenon and advance our knowledge of cinnamic acid derivatives as versatile defense metabolites. PMID

  13. Plant Metabolomics: An Indispensable System Biology Tool for Plant Science

    OpenAIRE

    Jun Hong; Litao Yang; Dabing Zhang; Jianxin Shi

    2016-01-01

    As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plan...

  14. Metabolomic Fingerprint of Heart Failure with Preserved Ejection Fraction

    OpenAIRE

    Beshay N Zordoky; Sung, Miranda M.; Justin Ezekowitz; Rupasri Mandal; Beomsoo Han; Trent C Bjorndahl; Souhaila Bouatra; Todd Anderson; Oudit, Gavin Y.; Wishart, David S.; Jason R.B. Dyck

    2015-01-01

    Background Heart failure (HF) with preserved ejection fraction (HFpEF) is increasingly recognized as an important clinical entity. Preclinical studies have shown differences in the pathophysiology between HFpEF and HF with reduced ejection fraction (HFrEF). Therefore, we hypothesized that a systematic metabolomic analysis would reveal a novel metabolomic fingerprint of HFpEF that will help understand its pathophysiology and assist in establishing new biomarkers for its diagnosis. Methods and ...

  15. Metabolomic Studies of Oral Biofilm, Oral Cancer, and Beyond

    OpenAIRE

    Jumpei Washio; Nobuhiro Takahashi

    2016-01-01

    Oral diseases are known to be closely associated with oral biofilm metabolism, while cancer tissue is reported to possess specific metabolism such as the ‘Warburg effect’. Metabolomics might be a useful method for clarifying the whole metabolic systems that operate in oral biofilm and oral cancer, however, technical limitations have hampered such research. Fortunately, metabolomics techniques have developed rapidly in the past decade, which has helped to solve these difficulties. In vivo meta...

  16. Metabolomic characteristics of Catharanthus roseus plants in time and space

    OpenAIRE

    Qifang, Pan

    2014-01-01

    The thesis aims at combining metabolomics with other methods to investigate the regulation of the TIA biosynthesis and how this is connected with other pathways and the plant’s physiology and development. It reviews the biosynthesis studies of Catharanthus roseus. An HPLC method is described for both precursors and alkaloids which was validated to analyze alkaloid contents in different organs, its relationship with leaf age and growth of C. roseus plants. A metabolomics investigation of C. ro...

  17. Metabolomics approach for discovering disease biomarkers and understanding metabolic pathway

    Directory of Open Access Journals (Sweden)

    Jeeyoun Jung

    2011-12-01

    Full Text Available Metabolomics, the multi-targeted analysis of endogenous metabolites from biological samples, can be efficiently applied to screen disease biomarkers and investigate pathophysiological processes. Metabolites change rapidly in response to physiological perturbations, making them the closest link to disease phenotypes. This study explored the role of metabolomics in gaining mechanistic insight into disease processes and in searching for novel biomarkers of human diseases

  18. SMART: Statistical Metabolomics Analysis-An R Tool.

    Science.gov (United States)

    Liang, Yu-Jen; Lin, Yu-Ting; Chen, Chia-Wei; Lin, Chien-Wei; Chao, Kun-Mao; Pan, Wen-Harn; Yang, Hsin-Chou

    2016-06-21

    Metabolomics data provide unprecedented opportunities to decipher metabolic mechanisms by analyzing hundreds to thousands of metabolites. Data quality concerns and complex batch effects in metabolomics must be appropriately addressed through statistical analysis. This study developed an integrated analysis tool for metabolomics studies to streamline the complete analysis flow from initial data preprocessing to downstream association analysis. We developed Statistical Metabolomics Analysis-An R Tool (SMART), which can analyze input files with different formats, visually represent various types of data features, implement peak alignment and annotation, conduct quality control for samples and peaks, explore batch effects, and perform association analysis. A pharmacometabolomics study of antihypertensive medication was conducted and data were analyzed using SMART. Neuromedin N was identified as a metabolite significantly associated with angiotensin-converting-enzyme inhibitors in our metabolome-wide association analysis (p = 1.56 × 10(-4) in an analysis of covariance (ANCOVA) with an adjustment for unknown latent groups and p = 1.02 × 10(-4) in an ANCOVA with an adjustment for hidden substructures). This endogenous neuropeptide is highly related to neurotensin and neuromedin U, which are involved in blood pressure regulation and smooth muscle contraction. The SMART software, a user guide, and example data can be downloaded from http://www.stat.sinica.edu.tw/hsinchou/metabolomics/SMART.htm . PMID:27248514

  19. Molecular cartography in acute Chlamydia pneumoniae infections--a non-targeted metabolomics approach.

    Science.gov (United States)

    Müller, Constanze; Dietz, Inga; Tziotis, Dimitrios; Moritz, Franco; Rupp, Jan; Schmitt-Kopplin, Philippe

    2013-06-01

    Infections with Chlamydia pneumoniae cause several respiratory diseases, such as community-acquired pneumonia, bronchitis or sinusitis. Here, we present an integrated non-targeted metabolomics analysis applying ultra-high-resolution mass spectrometry and ultra-performance liquid chromatography mass spectrometry to determine metabolite alterations in C. pneumoniae-infected HEp-2 cells. Most important permutations are elaborated using uni- and multivariate statistical analysis, logD retention time regression and mass defect-based network analysis. Classes of metabolites showing high variations upon infection are lipids, carbohydrates and amino acids. Moreover, we observed several non-annotated compounds as predominantly abundant after infection, which are promising biomarker candidates for drug-target and diagnostic research.

  20. New frontiers in pharmaceutical analysis: A metabolomic approach to check batch compliance of complex products based on natural substances.

    Science.gov (United States)

    Mattoli, L; Burico, M; Fodaroni, G; Tamimi, S; Bedont, S; Traldi, P; Stocchero, M

    2016-07-15

    Natural substances, particularly medicinal plants and their extracts, are still today intended as source for new Active Pharmaceutical Ingredients (APIs). Alternatively they can be validly employed to prepare medicines, food supplements or medical devices. The most adopted analytical approach used to verify quality of natural substances like medicinal plants is based still today on the traditional quantitative determination of marker compounds and/or active ingredients, besides the acquisition of a fingerprint by TLC, NIR, HPLC, GC. Here a new analytical approach based on untargeted metabolomic fingerprinting by means of Mass Spectrometry (MS) to verify the quality of grinTuss adulti syrup, a complex products based on medicinal plants, is proposed. Recently, untargeted metabolomic has been successfully applied to assess quality of natural substances, plant extracts, as well as corresponding formulated products, being the complexity a resource but not necessarily a limit. The untargeted metabolomic fingerprinting includes the monitoring of the main constituents, giving weighted relevance to the most abundant ones, but also considering minor components, that might be notable in view of an integrated - often synergistic - effect on the biological system. Two different years of production were investigated. The collected samples were analyzed by Flow Injection ElectroSpray Ionization Mass Spectrometry Analysis (FIA-ESI-MS) and a suitable data processing procedure was developed to transform the MS spectra into robust fingerprints. Multivariate Statistical Process Control (MSPC) was applied in order to obtain multivariate control charts that were validated to prove the effectiveness of the proposed method. PMID:27155737

  1. Comparative metabolomics in Glycine max and Glycine soja under salt stress to reveal the phenotypes of their offspring.

    Science.gov (United States)

    Lu, Yonghai; Lam, Honming; Pi, Erxu; Zhan, Qinglei; Tsai, Sauna; Wang, Chunmei; Kwan, Yiuwa; Ngai, Saiming

    2013-09-11

    Metabolomics is developing as an important functional genomics tool for understanding plant systems' response to genetic and environmental changes. Here, we characterized the metabolic changes of cultivated soybean C08 (Glycine max L. Merr) and wild soybean W05 (Glycine soja Sieb.et Zucc.) under salt stress using MS-based metabolomics, in order to reveal the phenotypes of their eight hybrid offspring (9H0086, 9H0124, 9H0391, 9H0736, 9H0380, 9H0400, 9H0434, and 9H0590). Total small molecule extracts of soybean seedling leaves were profiled by gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-Fourier transform mass spectrometry (LC-FT/MS). We found that wild soybean contained higher amounts of disaccharides, sugar alcohols, and acetylated amino acids than cultivated soybean, but with lower amounts of monosaccharides, carboxylic acids, and unsaturated fatty acids. Further investigations demonstrated that the ability of soybean to tolerate salt was mainly based on synthesis of compatible solutes, induction of reactive oxygen species (ROS) scavengers, cell membrane modifications, and induction of plant hormones. On the basis of metabolic phenotype, the salt-tolerance abilities of 9H0086, 9H0124, 9H0391, 9H0736, 9H0380, 9H0400, 9H0434, and 9H0590 were discriminated. Our results demonstrated that MS-based metabolomics provides a fast and powerful approach to discriminate the salt-tolerance characteristics of soybeans.

  2. Metabolomic phenotyping of af cloned pig model

    DEFF Research Database (Denmark)

    Clausen, Morten Rahr; Christensen, Kirstine Lykke; Hedemann, Mette Skou;

    2011-01-01

    Background Pigs are widely used as models for human physiological changes in intervention studies, because of the close resemblance between human and porcine physiology and the high degree of experimental control when using an animal model. Cloned animals have, in principle, identical genotypes...... and possibly also phenotypes and this offer an extra level of experimental control which could possibly make them a desirable tool for intervention studies. Therefore, in the present study, we address how phenotype and phenotypic variation is affected by cloning, through comparison of cloned pigs and normal...... outbred pigs. Results The metabolic phenotype of cloned pigs (n = 5) was for the first time elucidated by nuclear magnetic resonance (NMR)-based metabolomic analysis of multiple bio-fluids including plasma, bile and urine. The metabolic phenotype of the cloned pigs was compared with normal outbred pigs (n...

  3. Robust Early Pregnancy Prediction of Later Preeclampsia Using Metabolomic Biomarkers.

    LENUS (Irish Health Repository)

    Kenny, Louise C

    2010-09-13

    Preeclampsia is a pregnancy-specific syndrome that causes substantial maternal and fetal morbidity and mortality. The etiology is incompletely understood, and there is no clinically useful screening test. Current metabolomic technologies have allowed the establishment of metabolic signatures of preeclampsia in early pregnancy. Here, a 2-phase discovery\\/validation metabolic profiling study was performed. In the discovery phase, a nested case-control study was designed, using samples obtained at 15±1 weeks\\' gestation from 60 women who subsequently developed preeclampsia and 60 controls taking part in the prospective Screening for Pregnancy Endpoints cohort study. Controls were proportionally population matched for age, ethnicity, and body mass index at booking. Plasma samples were analyzed using ultra performance liquid chromatography-mass spectrometry. A multivariate predictive model combining 14 metabolites gave an odds ratio for developing preeclampsia of 36 (95% CI: 12 to 108), with an area under the receiver operator characteristic curve of 0.94. These findings were then validated using an independent case-control study on plasma obtained at 15±1 weeks from 39 women who subsequently developed preeclampsia and 40 similarly matched controls from a participating center in a different country. The same 14 metabolites produced an odds ratio of 23 (95% CI: 7 to 73) with an area under receiver operator characteristic curve of 0.92. The finding of a consistent discriminatory metabolite signature in early pregnancy plasma preceding the onset of preeclampsia offers insight into disease pathogenesis and offers the tantalizing promise of a robust presymptomatic screening test.

  4. Robust early pregnancy prediction of later preeclampsia using metabolomic biomarkers.

    LENUS (Irish Health Repository)

    Kenny, Louise C

    2012-01-31

    Preeclampsia is a pregnancy-specific syndrome that causes substantial maternal and fetal morbidity and mortality. The etiology is incompletely understood, and there is no clinically useful screening test. Current metabolomic technologies have allowed the establishment of metabolic signatures of preeclampsia in early pregnancy. Here, a 2-phase discovery\\/validation metabolic profiling study was performed. In the discovery phase, a nested case-control study was designed, using samples obtained at 15+\\/-1 weeks\\' gestation from 60 women who subsequently developed preeclampsia and 60 controls taking part in the prospective Screening for Pregnancy Endpoints cohort study. Controls were proportionally population matched for age, ethnicity, and body mass index at booking. Plasma samples were analyzed using ultra performance liquid chromatography-mass spectrometry. A multivariate predictive model combining 14 metabolites gave an odds ratio for developing preeclampsia of 36 (95% CI: 12 to 108), with an area under the receiver operator characteristic curve of 0.94. These findings were then validated using an independent case-control study on plasma obtained at 15+\\/-1 weeks from 39 women who subsequently developed preeclampsia and 40 similarly matched controls from a participating center in a different country. The same 14 metabolites produced an odds ratio of 23 (95% CI: 7 to 73) with an area under receiver operator characteristic curve of 0.92. The finding of a consistent discriminatory metabolite signature in early pregnancy plasma preceding the onset of preeclampsia offers insight into disease pathogenesis and offers the tantalizing promise of a robust presymptomatic screening test.

  5. Metabolomic analysis of sex specific metabolites in gonads of the mussel, Mytilus edulis.

    Science.gov (United States)

    Cubero-Leon, Elena; Minier, Christophe; Rotchell, Jeanette M; Hill, Elizabeth M

    2012-06-01

    Marine mussels have been used as sentinel organisms to monitor exposure to a variety of chemical contaminants, including endocrine disrupting chemicals, in the aquatic environment. Although they are an important species for use in ecotoxicology investigations, information on their reproductive physiology and biochemistry is fragmentary. Mass spectrometry-based profiling techniques are increasingly being used to study how the metabolome of an organism changes as a result of tissue differentiation, disease or in response to environmental stressors. In this study, ultraperformance liquid chromatography-time-of-flight-mass spectrometry (UPLC-TOFMS) was used to investigate sex specific differences in the mussel metabolome in order to further investigate the reproductive physiology of this species. Using this method, a comparison of female and male mantle tissues containing mature gonad, revealed significant differences in glycerophosphatidylcholine (PC) and lysophosphatidylcholine (LPC) metabolites. A number of other unidentified metabolites, including those putatively identified as conjugated sterols, were also differentially expressed between male and female mantle/gonadal tissue. PMID:22475636

  6. Analysis of Metabolomics Datasets with High-Performance Computing and Metabolite Atlases

    Directory of Open Access Journals (Sweden)

    Yushu Yao

    2015-07-01

    Full Text Available Even with the widespread use of liquid chromatography mass spectrometry (LC/MS based metabolomics, there are still a number of challenges facing this promising technique. Many, diverse experimental workflows exist; yet there is a lack of infrastructure and systems for tracking and sharing of information. Here, we describe the Metabolite Atlas framework and interface that provides highly-efficient, web-based access to raw mass spectrometry data in concert with assertions about chemicals detected to help address some of these challenges. This integration, by design, enables experimentalists to explore their raw data, specify and refine features annotations such that they can be leveraged for future experiments. Fast queries of the data through the web using SciDB, a parallelized database for high performance computing, make this process operate quickly. By using scripting containers, such as IPython or Jupyter, to analyze the data, scientists can utilize a wide variety of freely available graphing, statistics, and information management resources. In addition, the interfaces facilitate integration with systems biology tools to ultimately link metabolomics data with biological models.

  7. Seed metabolomic study reveals significant metabolite variations and correlations among different soybean cultivars

    Institute of Scientific and Technical Information of China (English)

    Hong Lin; Jun Rao; Jianxin Shi; Chaoyang Hu; Fang Cheng; Zoe AWilson; Dabing Zhang; Sheng Quan

    2014-01-01

    Soybean [Glycine max (L.) Merr.] is one of the world’s major crops, and soybean seeds are a rich and important resource for proteins and oils. While “omics”studies, such as genomics, transcriptomics, and proteomics, have been widely applied in soybean molecular research, fewer metabolomic studies have been conducted for large-scale detection of low molecular weight metabolites, especial y in soybean seeds. In this study, we investigated the seed metabolomes of 29 common soybean cultivars through combined gas chromatography-mass spectrometry and ultra-performance liquid chromatography-tandem mass spectrometry. One hundred sixty-nine named metabolites were identified and subsequently used to construct a metabolic network of mature soybean seed. Among the 169 detected metabolites, 104 were found to be significantly variable in their levels across tested cultivars. Metabolite markers that could be used to distinguish genetical y related soybean cultivars were also identified, and metabolite-metabolite correlation analysis revealed some significant associations within the same or among different metabolite groups. Findings from this work may potentially provide the basis for further studies on both soybean seed metabolism and metabolic engineering to improve soybean seed quality and yield.

  8. Exploring natural variation of Pinus pinaster Aiton using metabolomics: Is it possible to identify the region of origin of a pine from its metabolites?

    Science.gov (United States)

    Meijón, Mónica; Feito, Isabel; Oravec, Michal; Delatorre, Carolina; Weckwerth, Wolfram; Majada, Juan; Valledor, Luis

    2016-02-01

    Natural variation of the metabolome of Pinus pinaster was studied to improve understanding of its role in the adaptation process and phenotypic diversity. The metabolomes of needles and the apical and basal section of buds were analysed in ten provenances of P. pinaster, selected from France, Spain and Morocco, grown in a common garden for 5 years. The employment of complementary mass spectrometry techniques (GC-MS and LC-Orbitrap-MS) together with bioinformatics tools allowed the reliable quantification of 2403 molecular masses. The analysis of the metabolome showed that differences were maintained across provenances and that the metabolites characteristic of each organ are mainly related to amino acid metabolism, while provenances were distinguishable essentially through secondary metabolism when organs were analysed independently. Integrative analyses of metabolome, environmental and growth data provided a comprehensive picture of adaptation plasticity in conifers. These analyses defined two major groups of plants, distinguished by secondary metabolism: that is, either Atlantic or Mediterranean provenance. Needles were the most sensitive organ, where strong correlations were found between flavonoids and the water regime of the geographic origin of the provenance. The data obtained point to genome specialization aimed at maximizing the drought stress resistance of trees depending on their origin. PMID:26756581

  9. Applications of NMR-based metabolomics in biological and environmental research

    Science.gov (United States)

    As a complimentary tool to other omics platforms, metabolomics is increasingly being used by biologists to study the dynamic response of biological systems (cells, tissues, or whole organisms) under diverse physiological or pathological conditions. Metabolomics deals with the qu...

  10. Metabolomics in Toxicology and Preclinical Research, a t4 Workshop Report

    Science.gov (United States)

    Metabolomics, the comprehensive analysis of metabolites in a biological system, provides detailed information about the biochemical/physiological condition of the test system, and of changes affected by anthropogenic chemicals. Metabolomic analysis is used in many fields, ranging...

  11. Biomarker Identification and Pathway Analysis by Serum Metabolomics of Lung Cancer

    Directory of Open Access Journals (Sweden)

    Yingrong Chen

    2015-01-01

    Full Text Available Lung cancer is one of the most common causes of cancer death, for which no validated tumor biomarker is sufficiently accurate to be useful for diagnosis. Additionally, the metabolic alterations associated with the disease are unclear. In this study, we investigated the construction, interaction, and pathways of potential lung cancer biomarkers using metabolomics pathway analysis based on the Kyoto Encyclopedia of Genes and Genomes database and the Human Metabolome Database to identify the top altered pathways for analysis and visualization. We constructed a diagnostic model using potential serum biomarkers from patients with lung cancer. We assessed their specificity and sensitivity according to the area under the curve of the receiver operator characteristic (ROC curves, which could be used to distinguish patients with lung cancer from normal subjects. The pathway analysis indicated that sphingolipid metabolism was the top altered pathway in lung cancer. ROC curve analysis indicated that glycerophospho-N-arachidonoyl ethanolamine (GpAEA and sphingosine were potential sensitive and specific biomarkers for lung cancer diagnosis and prognosis. Compared with the traditional lung cancer diagnostic biomarkers carcinoembryonic antigen and cytokeratin 19 fragment, GpAEA and sphingosine were as good or more appropriate for detecting lung cancer. We report our identification of potential metabolic diagnostic and prognostic biomarkers of lung cancer and clarify the metabolic alterations in lung cancer.

  12. Determination of steroids in human plasma using temperature-dependent inclusion chromatography for metabolomic investigations.

    Science.gov (United States)

    Zarzycki, Paweł K; Kulhanek, Kathrin M; Smith, Roger; Clifton, Vicki L

    2006-02-01

    Clinical and metabolomic investigations of complex human fluids require cost-effective methodologies that can rapidly assess the steroid hormone milieu of individual samples. The efficiency of quantification of many steroids is limited using immunoassays as these methods can only measure a single component of biological samples and are dependent upon the specificity of the antiserum used in the protocol. In this study, we optimised the solid-phase extraction protocol for the extraction of a range of steroids of varied polarity from estetrol to progesterone from human plasma. The final SPE procedure for efficient extraction of steroids was a washing mixture of 5 ml of 30% methanol and an elution solvent of 2 ml of 100% methanol using 0.5 g C-18 cartridges. This protocol resulted in a high recovery rate, ranging from 85.2 to 99.9% for both the internal standard (7,8-dimethoxyflavone) and steroids of interest. We also improved the separation methodology of our previous work using temperature dependent inclusion chromatography with a mobile phase composition of 35% acetonitrile and 12 mM of beta-cyclodextrin at 29 degrees C. Under these conditions most of the fluid components including estetrol were detected in the first 10 min with progesterone appearing at 43 min. This method is simplistic, inexpensive and reproducible with the capabilities of accurate quantification of steroids. Therefore it could have numerous clinical and metabolomic applications. PMID:16364333

  13. Metabolomic assessment of induced and activated chemical defence in the invasive red alga Gracilaria vermiculophylla.

    Science.gov (United States)

    Nylund, Göran M; Weinberger, Florian; Rempt, Martin; Pohnert, Georg

    2011-01-01

    In comparison with terrestrial plants the mechanistic knowledge of chemical defences is poor for marine macroalgae. This restricts our understanding in the chemically mediated interactions that take place between algae and other organisms. Technical advances such as metabolomics, however, enable new approaches towards the characterisation of the chemically mediated interactions of organisms with their environment. We address defence responses in the red alga Gracilaria vermiculophylla using mass spectrometry based metabolomics in combination with bioassays. Being invasive in the north Atlantic this alga is likely to possess chemical defences according to the prediction that well-defended exotics are most likely to become successful invaders in systems dominated by generalist grazers, such as marine macroalgal communities. We investigated the effect of intense herbivore feeding and simulated herbivory by mechanical wounding of the algae. Both processes led to similar changes in the metabolic profile. Feeding experiments with the generalist isopod grazer Idotea baltica showed that mechanical wounding caused a significant increase in grazer resistance. Structure elucidation of the metabolites of which some were up-regulated more than 100 times in the wounded tissue, revealed known and novel eicosanoids as major components. Among these were prostaglandins, hydroxylated fatty acids and arachidonic acid derived conjugated lactones. Bioassays with pure metabolites showed that these eicosanoids are part of the innate defence system of macroalgae, similarly to animal systems. In accordance with an induced defence mechanism application of extracts from wounded tissue caused a significant increase in grazer resistance and the up-regulation of other pathways than in the activated defence. Thus, this study suggests that G. vermiculophylla chemically deters herbivory by two lines of defence, a rapid wound-activated process followed by a slower inducible defence. By unravelling

  14. Serum metabolome and lipidome changes in adult patients with primary dengue infection.

    Directory of Open Access Journals (Sweden)

    Liang Cui

    Full Text Available BACKGROUND: Dengue virus (DENV is the most widespread arbovirus with an estimated 100 million infections occurring every year. Endemic in the tropical and subtropical areas of the world, dengue fever/dengue hemorrhagic fever (DF/DHF is emerging as a major public health concern. The complex array of concurrent host physiologic changes has hampered a complete understanding of underlying molecular mechanisms of dengue pathogenesis. METHODOLOGY/PRINCIPLE FINDINGS: Systems level characterization of serum metabolome and lipidome of adult DF patients at early febrile, defervescence, and convalescent stages of DENV infection was performed using liquid chromatography- and gas chromatography-mass spectrometry. The tractability of following metabolite and lipid changes in a relatively large sample size (n = 44 across three prominent infection stages allowed the identification of critical physiologic changes that coincided with the different stages. Sixty differential metabolites were identified in our metabolomics analysis and the main metabolite classes were free fatty acids, acylcarnitines, phospholipids, and amino acids. Major perturbed metabolic pathways included fatty acid biosynthesis and β-oxidation, phospholipid catabolism, steroid hormone pathway, etc., suggesting the multifactorial nature of human host responses. Analysis of phospholipids and sphingolipids verified the temporal trends and revealed association with lymphocytes and platelets numbers. These metabolites were significantly perturbed during the early stages, and normalized to control levels at convalescent stage, suggesting their potential utility as prognostic markers. CONCLUSIONS/SIGNIFICANCE: DENV infection causes temporally distinct serum metabolome and lipidome changes, and many of the differential metabolites are involved in acute inflammatory responses. Our global analyses revealed early anti-inflammatory responses working in concert to modulate early pro-inflammatory processes

  15. Influence of Missing Values Substitutes on Multivariate Analysis of Metabolomics Data

    Directory of Open Access Journals (Sweden)

    Piotr S. Gromski

    2014-06-01

    Full Text Available Missing values are known to be problematic for the analysis of gas chromatography-mass spectrometry (GC-MS metabolomics data. Typically these values cover about 10%–20% of all data and can originate from various backgrounds, including analytical, computational, as well as biological. Currently, the most well known substitute for missing values is a mean imputation. In fact, some researchers consider this aspect of data analysis in their metabolomics pipeline as so routine that they do not even mention using this replacement approach. However, this may have a significant influence on the data analysis output(s and might be highly sensitive to the distribution of samples between different classes. Therefore, in this study we have analysed different substitutes of missing values namely: zero, mean, median, k-nearest neighbours (kNN and random forest (RF imputation, in terms of their influence on unsupervised and supervised learning and, thus, their impact on the final output(s in terms of biological interpretation. These comparisons have been demonstrated both visually and computationally (classification rate to support our findings. The results show that the selection of the replacement methods to impute missing values may have a considerable effect on the classification accuracy, if performed incorrectly this may negatively influence the biomarkers selected for an early disease diagnosis or identification of cancer related metabolites. In the case of GC-MS metabolomics data studied here our findings recommend that RF should be favored as an imputation of missing value over the other tested methods. This approach displayed excellent results in terms of classification rate for both supervised methods namely: principal components-linear discriminant analysis (PC-LDA (98.02% and partial least squares-discriminant analysis (PLS-DA (97.96% outperforming other imputation methods.

  16. Towards Improving Point-of-Care Diagnosis of Non-malaria Febrile Illness: A Metabolomics Approach.

    Directory of Open Access Journals (Sweden)

    Saskia Decuypere

    2016-03-01

    Full Text Available Non-malaria febrile illnesses such as bacterial bloodstream infections (BSI are a leading cause of disease and mortality in the tropics. However, there are no reliable, simple diagnostic tests for identifying BSI or other severe non-malaria febrile illnesses. We hypothesized that different infectious agents responsible for severe febrile illness would impact on the host metabolome in different ways, and investigated the potential of plasma metabolites for diagnosis of non-malaria febrile illness.We conducted a comprehensive mass-spectrometry based metabolomics analysis of the plasma of 61 children with severe febrile illness from a malaria-endemic rural African setting. Metabolite features characteristic for non-malaria febrile illness, BSI, severe anemia and poor clinical outcome were identified by receiver operating curve analysis.The plasma metabolome profile of malaria and non-malaria patients revealed fundamental differences in host response, including a differential activation of the hypothalamic-pituitary-adrenal axis. A simple corticosteroid signature was a good classifier of severe malaria and non-malaria febrile patients (AUC 0.82, 95% CI: 0.70-0.93. Patients with BSI were characterized by upregulated plasma bile metabolites; a signature of two bile metabolites was estimated to have a sensitivity of 98.1% (95% CI: 80.2-100 and a specificity of 82.9% (95% CI: 54.7-99.9 to detect BSI in children younger than 5 years. This BSI signature demonstrates that host metabolites can have a superior diagnostic sensitivity compared to pathogen-detecting tests to identify infections characterized by low pathogen load such as BSI.This study demonstrates the potential use of plasma metabolites to identify causality in children with severe febrile illness in malaria-endemic settings.

  17. The Swine Plasma Metabolome Chronicles "Many Days" Biological Timing and Functions Linked to Growth.

    Directory of Open Access Journals (Sweden)

    Timothy G Bromage

    Full Text Available The paradigm of chronobiology is based almost wholly upon the daily biological clock, or circadian rhythm, which has been the focus of intense molecular, cellular, pharmacological, and behavioral, research. However, the circadian rhythm does not explain biological timings related to fundamental aspects of life history such as rates of tissue/organ/body size development and control of the timing of life stages such as gestation length, age at maturity, and lifespan. This suggests that another biological timing mechanism is at work. Here we focus on a "many days" (multidien chronobiological period first observed as enigmatic recurring growth lines in developing mammalian tooth enamel that is strongly associate with all adult tissue, organ, and body masses as well as life history attributes such as gestation length, age at maturity, weaning, and lifespan, particularly among the well studied primates. Yet, knowledge of the biological factors regulating the patterning of mammalian life, such as the development of body size and life history structure, does not exist. To identify underlying molecular mechanisms we performed metabolome and genome analyses from blood plasma in domestic pigs. We show that blood plasma metabolites and small non-coding RNA (sncRNA drawn from 33 domestic pigs over a two-week period strongly oscillate on a 5-day multidien rhythm, as does the pig enamel rhythm. Metabolomics and genomics pathway analyses actually reveal two 5-day rhythms, one related to growth in which biological functions include cell proliferation, apoptosis, and transcription regulation/protein synthesis, and another 5-day rhythm related to degradative pathways that follows three days later. Our results provide experimental confirmation of a 5-day multidien rhythm in the domestic pig linking the periodic growth of enamel with oscillations of the metabolome and genome. This association reveals a new class of chronobiological rhythm and a snapshot of the

  18. The Swine Plasma Metabolome Chronicles "Many Days" Biological Timing and Functions Linked to Growth.

    Science.gov (United States)

    Bromage, Timothy G; Idaghdour, Youssef; Lacruz, Rodrigo S; Crenshaw, Thomas D; Ovsiy, Olexandra; Rotter, Björn; Hoffmeier, Klaus; Schrenk, Friedemann

    2016-01-01

    The paradigm of chronobiology is based almost wholly upon the daily biological clock, or circadian rhythm, which has been the focus of intense molecular, cellular, pharmacological, and behavioral, research. However, the circadian rhythm does not explain biological timings related to fundamental aspects of life history such as rates of tissue/organ/body size development and control of the timing of life stages such as gestation length, age at maturity, and lifespan. This suggests that another biological timing mechanism is at work. Here we focus on a "many days" (multidien) chronobiological period first observed as enigmatic recurring growth lines in developing mammalian tooth enamel that is strongly associate with all adult tissue, organ, and body masses as well as life history attributes such as gestation length, age at maturity, weaning, and lifespan, particularly among the well studied primates. Yet, knowledge of the biological factors regulating the patterning of mammalian life, such as the development of body size and life history structure, does not exist. To identify underlying molecular mechanisms we performed metabolome and genome analyses from blood plasma in domestic pigs. We show that blood plasma metabolites and small non-coding RNA (sncRNA) drawn from 33 domestic pigs over a two-week period strongly oscillate on a 5-day multidien rhythm, as does the pig enamel rhythm. Metabolomics and genomics pathway analyses actually reveal two 5-day rhythms, one related to growth in which biological functions include cell proliferation, apoptosis, and transcription regulation/protein synthesis, and another 5-day rhythm related to degradative pathways that follows three days later. Our results provide experimental confirmation of a 5-day multidien rhythm in the domestic pig linking the periodic growth of enamel with oscillations of the metabolome and genome. This association reveals a new class of chronobiological rhythm and a snapshot of the biological bases that

  19. Implications of genotypic differences in the generation of a urinary metabolomics radiation signature.

    Science.gov (United States)

    Laiakis, Evagelia C; Pannkuk, Evan L; Diaz-Rubio, Maria Elena; Wang, Yi-Wen; Mak, Tytus D; Simbulan-Rosenthal, Cynthia M; Brenner, David J; Fornace, Albert J

    2016-06-01

    The increased threat of radiological terrorism and accidental nuclear exposures, together with increased usage of radiation-based medical procedures, has made necessary the development of minimally invasive methods for rapid identification of exposed individuals. Genetically predisposed radiosensitive individuals comprise a significant number of the population and require specialized attention and treatments after such events. Metabolomics, the assessment of the collective small molecule content in a given biofluid or tissue, has proven effective in the rapid identification of radiation biomarkers and metabolic perturbations. To investigate how the genotypic background may alter the ionizing radiation (IR) signature, we analyzed urine from Parp1(-/-) mice, as a model radiosensitive genotype, exposed to IR by utilizing the analytical power of liquid chromatography coupled with mass spectrometry (LC-MS), as urine has been thoroughly investigated in wild type (WT) mice in previous studies from our laboratory. Samples were collected at days one and three after irradiation, time points that are important for the early and efficient triage of exposed individuals. Time-dependent perturbations in metabolites were observed in the tricarboxylic acid pathway (TCA). Other differentially excreted metabolites included amino acids and metabolites associated with dysregulation of energy metabolism pathways. Time-dependent apoptotic pathway activation between WT and mutant mice following IR exposure may explain the altered excretion patterns, although the origin of the metabolites remains to be determined. This first metabolomics study in urine from radiation exposed genetic mutant animal models provides evidence that this technology can be used to dissect the effects of genotoxic agents on metabolism by assessing easily accessible biofluids and identify biomarkers of radiation exposure. Applications of metabolomics could be incorporated in the future to further elucidate the

  20. AICAR stimulation metabolome widely mimics electrical contraction in isolated rat epitrochlearis muscle.

    Science.gov (United States)

    Miyamoto, Licht; Egawa, Tatsuro; Oshima, Rieko; Kurogi, Eriko; Tomida, Yosuke; Tsuchiya, Koichiro; Hayashi, Tatsuya

    2013-12-15

    Physical exercise has potent therapeutic and preventive effects against metabolic disorders. A number of studies have suggested that 5'-AMP-activated protein kinase (AMPK) plays a pivotal role in regulating carbohydrate and lipid metabolism in contracting skeletal muscles, while several genetically manipulated animal models revealed the significance of AMPK-independent pathways. To elucidate significance of AMPK and AMPK-independent signals in contracting skeletal muscles, we conducted a metabolomic analysis that compared the metabolic effects of 5-aminoimidazole-4-carboxamide-1-β-D-ribonucleoside (AICAR) stimulation with the electrical contraction ex vivo in isolated rat epitrochlearis muscles, in which both α1- and α2-isoforms of AMPK and glucose uptake were equally activated. The metabolomic analysis using capillary electrophoresis time-of-flight mass spectrometry detected 184 peaks and successfully annotated 132 small molecules. AICAR stimulation exhibited high similarity to the electrical contraction in overall metabolites. Principal component analysis (PCA) demonstrated that the major principal component characterized common effects whereas the minor principal component distinguished the difference. PCA and a factor analysis suggested a substantial change in redox status as a result of AMPK activation. We also found a decrease in reduced glutathione levels in both AICAR-stimulated and contracting muscles. The muscle contraction-evoked influences related to the metabolism of amino acids, in particular, aspartate, alanine, or lysine, are supposed to be independent of AMPK activation. Our results substantiate the significance of AMPK activation in contracting skeletal muscles and provide novel evidence that AICAR stimulation closely mimics the metabolomic changes in the contracting skeletal muscles.

  1. Normalization method for metabolomics data using optimal selection of multiple internal standards

    Directory of Open Access Journals (Sweden)

    Yetukuri Laxman

    2007-03-01

    Full Text Available Abstract Background Success of metabolomics as the phenotyping platform largely depends on its ability to detect various sources of biological variability. Removal of platform-specific sources of variability such as systematic error is therefore one of the foremost priorities in data preprocessing. However, chemical diversity of molecular species included in typical metabolic profiling experiments leads to different responses to variations in experimental conditions, making normalization a very demanding task. Results With the aim to remove unwanted systematic variation, we present an approach that utilizes variability information from multiple internal standard compounds to find optimal normalization factor for each individual molecular species detected by metabolomics approach (NOMIS. We demonstrate the method on mouse liver lipidomic profiles using Ultra Performance Liquid Chromatography coupled to high resolution mass spectrometry, and compare its performance to two commonly utilized normalization methods: normalization by l2 norm and by retention time region specific standard compound profiles. The NOMIS method proved superior in its ability to reduce the effect of systematic error across the full spectrum of metabolite peaks. We also demonstrate that the method can be used to select best combinations of standard compounds for normalization. Conclusion Depending on experiment design and biological matrix, the NOMIS method is applicable either as a one-step normalization method or as a two-step method where the normalization parameters, influenced by variabilities of internal standard compounds and their correlation to metabolites, are first calculated from a study conducted in repeatability conditions. The method can also be used in analytical development of metabolomics methods by helping to select best combinations of standard compounds for a particular biological matrix and analytical platform.

  2. Liquid–liquid extraction combined with differential isotope dimethylaminophenacyl labeling for improved metabolomic profiling of organic acids

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Jun; Li, Liang, E-mail: Liang.Li@ualberta.ca

    2013-11-25

    Graphical abstract: -- Highlights: •An improved method for profiling the carboxylic acid sub-metabolome is reported. •Liquid–liquid extraction was used for separating the organic acids from the amines. •{sup 12}C/{sup 13}C-p-dimethylaminophenacyl (DmPA) labeling of the organic acids was carried out on the extract. •Detection interference by amines and labeling efficiency reduction by water were reduced. •About 2500 {sup 12}C/{sup 13}C-peak pairs or putative metabolites could be detected from 20 μL of human urine. -- Abstract: A large fraction of the known human metabolome belong to organic acids. However, comprehensive profiling of the organic acid sub-metabolome is a major analytical challenge. In this work, we report an improved method for detecting organic acid metabolites. This method is based on the use of liquid–liquid extraction (LLE) to selectively extract the organic acids, followed by using differential isotope p-dimethylaminophenacyl (DmPA) labeling of the acid metabolites. The {sup 12}C-/{sup 13}C-labeled samples are analyzed by liquid chromatography Fourier-transform ion cyclotron resonance mass spectrometry (LC–FTICR–MS). It is shown that this LLE DmPA labeling method offers superior performance over the method of direct DmPA labeling of biofluids such as human urine. LLE of organic acids reduces the interference of amine-containing metabolites that may also react with DmPA. It can also remove water in a biofluid that can reduce the labeling efficiency. Using human urine as an example, it is demonstrated that about 2500 peak pairs or putative metabolites could be detected in a 30-min gradient LC–MS run, which is about 3 times more than that detected in a sample prepared using direct DmPA labeling. About 95% of the 1000 or so matched metabolites to the Human Metabolome Database (HMDB) are organic acids. It is further shown that this method can be used to handle as small as 10 μL of urine. We believe that this method opens the

  3. PLS-based and regularization-based methods for the selection of relevant variables in non-targeted metabolomics data

    Directory of Open Access Journals (Sweden)

    Renata Bujak

    2016-07-01

    Full Text Available Non-targeted metabolomics constitutes a part of systems biology and aims to determine many metabolites in complex biological samples. Datasets obtained in non-targeted metabolomics studies are multivariate and high-dimensional due to the sensitivity of mass spectrometry-based detection methods as well as complexity of biological matrices. Proper selection of variables which contribute into group classification is a crucial step, especially in metabolomics studies which are focused on searching for disease biomarker candidates. In the present study, three different statistical approaches were tested using two metabolomics datasets (RH and PH study. Orthogonal projections to latent structures-discriminant analysis (OPLS-DA without and with multiple testing correction as well as least absolute shrinkage and selection operator (LASSO were tested and compared. For the RH study, OPLS-DA model built without multiple testing correction, selected 46 and 218 variables based on VIP criteria using Pareto and UV scaling, respectively. In the case of the PH study, 217 and 320 variables were selected based on VIP criteria using Pareto and UV scaling, respectively. In the RH study, OPLS-DA model built with multiple testing correction, selected 4 and 19 variables as statistically significant in terms of Pareto and UV scaling, respectively. For PH study, 14 and 18 variables were selected based on VIP criteria in terms of Pareto and UV scaling, respectively. Additionally, the concept and fundaments of the least absolute shrinkage and selection operator (LASSO with bootstrap procedure evaluating reproducibility of results, was demonstrated. In the RH and PH study, the LASSO selected 14 and 4 variables with reproducibility between 99.3% and 100%. However, apart from the popularity of PLS-DA and OPLS-DA methods in metabolomics, it should be highlighted that they do not control type I or type II error, but only arbitrarily establish a cut-off value for PLS-DA loadings

  4. Comprehensive analysis of the metabolome of Pseudomonas putida S12 grown on different carbon sources

    NARCIS (Netherlands)

    Werf, M.J. van der; Overkamp, K.M.; Muilwijk, B.; Koek, M.M.; Werff van der - Vat, B.J.C. van der; Jellema, R.H.; Coulier, L.; Hankemeier, T.

    2008-01-01

    Metabolomics is an emerging, powerful, functional genomics technology that involves the comparative non-targeted analysis of the complete set of metabolites in an organism. We have set-up a robust quantitative metabolomics platform that allows the analysis of 'snapshot' metabolomes. In this study, w

  5. The Progress of Metabolomics Study in Traditional Chinese Medicine Research.

    Science.gov (United States)

    Wang, Pengcheng; Wang, Qiuhong; Yang, Bingyou; Zhao, Shan; Kuang, Haixue

    2015-01-01

    Traditional Chinese medicine (TCM) has played important roles in health protection and disease treatment for thousands of years in China and has gained the gradual acceptance of the international community. However, many intricate issues, which cannot be explained by traditional methods, still remain, thus, new ideas and technologies are needed. As an emerging system biology technology, the holistic view adopted by metabolomics is similar to that of TCM, which allows us to investigate TCM with complicated conditions and multiple factors in depth. In this paper, we tried to give a timely and comprehensive update about the methodology progression of metabolomics, as well as its applications, in different fields of TCM studies including quality control, processing, safety and efficacy evaluation. The herbs investigated by metabolomics were selected for detailed examination, including Anemarrhena asphodeloides Bunge, Atractylodes macrocephala Kidd, Pinellia ternate, etc.; furthermore, some valuable results have been obtained and summarized. In conclusion, although the study of metabolomics is at the early phase and requires further scrutiny and validation, it still provides bright prospects to dissect the synergistic action of multiple components from TCM. Overall, with the further development of analytical techniques, especially multi-analysis techniques, we expect that metabolomics will greatly promote TCM research and the establishment of international standards, which is beneficial to TCM modernization. PMID:26477800

  6. Metabolomics: Bridging the Gap between Pharmaceutical Development and Population Health

    Science.gov (United States)

    Tolstikov, Vladimir

    2016-01-01

    Metabolomics has emerged as an essential tool for studying metabolic processes, stratification of patients, as well as illuminating the fundamental metabolic alterations in disease onset, progression, or response to therapeutic intervention. Metabolomics materialized within the pharmaceutical industry as a standalone assay in toxicology and disease pathology and eventually evolved towards aiding in drug discovery and pre-clinical studies via supporting pharmacokinetic and pharmacodynamic characterization of a drug or a candidate. Recent progress in the field is illustrated by coining of the new term—Pharmacometabolomics. Integration of data from metabolomics with large-scale omics along with clinical, molecular, environmental and behavioral analysis has demonstrated the enhanced utility of deconstructing the complexity of health, disease, and pharmaceutical intervention(s), which further highlight it as an essential component of systems medicine. This review presents the current state and trend of metabolomics applications in pharmaceutical development, and highlights the importance and potential of clinical metabolomics as an essential part of multi-omics protocols that are directed towards shaping precision medicine and population health. PMID:27399792

  7. Metabolomics: Bridging the Gap between Pharmaceutical Development and Population Health.

    Science.gov (United States)

    Tolstikov, Vladimir

    2016-01-01

    Metabolomics has emerged as an essential tool for studying metabolic processes, stratification of patients, as well as illuminating the fundamental metabolic alterations in disease onset, progression, or response to therapeutic intervention. Metabolomics materialized within the pharmaceutical industry as a standalone assay in toxicology and disease pathology and eventually evolved towards aiding in drug discovery and pre-clinical studies via supporting pharmacokinetic and pharmacodynamic characterization of a drug or a candidate. Recent progress in the field is illustrated by coining of the new term-Pharmacometabolomics. Integration of data from metabolomics with large-scale omics along with clinical, molecular, environmental and behavioral analysis has demonstrated the enhanced utility of deconstructing the complexity of health, disease, and pharmaceutical intervention(s), which further highlight it as an essential component of systems medicine. This review presents the current state and trend of metabolomics applications in pharmaceutical development, and highlights the importance and potential of clinical metabolomics as an essential part of multi-omics protocols that are directed towards shaping precision medicine and population health. PMID:27399792

  8. Accurate determination of chlorine, bromine, and iodine in sedimentary rock reference samples by radiochemical neutron activation analysis and a detailed comparison with inductively coupled plasma mass spectrometry literature data.

    Science.gov (United States)

    Sekimoto, Shun; Ebihara, Mitsuru

    2013-07-01

    Trace amounts of three halogens (chlorine, bromine, and iodine) were determined using radiochemical neutron activation analysis (RNAA) for nine sedimentary rocks and three rhyolite samples. To obtain high-quality analytical data, the radiochemical procedure of RNAA was improved by lowering the background in gamma-ray spectrometry and completing the chemical procedure more rapidly than in conventional procedures. A comparison of the RNAA data of Br and I with corresponding inductively coupled plasma mass spectrometry (ICPMS) literature data revealed that the values obtained by ICPMS coupled with pyrohydrolysis preconcentration were systematically lower than the RNAA data for some reference samples, suggesting that the quantitative collection of Br and I cannot always be achieved by the pyrohydrolysis for some solid samples. The RNAA data of three halogens can classify sedimentary rock reference samples into two groups (the samples from inland water and those from seawater), implying the geochemical significance of halogen data. PMID:23710630

  9. Accurate determination of chlorine, bromine, and iodine in sedimentary rock reference samples by radiochemical neutron activation analysis and a detailed comparison with inductively coupled plasma mass spectrometry literature data.

    Science.gov (United States)

    Sekimoto, Shun; Ebihara, Mitsuru

    2013-07-01

    Trace amounts of three halogens (chlorine, bromine, and iodine) were determined using radiochemical neutron activation analysis (RNAA) for nine sedimentary rocks and three rhyolite samples. To obtain high-quality analytical data, the radiochemical procedure of RNAA was improved by lowering the background in gamma-ray spectrometry and completing the chemical procedure more rapidly than in conventional procedures. A comparison of the RNAA data of Br and I with corresponding inductively coupled plasma mass spectrometry (ICPMS) literature data revealed that the values obtained by ICPMS coupled with pyrohydrolysis preconcentration were systematically lower than the RNAA data for some reference samples, suggesting that the quantitative collection of Br and I cannot always be achieved by the pyrohydrolysis for some solid samples. The RNAA data of three halogens can classify sedimentary rock reference samples into two groups (the samples from inland water and those from seawater), implying the geochemical significance of halogen data.

  10. A high-throughput metabolomic approach to explore the regulatory effect of mangiferin on metabolic network disturbances of hyperlipidemia rats.

    Science.gov (United States)

    Zhou, Chengyan; Li, Gang; Li, Yanchuan; Gong, Liya; Huang, Yifan; Shi, Zhiping; Du, Shanshan; Li, Ying; Wang, Maoqing; Yin, Jun; Sun, Changhao

    2015-02-01

    This paper was designed to study metabolomic characters of the high-fat diet (HFD)-induced hyperlipidemia and the intervention effects of Mangiferin (MG). In this study, we aimed to investigate the intervention of MG on rats with hyperlipidemia induced by HFD and explore the possible mechanisms of hyperlipidemia. Urine metabolic profiles were analyzed using ultra-performance liquid chromatography/electrospray ionization quadruple time-of-flight mass spectrometry (UPLC-ESI-QTOF-MS) coupled with the principal component analysis (PCA) and partial least squares-discriminate analysis (PLS-DA) models, Heatmap and metabolism pathway analysis. PCA was applied to study the trajectory of the urinary metabolic phenotype of hyperlipidemia rat after administration of MG. The VIP-plot of orthogonal PLS-DA was used for discovering potential biomarkers to clarify the mechanism of MG. Biochemical analyses indicate that MG can alleviate the hyperlipidemia damage. Twenty significantly changed metabolites (potential biomarkers) were found to be reasonable in explaining the action mechanism of MG. The effectiveness of MG on hyperlipidemia is proved using the established metabolomic method and the regulated metabolic pathways involve the TCA cycle, taurine and hypotaurine metabolism, glyoxylate and dicarboxylate metabolism, glycine and serine and threonine metabolism, glycerophospholipid metabolism, primary bile acid biosynthesis etc. The results indicated that MG has a favourable protective effect on HFD-induced hyperlipidemia by adjusting the metabolic disorders. It also suggests that the metabolomic technology is a powerful approach for elucidation of the action mechanisms of MG.

  11. Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization

    Directory of Open Access Journals (Sweden)

    Guerzoni Maria

    2011-10-01

    -chromatography mass spectrometry-solid-phase microextraction and 1H-Nuclear Magnetic Resonance. As shown by Canonical Discriminant Analysis of Principal Coordinates, the levels of volatile organic compounds and free amino acids in faecal and/or urine samples were markedly affected by CD. Conclusion As shown by the parallel microbiology and metabolome approach, the gluten-free diet lasting at least two years did not completely restore the microbiota and, consequently, the metabolome of CD children. Some molecules (e.g., ethyl-acetate and octyl-acetate, some short chain fatty acids and free amino acids, and glutamine seems to be metabolic signatures of CD.

  12. How large is the metabolome? A critical analysis of data exchange practices in chemistry.

    Directory of Open Access Journals (Sweden)

    Tobias Kind

    Full Text Available BACKGROUND: Calculating the metabolome size of species by genome-guided reconstruction of metabolic pathways misses all products from orphan genes and from enzymes lacking annotated genes. Hence, metabolomes need to be determined experimentally. Annotations by mass spectrometry would greatly benefit if peer-reviewed public databases could be queried to compile target lists of structures that already have been reported for a given species. We detail current obstacles to compile such a knowledge base of metabolites. RESULTS: As an example, results are presented for rice. Two rice (oryza sativa subspecies have been fully sequenced, oryza japonica and oryza indica. Several major small molecule databases were compared for listing known rice metabolites comprising PubChem, Chemical Abstracts, Beilstein, Patent databases, Dictionary of Natural Products, SetupX/BinBase, KNApSAcK DB, and finally those databases which were obtained by computational approaches, i.e. RiceCyc, KEGG, and Reactome. More than 5,000 small molecules were retrieved when searching these databases. Unfortunately, most often, genuine rice metabolites were retrieved together with non-metabolite database entries such as pesticides. Overlaps from database compound lists were very difficult to compare because structures were either not encoded in machine-readable format or because compound identifiers were not cross-referenced between databases. CONCLUSIONS: We conclude that present databases are not capable of comprehensively retrieving all known metabolites. Metabolome lists are yet mostly restricted to genome-reconstructed pathways. We suggest that providers of (biochemical databases enrich their database identifiers to PubChem IDs and InChIKeys to enable cross-database queries. In addition, peer-reviewed journal repositories need to mandate submission of structures and spectra in machine readable format to allow automated semantic annotation of articles containing chemical structures

  13. Reconstruction of food webs in biological soil crusts using metabolomics.

    Science.gov (United States)

    Baran, Richard; Brodie, Eoin L.; Mayberry-Lewis, Jazmine; Nunes Da Rocha, Ulisses; Bowen, Benjamin P.; Karaoz, Ulas; Cadillo-Quiroz, Hinsby; Garcia-Pichel, Ferran; Northen, Trent R.

    2015-04-01

    Biological soil crusts (BSCs) are communities of organisms inhabiting the upper layer of soil in arid environments. BSCs persist in a dessicated dormant state for extended periods of time and experience pulsed periods of activity facilitated by infrequent rainfall. Microcoleus vaginatus, a non-diazotrophic filamentous cyanobacterium, is the key primary producer in BSCs in the Colorado Plateau and is an early pioneer in colonizing arid environments. Over decades, BSCs proceed through developmental stages with increasing complexity of constituent microorganisms and macroscopic properties. Metabolic interactions among BSC microorganisms probably play a key role in determining the community dynamics and cycling of carbon and nitrogen. However, these metabolic interactions have not been studied systematically. Towards this goal, exometabolomic analysis was performed using liquid chromatography coupled to tandem mass spectrometry on biological soil crust pore water and spent media of key soil bacterial isolates. Comparison of spent vs. fresh media was used to determine uptake or release of metabolites by specific microbes. To link pore water experiments with isolate studies, metabolite extracts of authentic soil were used as supplements for isolate exometabolomic profiling. Our soil metabolomics methods detected hundreds of metabolites from soils including many novel compounds. Overall, Microcoleus vaginatus was found to release and utilize a broad range of metabolites. Many of these metabolites were also taken up by heterotrophs but there were surprisingly few metabolites uptaken by all isolates. This points to a competition for a small set of central metabolites and specialization of individual heterotrophs towards a diverse pool of available organic nutrients. Overall, these data suggest that understanding the substrate specialization of biological soil crust bacteria can help link community structure to nutrient cycling.

  14. Size-dependent effects of low level cadmium and zinc exposure on the metabolome of the Asian clam, Corbicula fluminea

    Energy Technology Data Exchange (ETDEWEB)