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Sample records for accurate mass metabolomics

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

    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.

    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.

    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. Metabolome analysis - mass spectrometry and microbial primary metabolites

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

    2008-01-01

    While metabolite profiling has been carried out for decades, the scope for metabolite analysis have recently been broadened to aim at all metabolites in a living organism – also referred to as the metabolome. This is a great challenge, which requires versatile analytical technologies that are highly sensitive and specific, and to undertake this challenge mass spectrometry (MS) is among the best candidates. Along with analysis of the metabolome the research area of metabolomics has evolved. Me...

  5. Metabolome analysis - mass spectrometry and microbial primary metabolites

    Højer-Pedersen, Jesper Juul

    2008-01-01

    highly sensitive and specific, and to undertake this challenge mass spectrometry (MS) is among the best candidates. Along with analysis of the metabolome the research area of metabolomics has evolved. Metabolomics combines metabolite profiles, data mining and biochemistry and aims at understanding the...... glucose, galactose or ethanol, and metabolic footprinting by mass spectrometry was used to study the influence of carbon source on the extracellular metabolites. The results showed that footprints clustered according to the carbon source. Advances in technologies for analytical chemistry have mediated...

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

    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...

  7. Quantification in untargeted mass spectrometry-based metabolomics

    van der Kloet, Frans Meindert

    2014-01-01

    The aim of this thesis was to develop concepts and methods to extract qualitative and quantitative information about metabolites from untargeted mass spectrometric data of biological samples. Several typical challenges in data handling were addressed that prevent a straightforward interpretation (data analysis) of the data acquired with different types of mass spectrometric-based metabolomics methods (GC-MS, LC-MS, CE-MS or DI-MS) methods. The critical parameters causing variation in quantita...

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

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

    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.)

  10. The strengths and weaknesses of NMR spectroscopy and mass spectrometry with particular focus on metabolomics research.

    Emwas, Abdul-Hamid M

    2015-01-01

    Mass spectrometry (MS) and nuclear magnetic resonance (NMR) have evolved as the most common techniques in metabolomics studies, and each brings its own advantages and limitations. Unlike MS spectrometry, NMR spectroscopy is quantitative and does not require extra steps for sample preparation, such as separation or derivatization. Although the sensitivity of NMR spectroscopy has increased enormously and improvements continue to emerge steadily, this remains a weak point for NMR compared with MS. MS-based metabolomics provides an excellent approach that can offer a combined sensitivity and selectivity platform for metabolomics research. Moreover, different MS approaches such as different ionization techniques and mass analyzer technology can be used in order to increase the number of metabolites that can be detected. In this chapter, the advantages, limitations, strengths, and weaknesses of NMR and MS as tools applicable to metabolomics research are highlighted. PMID:25677154

  11. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology

    Aretz, Ina; Meierhofer, David

    2016-01-01

    Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology. PMID:27128910

  12. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology

    Ina Aretz

    2016-04-01

    Full Text Available Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

  13. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology.

    Aretz, Ina; Meierhofer, David

    2016-01-01

    Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology. PMID:27128910

  14. Metabolomics

    Kamstrup-Nielsen, Maja Hermann

    ) spectroscopy (Paper II), fluorescence spectroscopy (Paper III) and gas chromatography coupled to mass spectrometry (GC-MS). The principles of the three data acquisition techniques have been briefly described and the methods have been compared. The techniques complement each other, which makes room for data...... analysis (PCA), parallel factor analysis (PARAFAC), PARAFAC2 and partial least squares discriminant analysis (PLS-DA) all being described in depth. It can be a challenge to determine the appropriate number of components in PARAFAC2, since no specific tools have been developed for this purpose. Paper I is a...

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

    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

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

    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

  17. Development of a GC/Quadrupole-Orbitrap Mass Spectrometer, Part II: New Approaches for Discovery Metabolomics

    Peterson, Amelia C.; Balloon, Allison J.; Westphall, Michael S.; Coon, Joshua J.

    2014-01-01

    Identification of unknown peaks in gas chromatography/mass spectrometry (GC/MS)-based discovery metabolomics is challenging, and remains necessary to permit discovery of novel or unexpected metabolites that may elucidate disease processes and/or further our understanding of how genotypes relate to phenotypes. Here, we introduce two new technologies and an analytical workflow that can facilitate the identification of unknown peaks. First, we report on a GC/Quadrupole-Orbitrap mass spectrometer...

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

    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

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

    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

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

    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

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

    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

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

    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.

  3. Preliminary Metabolomic Analysis of Goat Milk from Different Breeds Using Mass Spectrometry

    Mohamad Razlan Abd Rahman

    2015-01-01

    Full Text Available Metabolomics facilitates the identification of numerous metabolites in a sample with mass less than 1 kD. The purpose of this study was to determine the effect of feed on the metabolites in raw goat milk samples obtained from two breeds namely Saanen and Shami that were collected from a farm in Selangor and Negeri Sembilan, Malaysia, respectively. The types of feed given to the goats were recorded. The fat in the samples were removed via centrifugation before analysis using liquid chromatography quadrupole time of flight mass spectrometry (LC-QToF-MS. From the chromatograms obtained the presence of veterinary drug residue, di- and tri-peptides, short and long-chain fatty acids, some components from plants, and insecticide residue were detected using HMP, KEGG, LMP, and METLIN databases identification. It is expected that through metabolomics study it may be possible to formulate the feed and determine the breed that give good quality milk.

  4. Mass Spectrometry-Based Metabolomics to Elucidate Functions in Marine Organisms and Ecosystems

    Sophie Goulitquer; Philippe Potin; Thierry Tonon

    2012-01-01

    Marine systems are very diverse and recognized as being sources of a wide range of biomolecules. This review provides an overview of metabolite profiling based on mass spectrometry (MS) approaches in marine organisms and their environments, focusing on recent advances in the field. We also point out some of the technical challenges that need to be overcome in order to increase applications of metabolomics in marine systems, including extraction of chemical compounds from different matrices an...

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

    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

  6. Neuronal metabolomics by ion mobility mass spectrometry in cocaine self-administering rats after early and late withdrawal.

    Zhang, Xing; Chiu, Veronica M; Todd, Ryan P; Sorg, Barbara A; Hill, Herbert H

    2016-06-01

    The neuronal metabolomes in rat striatum (STR), prefrontal cortex (PFC), and nucleus accumbens (NAC) were analyzed by Hadamard transform ion mobility mass spectrometry (HT-IMMS) in order to reveal global and specific metabolic changes induced by cocaine self-administration after 1-day or 3-week withdrawal. Metabolite features were comprehensively separated and detected using HPLC-IMMS within minutes. Global metabolic differences were observed by PCA for comparisons between cocaine and saline treatments at 1-day withdrawal time. Metabolite features that were significantly changed were selected using PCA loadings' plot and unpaired LLL test and then tentatively identified by accurate m/z, yielding a complete profile of metabolic changes induced by cocaine self-administration. The majority of these changes were found at the 1-day withdrawal time, but several of them endured even after 3-week withdrawal from cocaine, and these changes were generally brain region specific. Putatively identified metabolites associated with oxidative stress and energy metabolism were also specifically investigated. We discovered that the dysregulation of creatine/creatinine was different between the STR and NAC, demonstrating that metabolic alterations are brain region specific. Glutathione and adenosine were also changed in their abundance, and the results agreed with previous studies. In general, this study provided a high-throughput analytical platform to perform metabolomics analyses with putative identifications for altered metabolite features induced by cocaine treatment, therefore revealing additional metabolic targets of cocaine-induced changes after early and extended withdrawal times. PMID:27108279

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

    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

    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

    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.

  10. Mining tandem mass spectral data to develop a more accurate mass error model for peptide identification.

    Fu, Yan; Gao, Wen; He, Simin; Sun, Ruixiang; Zhou, Hu; Zeng, Rong

    2007-01-01

    The assumption on the mass error distribution of fragment ions plays a crucial role in peptide identification by tandem mass spectra. Previous mass error models are the simplistic uniform or normal distribution with empirically set parameter values. In this paper, we propose a more accurate mass error model, namely conditional normal model, and an iterative parameter learning algorithm. The new model is based on two important observations on the mass error distribution, i.e. the linearity between the mean of mass error and the ion mass, and the log-log linearity between the standard deviation of mass error and the peak intensity. To our knowledge, the latter quantitative relationship has never been reported before. Experimental results demonstrate the effectiveness of our approach in accurately quantifying the mass error distribution and the ability of the new model to improve the accuracy of peptide identification. PMID:17990507

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

    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.

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

    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

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

    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...

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

    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.

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

    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.

  16. Development of a GC/Quadrupole-Orbitrap mass spectrometer, part II: new approaches for discovery metabolomics.

    Peterson, Amelia C; Balloon, Allison J; Westphall, Michael S; Coon, Joshua J

    2014-10-21

    Identification of unknown peaks in gas chromatography/mass spectrometry (GC/MS)-based discovery metabolomics is challenging, and remains necessary to permit discovery of novel or unexpected metabolites that may elucidate disease processes and/or further our understanding of how genotypes relate to phenotypes. Here, we introduce two new technologies and an analytical workflow that can facilitate the identification of unknown peaks. First, we report on a GC/Quadrupole-Orbitrap mass spectrometer that provides high mass accuracy, high resolution, and high sensitivity analyte detection. Second, with an "intelligent" data-dependent algorithm, termed molecular-ion directed acquisition (MIDA), we maximize the information content generated from unsupervised tandem MS (MS/MS) and selected ion monitoring (SIM) by directing the MS to target the ions of greatest information content, that is, the most-intact ionic species. We combine these technologies with (13)C- and (15)N-metabolic labeling, multiple derivatization and ionization types, and heuristic filtering of candidate elemental compositions to achieve (1) MS/MS spectra of nearly all intact ion species for structural elucidation, (2) knowledge of carbon and nitrogen atom content for every ion in MS and MS/MS spectra, (3) relative quantification between alternatively labeled samples, and (4) unambiguous annotation of elemental composition. PMID:25166283

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

    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.

  18. Targeted metabolomic analysis of Escherichia coli by desorption electrospray ionization and extractive electrospray ionization mass spectrometry.

    Jackson, Ayanna U; Werner, Sean R; Talaty, Nari; Song, Yishu; Campbell, Karinna; Cooks, R Graham; Morgan, John A

    2008-04-15

    Desorption electrospray ionization (DESI) was utilized to monitor the presence of targeted central carbon metabolites within bacterial cell extracts and the quench supernatant of Escherichia coli. The targeted metabolites were identified through tandem mass spectrometry (MS/MS) product ion scans using collision-induced dissociation in the negative ion mode. Picogram detection limits were achieved for a majority of the metabolites during MS/MS analysis of standard metabolite solutions. In a [U-(13)C]glucose pulse experiment, where uniformly labeled glucose was fed to E. coli, the corresponding fragment ions from labeled metabolites in extracts were generally observed. There was evidence of matrix effects including moderate suppression by other metabolites within the spectra of the labeled and unlabeled extracts. To improve the specificity and sensitivity of detection, optimized in situ ambient chemical reactions using DESI and extractive electrospray ionization (EESI) were carried out for targeted compounds. This study provides the first indication of the potential to perform in situ targeted metabolomics of a bacterial sample via ambient ionization mass spectrometry. PMID:18243123

  19. 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

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

    2008-01-01

    with the specificity of MS up to 84% of the metabolites can be identified in a high mass accuracy ESI-spectrum. A total of 66 metabolites were systematically analyzed by positive and negative ESI-MS/MS with the aim of initiating a spectral library for ESI of microbial metabolites. This systematic...... 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 for extraction of metabolic differences, which can...

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

    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

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

    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.

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

    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%.

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

    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

  4. Metabolomic Approaches in Cancer Epidemiology

    Mukesh Verma

    2015-08-01

    Full Text Available Metabolomics is the study of low molecular weight molecules or metabolites produced within cells and biological systems. It involves technologies such as mass spectrometry (MS and nuclear magnetic resonance spectroscopy (NMR that can measure hundreds of thousands of unique chemical entities (UCEs. The metabolome provides one of the most accurate reflections of cellular activity at the functional level and can be leveraged to discern mechanistic information during normal and disease states. The advantages of metabolomics over other “omics” include its high sensitivity and ability to enable the analysis of relatively few metabolites compared with the number of genes and messenger RNAs (mRNAs. In clinical samples, metabolites are more stable than proteins or RNA. In fact, metabolomic profiling in basic, epidemiologic, clinical, and translational studies has revealed potential new biomarkers of disease and therapeutic outcome and has led to a novel mechanistic understanding of pathogenesis. These potential biomarkers include novel metabolites associated with cancer initiation, regression, and recurrence. Unlike genomics or even proteomics, however, the degree of metabolite complexity and heterogeneity within biological systems presents unique challenges that require specialized skills and resources to overcome. This article discusses epidemiologic studies of altered metabolite profiles in several cancers as well as challenges in the field and potential approaches to overcoming them.

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

    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

  6. Accurate Mass Determinations in Decay Chains with Missing Energy

    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.

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

    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...

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

    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

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

    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

  10. Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification

    Weisbrod, Chad R.; Eng, Jimmy K.; Hoopmann, Michael R.; Baker, Tahmina; Bruce, James E.

    2012-01-01

    FT All Reaction Monitoring (FT-ARM) is a novel approach for the identification and quantification of peptides that relies upon the selectivity of high mass accuracy data and the specificity of peptide fragmentation patterns. An FT-ARM experiment involves continuous, data-independent, high mass accuracy MS/MS acquisition spanning a defined m/z range. Custom software was developed to search peptides against the multiplexed fragmentation spectra by comparing theoretical or empirical fragment ion...

  11. On uplimit of accurate measurement of tau mass

    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.

  12. Accurate mass filtering of ion chromatograms for metabolite identification using a unit mass resolution liquid chromatography/mass spectrometry system.

    Gu, Ming; Wang, Yongdong; Zhao, Xian-Guo; Gu, Zhe-Ming

    2006-01-01

    Acceleration of liquid chromatography/mass spectrometric (LC/MS) analysis for metabolite identification critically relies on effective data processing since the rate of data acquisition is much faster than the rate of data mining. The rapid and accurate identification of metabolite peaks from complex LC/MS data is a key component to speeding up the process. Current approaches routinely use selected ion chromatograms that can suffer severely from matrix effects. This paper describes a new method to automatically extract and filter metabolite-related information from LC/MS data obtained at unit mass resolution in the presence of complex biological matrices. This approach is illustrated by LC/MS analysis of the metabolites of verapamil from a rat microsome incubation spiked with biological matrix (bile). MS data were acquired in profile mode on a unit mass resolution triple-quadrupole instrument, externally calibrated using a unique procedure that corrects for both mass axis and mass spectral peak shape to facilitate metabolite identification with high mass accuracy. Through the double-filtering effects of accurate mass and isotope profile, conventional extracted ion chromatograms corresponding to the parent drug (verapamil at m/z 455), demethylated verapamil (m/z 441), and dealkylated verapamil (m/z 291), that contained substantial false-positive peaks, were simplified into chromatograms that are substantially free from matrix interferences. These filtered chromatograms approach what would have been obtained by using a radioactivity detector to detect radio-labeled metabolites of interest. PMID:16463359

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

    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

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

    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.

  15. Alignment of capillary electrophoresis-mass spectrometry datasets using accurate mass information.

    Nevedomskaya, Ekaterina; Derks, Rico; Deelder, André M; Mayboroda, Oleg A; Palmblad, Magnus

    2009-12-01

    Capillary electrophoresis-mass spectrometry (CE-MS) is a powerful technique for the analysis of small soluble compounds in biological fluids. A major drawback of CE is the poor migration time reproducibility, which makes it difficult to combine data from different experiments and correctly assign compounds. A number of alignment algorithms have been developed but not all of them can cope with large and irregular time shifts between CE-MS runs. Here we present a genetic algorithm designed for alignment of CE-MS data using accurate mass information. The utility of the algorithm was demonstrated on real data, and the results were compared with one of the existing packages. The new algorithm showed a significant reduction of elution time variation in the aligned datasets. The importance of mass accuracy for the performance of the algorithm was also demonstrated by comparing alignments of datasets from a standard time-of-flight (TOF) instrument with those from the new ultrahigh resolution TOF maXis (Bruker Daltonics). PMID:19826795

  16. Mass spectrometry-based metabolomic fingerprinting for screening cold tolerance in Arabidopsis thaliana accessions

    Václavík, L.; Mishra, Anamika; Mishra, Kumud; Hajslova, J.

    2013-01-01

    Roč. 405, č. 8 (2013), s. 2671-2683. ISSN 1618-2642 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0073; GA MŠk OC08055 Institutional support: RVO:67179843 Keywords : cold tolerance * Arabidopsis thaliana * metabolomic fingerprinting * LC-MS * DART-MS * chemometric analysis Subject RIV: EH - Ecology, Behaviour Impact factor: 3.578, year: 2013

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

    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.

  18. Benzoyl chloride derivatization with liquid chromatography-mass spectrometry for targeted metabolomics of neurochemicals in biological samples.

    Wong, Jenny-Marie T; Malec, Paige A; Mabrouk, Omar S; Ro, Jennifer; Dus, Monica; Kennedy, Robert T

    2016-05-13

    Widely targeted metabolomic assays are useful because they provide quantitative data on large groups of related compounds. We report a high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method that utilizes benzoyl chloride labeling for 70 neurologically relevant compounds, including catecholamines, indoleamines, amino acids, polyamines, trace amines, antioxidants, energy compounds, and their metabolites. The method includes neurotransmitters and metabolites found in both vertebrates and insects. This method was applied to analyze microdialysate from rats, human cerebrospinal fluid, human serum, fly tissue homogenate, and fly hemolymph, demonstrating its broad versatility for multiple physiological contexts and model systems. Limits of detection for most assayed compounds were below 10nM, relative standard deviations were below 10%, and carryover was less than 5% for 70 compounds separated in 20min, with a total analysis time of 33min. This broadly applicable method provides robust monitoring of multiple analytes, utilizes small sample sizes, and can be applied to diverse matrices. The assay will be of value for evaluating normal physiological changes in metabolism in neurochemical systems. The results demonstrate the utility of benzoyl chloride labeling with HPLC-MS/MS for widely targeted metabolomics assays. PMID:27083258

  19. Liquid Chromatography–Mass Spectrometry Based Metabolomics Study of Cloned versus Normal Pigs Fed Either Restricted or Ad Libitum High-Energy Diets

    Christensen, Kirstine Lykke; Hedemann, Mette Skou; Jørgensen, Henry; Stagsted, Jan; Knudsen, Knud Erik Bach

    2012-01-01

    manner (60% of ad libitum) for 6 months, and plasma was subjected to liquid chromatography–mass spectrometry nontargeted metabolomics and biochemical analyses. Low systemic levels of IGF-1 could indicate altered growth conditions and energy metabolism in cloned pigs. In response to ad libitum feeding...

  20. The Brain Metabolome of Male Rats across the Lifespan

    Zheng, Xiaojiao; Chen, Tianlu; Zhao, Aihua; Wang, Xiaoyan; Xie, Guoxiang; Huang, Fengjie; Liu, Jiajian; Zhao, Qing; Wang, Shouli; Wang, Chongchong; Zhou, Mingmei; Panee, Jun; He, Zhigang; Jia, Wei

    2016-01-01

    Comprehensive and accurate characterization of brain metabolome is fundamental to brain science, but has been hindered by technical limitations. We profiled the brain metabolome in male Wistar rats at different ages (day 1 to week 111) using high-sensitivity and high-resolution mass spectrometry. Totally 380 metabolites were identified and 232 of them were quantitated. Compared with anatomical regions, age had a greater effect on variations in the brain metabolome. Lipids, fatty acids and amino acids accounted for the largest proportions of the brain metabolome, and their concentrations varied across the lifespan. The levels of polyunsaturated fatty acids were higher in infancy (week 1 to week 3) compared with later ages, and the ratio of omega-6 to omega-3 fatty acids increased in the aged brain (week 56 to week 111). Importantly, a panel of 20 bile acids were quantitatively measured, most of which have not previously been documented in the brain metabolome. This study extends the breadth of the mammalian brain metabolome as well as our knowledge of functional brain development, both of which are critically important to move the brain science forward. PMID:27063670

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

    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

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

    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

  3. Metabolomic analysis of saponins in crude extracts of Quillaja saponaria by liquid chromatography/mass spectrometry for product authentication.

    Kite, Geoffrey C; Howes, Melanie-Jayne R; Simmonds, Monique S J

    2004-01-01

    Analysis of 50% aqueous methanolic extracts of bark of Quillaja saponaria Molina (quillaja) by liquid chromatography/mass spectrometry (LC/MS), using negative ion electrospray, revealed over 100 saponins. The majority could be assigned to known structures or generalised variations of these from the product ion spectra obtained by serial mass spectrometry in a quadrupole ion trap mass spectrometer. Ten saponins contained a fatty acid domain terminated with both a pentose and deoxyhexose unit, a feature thus far only reported in QS-III. Twenty saponins were based on a hydroxylated derivative of quillaic acid, whereas only six 22beta-hydroxyquillaic acid saponins have been described. The occurrence of pairs of saponins differing only by the presence of a rhamnose or xylose unit in the C-3-substituted saccharide was readily observed in two-dimensional mass maps, and these showed the presence of the unreported 'rhamnose partner' of QS-III. However, one sample labelled as Q. saponaria appeared to lack all saponins containing rhamnose in the C-3 saccharide. Methods to authenticate saponin extracts of quillaja by LC/MS are suggested based on the general metabolomic profile, the occurrence of specific major saponins covering known structural variations, or the presence of saponins containing the unusual fatty acid domain, revealed by neutral loss analysis. PMID:15517552

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

    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

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

    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.

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

    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.

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

    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.

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

    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

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

    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

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

    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...

  11. The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience

    Griss, J.; A.R. Jones; Sachsenberg, T.; Walzer, M.; L. Gatto; Hartler, J.; Thallinger, G. G.; Salek, R. M.; Steinbeck, C.; Neuhauser, N.; Cox, J; Neumann, S.; Fan, J; Reisinger, F; Xu, Q.-W.

    2014-01-01

    The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experime...

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

    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. Discovery of safety biomarkers for atorvastatin in rat urine using mass spectrometry based metabolomics combined with global and targeted approach

    Kumar, Bhowmik Salil [Bioanalysis and Biotransformation Research Center, Korea Institute of Science and Technology, P.O. Box 131, Cheongryang, Seoul 130-650 (Korea, Republic of); University of Science and Technology, (305-333) 113 Gwahangno, Yuseong-gu, Daejeon (Korea, Republic of); Lee, Young-Joo; Yi, Hong Jae [College of Pharmacy, Kyung Hee University, Hoegi-dong, Dongdaemun-gu, Seoul 130-791 (Korea, Republic of); Chung, Bong Chul [Bioanalysis and Biotransformation Research Center, Korea Institute of Science and Technology, P.O. Box 131, Cheongryang, Seoul 130-650 (Korea, Republic of); Jung, Byung Hwa, E-mail: jbhluck@kist.re.kr [Bioanalysis and Biotransformation Research Center, Korea Institute of Science and Technology, P.O. Box 131, Cheongryang, Seoul 130-650 (Korea, Republic of); University of Science and Technology, (305-333) 113 Gwahangno, Yuseong-gu, Daejeon (Korea, Republic of)

    2010-02-19

    In order to develop a safety biomarker for atorvastatin, this drug was orally administrated to hyperlipidemic rats, and a metabolomic study was performed. Atorvastatin was given in doses of either 70 mg kg{sup -1} day{sup -1} or 250 mg kg{sup -1} day{sup -1} for a period of 7 days (n = 4 for each group). To evaluate any abnormal effects of the drug, physiological and plasma biochemical parameters were measured and histopathological tests were carried out. Safety biomarkers were derived by comparing these parameters and using both global and targeted metabolic profiling. Global metabolic profiling was performed using liquid chromatography/time of flight/mass spectrometry (LC/TOF/MS) with multivariate data analysis. Several safety biomarker candidates that included various steroids and amino acids were discovered as a result of global metabolic profiling, and they were also confirmed by targeted metabolic profiling using gas chromatography/mass spectrometry (GC/MS) and capillary electrophoresis/mass spectrometry (CE/MS). Serum biochemical and histopathological tests were used to detect abnormal drug reactions in the liver after repeating oral administration of atorvastatin. The metabolic differences between control and the drug-treated groups were compared using PLS-DA score plots. These results were compared with the physiological and plasma biochemical parameters and the results of a histopathological test. Estrone, cortisone, proline, cystine, 3-ureidopropionic acid and histidine were proposed as potential safety biomarkers related with the liver toxicity of atorvastatin. These results indicate that the combined application of global and targeted metabolic profiling could be a useful tool for the discovery of drug safety biomarkers.

  14. Discovery of safety biomarkers for atorvastatin in rat urine using mass spectrometry based metabolomics combined with global and targeted approach

    In order to develop a safety biomarker for atorvastatin, this drug was orally administrated to hyperlipidemic rats, and a metabolomic study was performed. Atorvastatin was given in doses of either 70 mg kg-1 day-1 or 250 mg kg-1 day-1 for a period of 7 days (n = 4 for each group). To evaluate any abnormal effects of the drug, physiological and plasma biochemical parameters were measured and histopathological tests were carried out. Safety biomarkers were derived by comparing these parameters and using both global and targeted metabolic profiling. Global metabolic profiling was performed using liquid chromatography/time of flight/mass spectrometry (LC/TOF/MS) with multivariate data analysis. Several safety biomarker candidates that included various steroids and amino acids were discovered as a result of global metabolic profiling, and they were also confirmed by targeted metabolic profiling using gas chromatography/mass spectrometry (GC/MS) and capillary electrophoresis/mass spectrometry (CE/MS). Serum biochemical and histopathological tests were used to detect abnormal drug reactions in the liver after repeating oral administration of atorvastatin. The metabolic differences between control and the drug-treated groups were compared using PLS-DA score plots. These results were compared with the physiological and plasma biochemical parameters and the results of a histopathological test. Estrone, cortisone, proline, cystine, 3-ureidopropionic acid and histidine were proposed as potential safety biomarkers related with the liver toxicity of atorvastatin. These results indicate that the combined application of global and targeted metabolic profiling could be a useful tool for the discovery of drug safety biomarkers.

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

    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

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

    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

  17. A hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS) based metabolomics study on colour stability of ovine meat.

    Subbaraj, Arvind K; Kim, Yuan H Brad; Fraser, Karl; Farouk, Mustafa M

    2016-07-01

    Meat colour is one of the cues available to the consumer to gauge overall meat quality and wholesomeness. Colour stability of meat is determined by several factors both inherent to the animal and post-slaughter conditions, including ageing, storage/packaging and display times. A hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS) based metabolomics study was undertaken to identify and compare polar metabolites between ovine meat samples that were exposed to different durations of ageing, storage conditions, and display times. Primary metabolites comprising amino acids, sugars, nucleotides, nucleosides, organic acids and their breakdown products were mainly identified as discriminating factors. For the first time, boron complexes of sugar and malic acid were also tentatively identified. As expected, most compounds identified were related to myoglobin chemistry, and compounds with antioxidant properties were found in higher levels in colour stable samples. Supplementary studies identifying semi-polar, non-polar and volatile compounds will provide a holistic understanding of the chemical basis of colour stability in ovine meat. PMID:26986230

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

    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

  19. Can NMR solve some significant challenges in metabolomics?

    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.

  20. Analysis of hydraulic fracturing flowback and produced waters using accurate mass: identification of ethoxylated surfactants.

    Thurman, E Michael; Ferrer, Imma; Blotevogel, Jens; Borch, Thomas

    2014-10-01

    Two series of ethylene oxide (EO) surfactants, polyethylene glycols (PEGs from EO3 to EO33) and linear alkyl ethoxylates (LAEs C-9 to C-15 with EO3-EO28), were identified in hydraulic fracturing flowback and produced water using a new application of the Kendrick mass defect and liquid chromatography/quadrupole-time-of-flight mass spectrometry. The Kendrick mass defect differentiates the proton, ammonium, and sodium adducts in both singly and doubly charged forms. A structural model of adduct formation is presented, and binding constants are calculated, which is based on a spherical cagelike conformation, where the central cation (NH4(+) or Na(+)) is coordinated with ether oxygens. A major purpose of the study was the identification of the ethylene oxide (EO) surfactants and the construction of a database with accurate masses and retention times in order to unravel the mass spectral complexity of surfactant mixtures used in hydraulic fracturing fluids. For example, over 500 accurate mass assignments are made in a few seconds of computer time, which then is used as a fingerprint chromatogram of the water samples. This technique is applied to a series of flowback and produced water samples to illustrate the usefulness of ethoxylate "fingerprinting", in a first application to monitor water quality that results from fluids used in hydraulic fracturing. PMID:25164376

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

    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

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

    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...

  3. Analysis of plant galactolipids by reversed-phase high-performance liquid chromatography/mass spectrometry with accurate mass measurement

    Zábranská, Marie; Vrkoslav, Vladimír; Sobotníková, J.; Cvačka, Josef

    2012-01-01

    Roč. 165, č. 5 (2012), s. 601-607. ISSN 0009-3084 R&D Projects: GA ČR GA203/09/0139 Grant ostatní: GA UK(CZ) SVV 2012-265201 Institutional research plan: CEZ:AV0Z40550506 Keywords : accurate mass measurement * DGDG * equivalent carbon number * MGDG * RP-HPLC/MS Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 2.147, year: 2012

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

    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

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

    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.

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

    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 ...

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

    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.

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

    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 $\

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

    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 ...

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

    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...

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

    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

  12. Combining desorption electrospray ionization mass spectrometry and nuclear magnetic resonance for differential metabolomics without sample preparation.

    Chen, Huanwen; Pan, Zhengzheng; Talaty, Nari; Raftery, Daniel; Cooks, R Graham

    2006-01-01

    Desorption electrospray ionization mass spectrometry (DESI-MS) and nuclear magnetic resonance (NMR) spectroscopy are used to provide data on urine examined without sample preparation to allow differentiation between diseased (lung cancer) and healthy mice. Principal component analysis (PCA) is used to shortlist compounds with potential for biomarker screening which are responsible for significant differences between control urine samples and samples from diseased animals. Similar PCA score plots have been achieved by DESI-MS and NMR, using a subset of common detected metabolites. The common compounds detected by DESI and NMR have the same changes in sign of their concentrations thereby indicating the usefulness of corroborative analytical methods. The effects of different solvents and surfaces on the DESI mass spectra are also evaluated and optimized. Over 80 different metabolites were successfully identified by DESI-MS and tandem mass spectrometry experiments, with no prior sample preparation. PMID:16628593

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

    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

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

    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...

  15. Towards fruitful metabolomics: high throughput analyses of polyphenol composition in berries using direct infusion mass spectrometry.

    McDougall, Gordon; Martinussen, Inger; Stewart, Derek

    2008-08-15

    Tannin-enriched extracts from raspberry, cloudberry and strawberry were analysed by liquid chromatography-mass spectrometric (LC-MS) techniques. The raspberry and cloudberry extracts contained a similar mixture of identifiable ellagitannin components and ellagic acid. However, the strawberry extract contained a complex mixture of ellagitannin and proanthocyanidin components that could not be adequately resolved to allow identification of individual peaks. Nevertheless, the negative ESI-MS spectra obtained by direct infusion mass spectrometric (DIMS) analysis described the diversity of these samples. For example, the predominance of signals associated with Lambertianin C in cloudberry and Sanguiin H6 in raspberry tannin extracts could be discerned and the diversity of signals from procyanidin and propelargonidin oligomers could be identified in the strawberry extract. The dose response for the main ellagitannin-derived signals in the raspberry tannin sample revealed a saturation effect probably due to ion suppression effects in the ion trap spectrometer. Nevertheless, DIMS spectra of whole berry extracts described qualitative differences in ellagitannin-derived peaks in raspberry, cloudberry and strawberry samples. In addition, positive mode DIMS spectra illustrated qualitative differences in the anthocyanin composition of berries of progeny from a raspberry breeding population that had been previously analysed by LC-MS. This suggests that DIMS could be applied to rapidly assess differences in polyphenol content, especially in large sample sets such as the progeny from breeding programmes. PMID:18650134

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

    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

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

    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.

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

    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.

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

    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...

  20. Understanding Metabolomics in Biomedical Research.

    Kim, Su Jung; Kim, Su Hee; Kim, Ji Hyun; Hwang, Shin; Yoo, Hyun Ju

    2016-03-01

    The term "omics" refers to any type of specific study that provides collective information on a biological system. Representative omics includes genomics, proteomics, and metabolomics, and new omics is constantly being added, such as lipidomics or glycomics. Each omics technique is crucial to the understanding of various biological systems and complements the information provided by the other approaches. The main strengths of metabolomics are that metabolites are closely related to the phenotypes of living organisms and provide information on biochemical activities by reflecting the substrates and products of cellular metabolism. The transcriptome does not always correlate with the proteome, and the translated proteome might not be functionally active. Therefore, their changes do not always result in phenotypic alterations. Unlike the genome or proteome, the metabolome is often called the molecular phenotype of living organisms and is easily translated into biological conditions and disease states. Here, we review the general strategies of mass spectrometry-based metabolomics. Targeted metabolome or lipidome analysis is discussed, as well as nontargeted approaches, with a brief explanation of the advantages and disadvantages of each platform. Biomedical applications that use mass spectrometry-based metabolomics are briefly introduced. PMID:26676338

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

    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.

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

    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

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

    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

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

    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

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

    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.

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

    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

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

    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

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

    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.

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

    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

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

    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...

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

    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.

  12. Accurate determination and certification of bromine in plastic by isotope dilution inductively coupled plasma mass spectrometry

    Highlights: • Accurate analytical method of Br in plastic was studied by isotope dilution ICPMS. • A microwave acid digestion using quartz vessel was suitable for Br analysis. • Sample dilution by NH3 solution could remove memory effect for ICPMS measurement. • The analytical result of the ID-ICPMS showed consistency with that of INAA. • The ID-ICPMS developed could apply to certification of Br in candidate plastic CRM. - Abstract: The accurate analytical method of bromine (Br) in plastic was developed by an isotope dilution inductively coupled plasma mass spectrometry (ID-ICPMS). The figures of merit of microwave acid digestion procedures using polytetrafluoroethylene (PTFE) or quartz vessels were studied and the latter one was suitable for Br analysis since its material was free from Br contamination. The sample dilution procedures using Milli-Q water or ammonium (NH3) solution were also studied to remove memory effect for ICPMS measurement. Although severe memory effect was observed on Milli-Q water dilution, NH3 solution could remove it successfully. The accuracy of the ID-ICPMS was validated by a certified reference material (CRM) as well as the comparison with the analytical result obtained by an instrumental neutron activation analysis (INAA) as different analytical method. From these results, the ID-ICPMS developed in the present study could be evaluated as accurate analytical method of Br in plastic materials and it could apply to certification of Br in candidate plastic CRM with respect to such regulations related to RoHS (restriction of the use of hazardous substances in electrical and electronics equipment) directive

  13. Accurate determination and certification of bromine in plastic by isotope dilution inductively coupled plasma mass spectrometry

    Ohata, Masaki, E-mail: m-oohata@aist.go.jp; Miura, Tsutomu

    2014-07-21

    Highlights: • Accurate analytical method of Br in plastic was studied by isotope dilution ICPMS. • A microwave acid digestion using quartz vessel was suitable for Br analysis. • Sample dilution by NH{sub 3} solution could remove memory effect for ICPMS measurement. • The analytical result of the ID-ICPMS showed consistency with that of INAA. • The ID-ICPMS developed could apply to certification of Br in candidate plastic CRM. - Abstract: The accurate analytical method of bromine (Br) in plastic was developed by an isotope dilution inductively coupled plasma mass spectrometry (ID-ICPMS). The figures of merit of microwave acid digestion procedures using polytetrafluoroethylene (PTFE) or quartz vessels were studied and the latter one was suitable for Br analysis since its material was free from Br contamination. The sample dilution procedures using Milli-Q water or ammonium (NH{sub 3}) solution were also studied to remove memory effect for ICPMS measurement. Although severe memory effect was observed on Milli-Q water dilution, NH{sub 3} solution could remove it successfully. The accuracy of the ID-ICPMS was validated by a certified reference material (CRM) as well as the comparison with the analytical result obtained by an instrumental neutron activation analysis (INAA) as different analytical method. From these results, the ID-ICPMS developed in the present study could be evaluated as accurate analytical method of Br in plastic materials and it could apply to certification of Br in candidate plastic CRM with respect to such regulations related to RoHS (restriction of the use of hazardous substances in electrical and electronics equipment) directive.

  14. Enantiomeric separation in comprehensive two-dimensional gas chromatography with accurate mass analysis.

    Chin, Sung-Tong; Nolvachai, Yada; Marriott, Philip J

    2014-11-01

    Chiral comprehensive two-dimensional gas chromatography (eGC×GC) coupled to quadrupole-accurate mass time-of-flight mass spectrometry (QTOFMS) was evaluated for its capability to report the chiral composition of several monoterpenes, namely, α-pinene, β-pinene, and limonene in cardamom oil. Enantiomers in a standard mixture were fully resolved by direct enantiomeric-GC analysis with a 2,3-di-O-methyl-6-t-butylsilyl derivatized β-cyclodextrin phase; however, the (+)-(R)-limonene enantiomer in cardamom oil was overlapped with other background components including cymene and cineole. Verification of (+)-(R)-limonene components based on characteristic ions at m/z 136, 121, and 107 acquired by chiral single-dimension GC-QTOFMS in the alternate MS/MSMS mode of operation was unsuccessful due to similar parent/daughter ions generated by interfering or co-eluting cymene and cineole. Column phases SUPELCOWAX, SLB-IL111, HP-88, and SLB-IL59, were incorporated as the second dimension column ((2)D) in chiral GC×GC analysis; the SLB-IL59 offered the best resolution for the tested monoterpene enantiomers from the matrix background. Enantiomeric ratios for α-pinene, β-pinene, and limonene were determined to be 1.325, 2.703, and 1.040, respectively, in the cardamom oil sample based on relative peak area data. PMID:24420979

  15. CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra

    Novák, Jiří; Lemr, Karel; Schug, Kevin A.; Havlíček, Vladimír

    2015-07-01

    Nonribosomal peptides have a wide range of biological and medical applications. Their identification by tandem mass spectrometry remains a challenging task. A new open-source de novo peptide identification engine CycloBranch was developed and successfully applied in identification or detailed characterization of 11 linear, cyclic, branched, and branch-cyclic peptides. CycloBranch is based on annotated building block databases the size of which is defined by the user according to ribosomal or nonribosomal peptide origin. The current number of involved nonisobaric and isobaric building blocks is 287 and 521, respectively. Contrary to all other peptide sequencing tools utilizing either peptide libraries or peptide fragment libraries, CycloBranch represents a true de novo sequencing engine developed for accurate mass spectrometric data. It is a stand-alone and cross-platform application with a graphical and user-friendly interface; it supports mzML, mzXML, mgf, txt, and baf file formats and can be run in parallel on multiple threads. It can be downloaded for free from http://ms.biomed.cas.cz/cyclobranch/, where the User's manual and video tutorials can be found.

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

    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

  17. Integrated Post-Experiment Monoisotopic Mass Refinement: An Integrated Approach to Accurately Assign Monoisotopic Precursor Masses to Tandem Mass Spectrometric Data

    Jung, Hee-Jung; Purvine, Samuel O.; Kim, Hokeun; Petyuk, Vladislav A.; Hyung, Seok-Won; Monroe, Matthew E.; Mun, Dong-Gi; Kim, Kyong-Chul; Park, Jong-Moon; Kim, Su-Jin; Tolic, Nikola; Slysz, Gordon W.; Moore, Ronald J.; Zhao, Rui; Adkins, Joshua N.; Anderson, Gordon A.; Lee, Hookeun; Camp, David G.; Yu, Myeong-Hee; Smith, Richard D.; Lee, Sang-Won

    2010-10-15

    Accurate assignment of monoisotopic precursor masses to tandem mass spectrometric (MS/MS) data is a fundamental and critically important step for successful peptide identifications in mass spectrometry based proteomics. Here we describe an integrated approach that combines three previously reported methods of treating MS/MS data for precursor mass refinement. This combined method, “integrated Post-Experiment Monoisotopic Mass Refinement” (iPE MMR), integrates steps: 1) generation of refined MS/MS data by DeconMSn, 2) additional refinement of the resultant MS/MS data by a modified version of PE-MMR, and 3) elimination of systematic errors of precursor masses using DtaRefinery. iPE-MMR is the first method that utilizes all MS information from multiple MS scans of a precursor ion and multiple charge states of it in an MS scan to determine precursor mass. By combining the synergistic features of each of method, iPE MMR increases sensitivity in peptide identification and provides increased accuracy when applied to complex high-throughput proteomics data. iPE MMR also allows incorporating additional data processing step(s) or skipping step(s), if necessary, to enable new developments or applications of the tools, as each step of iPE MMR produces output data in a common and conventional format used in proteomics data processing.

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

    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

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

    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.

  20. Metabolomics in transfusion medicine.

    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. PMID:26662506

  1. Nutritional Metabolomics

    Gürdeniz, Gözde

    . Application of multiple analytical strategies may provide comprehensive information to reach a valid answer to these research questions. In this thesis, I investigated several analytical technologies and data handling strategies in order to evaluate their effects on the biological answer. In metabolomics, one...... strategy influences the patterns identified as important for the nutritional question under study. Therefore, in depth understanding of the study design and the specific effects of the analytical technology on the produced data is extremely important to achieve high quality data handling. Besides data...

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

    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

  3. 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.

    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

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

    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.

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

    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...

  6. YMDB: the Yeast Metabolome Database.

    Jewison, Timothy; Knox, Craig; Neveu, Vanessa; Djoumbou, Yannick; Guo, An Chi; Lee, Jacqueline; Liu, Philip; Mandal, Rupasri; Krishnamurthy, Ram; Sinelnikov, Igor; Wilson, Michael; Wishart, David S

    2012-01-01

    The Yeast Metabolome Database (YMDB, http://www.ymdb.ca) is a richly annotated 'metabolomic' database containing detailed information about the metabolome of Saccharomyces cerevisiae. Modeled closely after the Human Metabolome Database, the YMDB contains >2000 metabolites with links to 995 different genes/proteins, including enzymes and transporters. The information in YMDB has been gathered from hundreds of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the YMDB also contains an extensive collection of experimental intracellular and extracellular metabolite concentration data compiled from detailed Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) metabolomic analyses performed in our lab. This is further supplemented with thousands of NMR and MS spectra collected on pure, reference yeast metabolites. Each metabolite entry in the YMDB contains an average of 80 separate data fields including comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, intracellular/extracellular concentrations, growth conditions and substrates, pathway information, enzyme data, gene/protein sequence data, as well as numerous hyperlinks to images, references and other public databases. 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 S. cervesiae'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 yeast biologists, systems biologists, the industrial fermentation industry, as well as the beer, wine and spirit industry. PMID:22064855

  7. Metabolomic analysis of swine urine treated with β2-agonists by ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry.

    Wu, Yuping; Bi, Yanfeng; Bingga, Gali; Li, Xiaowei; Zhang, Suxia; Li, Jiancheng; Li, Hui; Ding, Shuangyang; Xia, Xi

    2015-06-26

    The illegal use of β2-agonists in livestock production was previously detected by efficient methods based on mass spectrometry to control the residues of these drugs. Nevertheless, such methods still remain a challenging task for authorities who monitor these residues because 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 of illegal use of growth-promoting agents. Here, we outlined a metabolomics-based strategy for detecting the use of "cocktails" composed of mixtures of low amounts of three β2-agonists via urine profiling. Urine profiles of controls and swine treated with mixture of low amounts of three substances (clenbuterol, salbutamol, and ractopamine) were analyzed with ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. The metabolic differences between controls and β2-agonists-treated groups were compared using multivariate data analysis. Fourteen metabolites were identified related with the β2-agonists treatment, while two co-biomarkers, 2-indolecarboxylic acid and fluorometholone acetate, either in single or "cocktails" of low-dose mixture of clenbuterol, salbutamol, and ractopamine, could be considered as diagnostic markers for the detection of illegal use of β2-agonists. The results of depletion study demonstrated that it is practical to use the markers for monitoring of β2-agonists. PMID:25980694

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

    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

  9. Metabolomic Heterogeneity of Pulmonary Arterial Hypertension

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

    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.

  11. The Human Serum Metabolome

    Psychogios, Nikolaos; Hau, David. D.; Peng, Jun; Guo, An Chi; Mandal, Rupasri; Bouatra, Souhaila; Sinelnikov, Igor; Krishnamurthy, Ramanarayan; Eisner, Roman; Gautam, Bijaya; Young, Nelson; Xia, Jianguo; Knox, Craig; Dong, Edison; Huang, Paul

    2011-01-01

    Continuing improvements in analytical technology along with an increased interest in performing comprehensive, quantitative metabolic profiling, is leading to increased interest pressures within the metabolomics community to develop centralized metabolite reference resources for certain clinically important biofluids, such as cerebrospinal fluid, urine and blood. As part of an ongoing effort to systematically characterize the human metabolome through the Human Metabolome Project, we have unde...

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

    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

  13. A fast and accurate method to compute the mass return from multiple stellar populations

    Calura, F; Nipoti, C

    2013-01-01

    The mass returned to the ambient medium by aging stellar populations over cosmological times sums up to a significant fraction (20% - 30% or more) of their initial mass. This continuous mass injection plays a fundamental role in phenomena such as galaxy formation and evolution, fueling of supermassive black holes in galaxies and the consequent (negative and positive) feedback phenomena, and the origin of multiple stellar populations in globular clusters. In numerical simulations the calculation of the mass return can be time consuming, since it requires at each time step the evaluation of a convolution integral over the whole star formation history, so the computational time increases quadratically with the number of time-steps. The situation can be especially critical in hydrodynamical simulations, where different grid points are characterized by different star formation histories, and the gas cooling and heating times are shorter by orders of magnitude than the characteristic stellar lifetimes. In this pape...

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

    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. PMID:26981882

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

    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...

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

    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...

  17. Validation of Metabolic Alterations in Microscale Cell Culture Lysates Using Hydrophilic Interaction Liquid Chromatography (HILIC)-Tandem Mass Spectrometry-Based Metabolomics

    Gunda, Venugopal; Yu, Fang; Singh, Pankaj K.

    2016-01-01

    By standard convention, in order to increase the efficacy of metabolite detection from cell culture lysates, metabolite extracts from a large quantity of cells are utilized for multiple reaction monitoring-based metabolomic studies. Metabolomics from a small number of cell extracts offers a potential economical alternative to increased cell numbers, in turn increasing the utility of cell culture-based metabolomics. However, the effect of reduced cell numbers on targeted metabolomic profiling is relatively unstudied. Considering the limited knowledge available of the feasibility and accuracy of microscale cell culture metabolomics, the present study analyzes differences in metabolomic profiles of different cell numbers of three pancreatic cancer cell lines. Specifically, it examines the effects of reduced cell numbers on metabolite profiles by obtaining extracts either directly from microscale culture plates or through serial dilution of increased numbers of cellular metabolite extracts. Our results indicate reduced cell numbers only modestly affect the number of metabolites detected (93% of metabolites detected in cell numbers as low as 104 cells and 97% for 105 cells), independent of the method used to obtain the cells. However, metabolite peak intensities were differentially affected by the reduced cell numbers, with some peak intensities inversely proportional to the cell numbers. To help eliminate such potential inverse relationships, peak intensities for increased cell numbers were excluded from the comparative analysis. Overall, metabolite profiles from microscale culture plates were observed to differ from the serial dilution samples, which may be attributable to the medium-to-cell-number ratios. Finally, findings identify perturbations in metabolomic profiling for cellular extracts from reduced cell numbers, which offer future applications in microscale metabolomic evaluations. PMID:27120458

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

    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...

  19. PhytoHub version 1.0: a food metabolome database dedicated to dietary phytochemicals

    Giacomoni, Franck; Fillatre, Yoann; Rothwell, Joseph; Eisner, R.; Cesaire, Daniel; Pujos-Guillot, Estelle; Knox, C; Manach, Claudine

    2014-01-01

    The 1st international workshop on the ‘Food metabolome and biomarkers for dietary exposure’, organized in Glasgow last year, identified as a priority the development of databases and libraries of spectra for the food metabolome. The food metabolome comprises all metabolites present in human biofluids and tissues that directly derive from the digestion and metabolism of food chemicals. Exploration of the food metabolome through mass spectrometry untargeted profiling has opened new avenues...

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

    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

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

    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

  2. Oxidized Fatty Acid Analysis by Charge Switch Derivatization, Selected Reaction Monitoring and Accurate Mass Quantification

    Liu, Xinping; Moon, Sung Ho; Mancuso, David J.; Jenkins, Christopher M.; Guan, Shaoping; Sims, Harold F.; Gross, Richard W.

    2013-01-01

    A highly sensitive, specific and robust method for the analysis of oxidized metabolites of linoleic, acid (LA), arachidonic acid (AA) and docosahexaenoic acid (DHA) was developed using charge-switch derivatization, LC-ESI MS/MS with selected reaction monitoring (SRM) and quantitation by high mass accuracy analysis of product ions thereby minimizing interferences from contaminating ions. Charge-switch derivatization of LA, AA and DHA metabolites with N-(4-aminomethylphenyl)-pyridinium resulted...

  3. Metabolomics and Epidemiology Working Group

    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.

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

    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 ...

  5. Accurate mass measurements of short-lived isotopes with the MISTRAL rf spectrometer

    Toader, C F; Borcea, C; Doubre, H; Duma, M; Jacotin, M; Henry, S; Képinski, J F; Lebée, G; Le Scornet, G; Lunney, M D; Monsanglant, C; De Saint-Simon, M; Thibault, C

    1999-01-01

    The MISTRAL experiment has measured its first masses at ISOLDE. Installed in May 1997, this radiofrequency transmission spectrometer is to concentrate on nuclides with particularly short half-lives. MISTRAL received its first stable beam in October and first radioactive beam in November 1997. These first tests, with a plasma ion source, resulted in excellent isobaric separation and reasonable transmission. Further testing and development enabled first data taking in July 1998 on neutron-rich Na isotopes having half-lives as short as 31 ms.

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

    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...

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

    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

  8. ECMDB: the E. coli Metabolome Database.

    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. PMID:23109553

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

    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

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

    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

  11. Accurate evolutions of unequal-mass neutron-star binaries: properties of the torus and short GRB engines

    We present new results from accurate and fully general-relativistic simulations of the coalescence of unmagnetized binary neutron stars with various mass ratios. The evolution of the stars is followed through the inspiral phase, the merger, and the prompt collapse to a black hole, up until the appearance of a thick accretion disc, which is studied as it enters and remains in a regime of quasi-steady accretion. Although a simple ideal-fluid equation of state with Γ = 2 is used, this work presents a systematic study within a fully general-relativistic framework of the properties of the resulting black-hole-torus system produced by the merger of unequal-mass binaries. More specifically, we show that (1) the mass of the torus increases considerably with the mass asymmetry, and equal-mass binaries do not produce significant tori if they have a total baryonic mass Mtot ∼> 3.7 Mo-dot; (2) tori with masses Mtor ∼ 0.2 Mo-dot are measured for binaries with Mtot ∼ 3.4 Mo-dot and mass ratios q ∼ 0.75-0.85; (3) the mass of the torus can be estimated by the simple expression Mtor-bar(q,Mtot = [c1 (1-q) + c2](Mmax-Mot), involving the maximum mass for the binaries and coefficients constrained from the simulations, and suggesting that the tori can have masses as large as Mtor-bar ∼ 0.35Modot for Mtot ∼ 2.8 Mo-dot and q ∼ 0.75-0.85; (4) using a novel technique to analyze the evolution of the tori, we find no evidence for the onset of non-axisymmetric instabilities and that very little, if any, of their mass is unbound; (5) finally, for all the binaries considered, we compute the complete gravitational waveforms and the recoils imparted to the black holes, discussing the prospects of the detection of these sources for a number of present and future detectors.

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

    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

  13. Fast and Accurate Fourier Series Solutions to Gravitational Lensing by A General Family of Two Power-Law Mass Distributions

    Chae, K H

    2002-01-01

    Fourier series solutions to the deflection and magnification by a family of three-dimensional cusped two power-law ellipsoidal mass distributions are presented. The cusped two power-law ellipsoidal mass distributions are characterized by inner and outer power-law radial indices and a break (or, transition) radius. The model family includes mass models mimicking Jaffe, Hernquist, and $\\eta$ models and dark matter halo profiles from numerical simulations. The Fourier series solutions for the cusped two power-law mass distributions are relatively simple, and allow a very fast calculation even for a chosen small fractional calculational error (e.g. $10^{-5}$). These results will be particularly useful for studying lensed systems which provide a number of accurate lensing constraints and for systematic analyses of large numbers of lenses. Subroutines employing these results for the two power-law model and the results by Chae, Khersonsky, & Turnshek for the generalized single power-law mass model are made publi...

  14. Fast and Accurate Fourier Series Solutions to Gravitational Lensing by a General Family of Two-Power-Law Mass Distributions

    Chae, Kyu-Hyun

    2002-04-01

    Fourier series solutions to the deflection and magnification by a family of three-dimensional cusped two-power-law ellipsoidal mass distributions are presented. The cusped two-power-law ellipsoidal mass distributions are characterized by inner and outer power-law radial indices and a break (or transition) radius. The model family includes mass models mimicking Jaffe, Hernquist, and η models and dark matter halo profiles from numerical simulations. The Fourier series solutions for the cusped two-power-law mass distributions are relatively simple and allow a very fast calculation, even for a chosen small fractional calculational error (e.g., 10-5). These results will be particularly useful for studying lensed systems that provide a number of accurate lensing constraints and for systematic analyses of large numbers of lenses. Subroutines employing these results for the two-power-law model and the results by Chae, Khersonsky, & Turnshek for the generalized single-power-law mass model are made publicly available.

  15. Cancer Metabolomics and the Human Metabolome Database

    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.

  16. The emergence of proton nuclear magnetic resonance metabolomics in the cardiovascular arena as viewed from a clinical perspective

    Rankin, Naomi J.; Preiss, David; Welsh, Paul; Burgess, Karl E. V.; Nelson, Scott M; Lawlor, Debbie A.; Sattar, Naveed

    2014-01-01

    The ability to phenotype metabolic profiles in serum has increased substantially in recent years with the advent of metabolomics. Metabolomics is the study of the metabolome, defined as those molecules with an atomic mass less than 1.5 kDa. There are two main metabolomics methods: mass spectrometry (MS) and proton nuclear magnetic resonance (1H NMR) spectroscopy, each with its respective benefits and limitations. MS has greater sensitivity and so can detect many more metabolites. However, its...

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

    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.

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

    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

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

    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.

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

    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 ...

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

    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...

  2. Metabolomic analysis of the food-borne pathogen Campylobacter jejuni: application of direct injection mass spectrometry for mutant characterisation

    Howlett, R.M; Kelly, D. J.; Davey, M P; Paul Quick, W

    2014-01-01

    Campylobacter jejuni is the most frequent cause of human food-borne bacterial gastroenteritis but its physiology and biochemistry are poorly understood. Only a few amino-acids can be catabolised and these are known to be important for host colonization. Here we have established methods for rapid high throughput analyses of global metabolism in C. jejuni using direct injection mass spectrometry (DIMS) to compare metabolite fingerprints of wild-type and mutant strains. Principal component analy...

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

    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

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

    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

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

    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.

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

    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

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

    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

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

    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

  9. A gas chromatography-mass spectrometry-based metabolomic approach for the characterization of goat milk compared with cow milk.

    Scano, Paola; Murgia, Antonio; Pirisi, Filippo M; Caboni, Pierluigi

    2014-10-01

    In this work, the polar metabolite pool of commercial caprine milk was studied by gas chromatography-mass spectrometry and multivariate statistical data analysis. Experimental data were compared with those of cow milk and the discriminant analysis correctly classified milk. By the same means, differences due to heat treatments (UHT or pasteurization) on milk samples were also investigated. Results of the 2 discriminant analyses were combined, with the aim of finding the discriminant metabolites unique for each class and shared by 2 classes. Valine and glycine were specific to goat milk, talose and malic acid to cow milk, and hydroxyglutaric acid to pasteurized samples. Glucose and fructose were shared by cow milk and UHT-treated samples, whereas ribose was shared by pasteurized and goat milk. Other discriminant variables were not attributed to specific metabolites. Furthermore, with the aim to reduce food fraud, the issue of adulteration of caprine milk by addition of cheaper bovine milk has been also addressed. To this goal, mixtures of goat and cow milk were prepared by adding the latter in a range from 0 to 100% (vol/vol) and studied by multivariate regression analysis. The error in the level of cow milk detectable was approximately 5%. These overall results demonstrated that, through the combined approach of gas chromatography-mass spectrometry and multivariate statistical data analysis, we were able to discriminate between milk typologies on the basis of their polar metabolite profiles and to propose a new analytical method to easily discover food fraud and to protect goat milk uniqueness. The use of appropriate visualization tools improved the interpretation of multivariate model results. PMID:25108860

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

    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

  11. The food metabolome

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

    2014-01-01

    efforts; 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...

  12. Metabolomics data normalization with EigenMS.

    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.

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

    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

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

    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

  15. 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.

    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

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

    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

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

    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

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

    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.

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

    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

  20. Application of Metabolomics in Thyroid Cancer Research

    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.

  1. Metabolomic heterogeneity of pulmonary arterial hypertension.

    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.

  2. ICP-MS and ESI orbitrap MS/MS for plant elemental speciation. The need for accurate mass measurements

    Complete text of publication follows. Metallomics approaches based on the combined use of elemental and molecular mass spectrometry have been developed to gain a better understanding of the factors involved in the uptake and distribution of selenium (Se) and arsenic (As) in a well-known hyperaccumulator, Arabidopsis thaliana. Plants, individually and simultaneously supplemented with As and Se (1, 3, 5 μg g-1), were grown hydroponically for 7 weeks in a controlled environment. The effect of the presence of Se on the As uptake by the plant leaves was investigated here for the first time; Se in the growing media was found not to affect As concentrations of the leaves in comparison with individual exposure to As. The use of 1% formic acid (1 deg C, 1 h), compared with buffer extraction (2, 5, 12 h) by sonication, was found to be the choice as a compromise between extraction efficiency and preservation of the compound entity. Using size-exclusion HPLC-ICP-MS, the coelution of the main As peak (70% of the total chromatogram area) with sulphur was observed, suggesting the presence of biomolecules containing S and As in the leaves. A deeper insight into the As species distribution in the leaves was achieved using reversed phase HPLC in combination with ICP-MS and ESI Orbitrap MS/MS. The need for accurate mass measurements (using ESI Orbitrap MS/MS) to minimize ambiguity in species identification will be demonstrated.

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

    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

  4. THE ARAUCARIA PROJECT: ACCURATE DETERMINATION OF THE DYNAMICAL MASS OF THE CLASSICAL CEPHEID IN THE ECLIPSING SYSTEM OGLE-LMC-CEP-1812

    We have analyzed the double-lined eclipsing binary system OGLE-LMC-CEP-1812 in the LMC and demonstrate that it contains a classical fundamental mode Cepheid pulsating with a period of 1.31 days. The secondary star is a stable giant. We derive the dynamical masses for both stars with an accuracy of 1.5%, making the Cepheid in this system the second classical Cepheid with a very accurate dynamical mass determination, following the OGLE-LMC-CEP-0227 system studied by Pietrzyński et al. The measured dynamical mass agrees very well with that predicted by pulsation models. We also derive the radii of both components and accurate orbital parameters for the binary system. This new, very accurate dynamical mass for a classical Cepheid will greatly contribute to the solution of the Cepheid mass discrepancy problem, and to our understanding of the structure and evolution of classical Cepheids.

  5. Metabolomics in dyslipidemia.

    Chen, Hua; Miao, Hua; Feng, Ya-Long; Zhao, Ying-Yong; Lin, Rui-Chao

    2014-01-01

    Hyperlipidemia is an important public health problem with increased incidence and prevalence worldwide. Current clinical biomarkers, triglyceride, total cholesterol, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol lack the necessary specificity and sensitivity and only increase significantly after serious dyslipidemia. Therefore, sensitive biomarkers are needed for hyperlipidemia. Hyperlipidemia-specific biomarkers would improve clinical diagnosis and therapeutic treatment at early disease stages. The aim of metabolomics is to identify untargeted and global small-molecule metabolite profiles from cells, biofluids, and tissues. This method offers the potential for a holistic approach to improve disease diagnoses and our understanding of underlying pathologic mechanisms. This review summarizes analytical techniques, data collection and analysis for metabolomics, and metabolomics in hyperlipidemia animal models and clinical studies. Mechanisms of hypolipemia and antilipemic drug therapy are also discussed. Metabolomics provides a new opportunity to gain insight into metabolic profiling and pathophysiologic mechanisms of hyperlipidemia. PMID:25344987

  6. Metabolomics in multiple sclerosis.

    Bhargava, Pavan; Calabresi, Peter A

    2016-04-01

    Multiple sclerosis (MS) is a chronic demyelinating disorder of the central nervous system with inflammatory and degenerative components. The cause of MS remains unknown although genetic and environmental factors appear to play a role in its etiopathogenesis. Metabolomics is a new "omics" technology that aims at measuring small molecules in various biological matrices and can provide information that is not readily obtained from genomics, transcriptomics, or proteomics. Currently, several different analytical platforms exist for metabolomics, and both untargeted and targeted approaches are being employed. Methods of analysis of metabolomics data are also being developed and no consensus currently exists on the optimal approach to analysis and interpretation of these data. Metabolomics has the potential to provide putative biomarkers, insights into the pathophysiology of the disease, and to aid in precision medicine for patients with MS. PMID:26754801

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

    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

  8. Metabolomics er fremtiden

    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...

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

    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)

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

    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.

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

    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

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

    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

  13. Determination of the presence or absence of sulfur materials in drywall using direct analysis in real time in conjunction with an accurate-mass time-of-flight mass spectrometer.

    Curtis, Matthew E; Jones, Patrick R; Sparkman, O David; Cody, Robert B

    2009-11-01

    Based on the concern about the presence of sulfur materials being in drywall (wallboard), a quick and reliable test to confirm the presence or absence of these materials using direct analysis in real time (DART) mass spectrometry in conjunction with an accurate-mass time-of-flight (TOF) mass spectrometer has been developed and is described here. PMID:19700343

  14. Accurate Mass GC/LC-Quadrupole Time of Flight Mass Spectrometry Analysis of Fatty Acids and Triacylglycerols of Spicy Fruits from the Apiaceae Family

    Nguyen, Thao; Aparicio, Mario; Saleh, Mahmoud A.

    2016-01-01

    The triacylglycerol (TAG) structure and the regio-stereospecific distribution of fatty acids (FA) of seed oils from most of the Apiaceae family are not well documented. The TAG structure ultimately determines the final physical properties of the oils and the position of FAs in the TAG molecule affects the digestion; absorption and metabolism; and physical and technological properties of TAGs. Fixed oils from the fruits of dill (Anethum graveolens), caraway (Carum carvi), cumin (Cuminum cyminum), coriander (Coriandrum sativum), anise (Pimpinella anisum), carrot (Daucus carota), celery (Apium graveolens), fennel (Foeniculum vulgare), and Khella (Ammi visnaga), all from the Apiaceae family, were extracted at room temperature in chloroform/methanol (2:1 v/v) using percolators. Crude lipids were fractionated by solid phase extraction to separate neutral triacylglycerols (TAGs) from other lipids components. Neutral TAGs were subjected to transesterification process to convert them to their corresponding fatty acids methyl esters (FAMES) using 1% boron trifluoride (BF3) in methanol. FAMES were analyzed by gas chromatography-quadrupole time of flight (GC-QTOF) mass spectrometry. Triglycerides were analyzed using high performance liquid chromatography-quadrupole time of flight (LC-QTOF) mass spectrometry. Petroselinic acid was the major fatty acid in all samples ranging from 57% of the total fatty acids in caraway up to 82% in fennel. All samples contained palmitic (16:0), palmitoleic (C16:1n-9), stearic (C18:0), petroselinic (C18:1n-12), linoleic (C18:2n-6), linolinic (18:3n-3), and arachidic (C20:0) acids. TAG were analyzed using LC-QTOF for accurate mass identification and mass spectrometry/mass spectrometry (MS/MS) techniques for regiospesific elucidation of the identified TAGs. Five major TAGs were detected in all samples but with different relative concentrations in all of the tested samples. Several other TAGs were detected as minor components and were present in

  15. Accurate Mass GC/LC-Quadrupole Time of Flight Mass Spectrometry Analysis of Fatty Acids and Triacylglycerols of Spicy Fruits from the Apiaceae Family

    Thao Nguyen

    2015-12-01

    Full Text Available The triacylglycerol (TAG structure and the regio-stereospecific distribution of fatty acids (FA of seed oils from most of the Apiaceae family are not well documented. The TAG structure ultimately determines the final physical properties of the oils and the position of FAs in the TAG molecule affects the digestion; absorption and metabolism; and physical and technological properties of TAGs. Fixed oils from the fruits of dill (Anethum graveolens, caraway (Carum carvi, cumin (Cuminum cyminum, coriander (Coriandrum sativum, anise (Pimpinella anisum, carrot (Daucus carota, celery (Apium graveolens, fennel (Foeniculum vulgare, and Khella (Ammi visnaga, all from the Apiaceae family, were extracted at room temperature in chloroform/methanol (2:1 v/v using percolators. Crude lipids were fractionated by solid phase extraction to separate neutral triacylglycerols (TAGs from other lipids components. Neutral TAGs were subjected to transesterification process to convert them to their corresponding fatty acids methyl esters (FAMES using 1% boron trifluoride (BF3 in methanol. FAMES were analyzed by gas chromatography-quadrupole time of flight (GC-QTOF mass spectrometry. Triglycerides were analyzed using high performance liquid chromatography-quadrupole time of flight (LC-QTOF mass spectrometry. Petroselinic acid was the major fatty acid in all samples ranging from 57% of the total fatty acids in caraway up to 82% in fennel. All samples contained palmitic (16:0, palmitoleic (C16:1n-9, stearic (C18:0, petroselinic (C18:1n-12, linoleic (C18:2n-6, linolinic (18:3n-3, and arachidic (C20:0 acids. TAG were analyzed using LC-QTOF for accurate mass identification and mass spectrometry/mass spectrometry (MS/MS techniques for regiospesific elucidation of the identified TAGs. Five major TAGs were detected in all samples but with different relative concentrations in all of the tested samples. Several other TAGs were detected as minor components and were present in some

  16. Accurate Mass GC/LC-Quadrupole Time of Flight Mass Spectrometry Analysis of Fatty Acids and Triacylglycerols of Spicy Fruits from the Apiaceae Family.

    Nguyen, Thao; Aparicio, Mario; Saleh, Mahmoud A

    2015-01-01

    The triacylglycerol (TAG) structure and the regio-stereospecific distribution of fatty acids (FA) of seed oils from most of the Apiaceae family are not well documented. The TAG structure ultimately determines the final physical properties of the oils and the position of FAs in the TAG molecule affects the digestion; absorption and metabolism; and physical and technological properties of TAGs. Fixed oils from the fruits of dill (Anethum graveolens), caraway (Carum carvi), cumin (Cuminum cyminum), coriander (Coriandrum sativum), anise (Pimpinella anisum), carrot (Daucus carota), celery (Apium graveolens), fennel (Foeniculum vulgare), and Khella (Ammi visnaga), all from the Apiaceae family, were extracted at room temperature in chloroform/methanol (2:1 v/v) using percolators. Crude lipids were fractionated by solid phase extraction to separate neutral triacylglycerols (TAGs) from other lipids components. Neutral TAGs were subjected to transesterification process to convert them to their corresponding fatty acids methyl esters (FAMES) using 1% boron trifluoride (BF₃) in methanol. FAMES were analyzed by gas chromatography-quadrupole time of flight (GC-QTOF) mass spectrometry. Triglycerides were analyzed using high performance liquid chromatography-quadrupole time of flight (LC-QTOF) mass spectrometry. Petroselinic acid was the major fatty acid in all samples ranging from 57% of the total fatty acids in caraway up to 82% in fennel. All samples contained palmitic (16:0), palmitoleic (C16:1n-9), stearic (C18:0), petroselinic (C18:1n-12), linoleic (C18:2n-6), linolinic (18:3n-3), and arachidic (C20:0) acids. TAG were analyzed using LC-QTOF for accurate mass identification and mass spectrometry/mass spectrometry (MS/MS) techniques for regiospesific elucidation of the identified TAGs. Five major TAGs were detected in all samples but with different relative concentrations in all of the tested samples. Several other TAGs were detected as minor components and were present in

  17. COnsortium of METabolomics Studies (COMETS)

    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.

  18. LC-MS-based metabolomics

    Zhou, Bin; Xiao, Jun Feng; Tuli, Leepika; Ressom, Habtom W

    2011-01-01

    Metabolomics aims at identification and quantitation of small molecules involved in metabolic reactions. LC-MS has enjoyed a growing popularity as the platform for metabolomic studies due to its high throughput, soft ionization, and good coverage of metabolites. The success of LC-MS-based metabolomic study often depends on multiple experimental, analytical, and computational steps. This review presents a workflow of a typical LC-MS-based metabolomic analysis for identification and quantitatio...

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

    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

  20. Metabolomics in the fight against malaria

    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.

  1. Microbial metabolomics in open microscale platforms.

    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

  2. Establishing Substantial Equivalence: Metabolomics

    Beale, Michael H.; Ward, Jane L.; Baker, John M.

    Modern ‘metabolomic’ methods allow us to compare levels of many structurally diverse compounds in an automated fashion across a large number of samples. This technology is ideally suited to screening of populations of plants, including trials where the aim is the determination of unintended effects introduced by GM. A number of metabolomic methods have been devised for the determination of substantial equivalence. We have developed a methodology, using [1H]-NMR fingerprinting, for metabolomic screening of plants and have applied it to the study of substantial equivalence of field-grown GM wheat. We describe here the principles and detail of that protocol as applied to the analysis of flour generated from field plots of wheat. Particular emphasis is given to the downstream data processing and comparison of spectra by multivariate analysis, from which conclusions regarding metabolome changes due to the GM can be assessed against the background of natural variation due to environment.

  3. Accurate physical laws can permit new standard units: The two laws F→=ma→ and the proportionality of weight to mass

    Saslow, Wayne M.

    2014-04-01

    Three common approaches to F→=ma→ are: (1) as an exactly true definition of force F→ in terms of measured inertial mass m and measured acceleration a→; (2) as an exactly true axiom relating measured values of a→, F→ and m; and (3) as an imperfect but accurately true physical law relating measured a→ to measured F→, with m an experimentally determined, matter-dependent constant, in the spirit of the resistance R in Ohm's law. In the third case, the natural units are those of a→ and F→, where a→ is normally specified using distance and time as standard units, and F→ from a spring scale as a standard unit; thus mass units are derived from force, distance, and time units such as newtons, meters, and seconds. The present work develops the third approach when one includes a second physical law (again, imperfect but accurate)—that balance-scale weight W is proportional to m—and the fact that balance-scale measurements of relative weight are more accurate than those of absolute force. When distance and time also are more accurately measurable than absolute force, this second physical law permits a shift to standards of mass, distance, and time units, such as kilograms, meters, and seconds, with the unit of force—the newton—a derived unit. However, were force and distance more accurately measurable than time (e.g., time measured with an hourglass), this second physical law would permit a shift to standards of force, mass, and distance units such as newtons, kilograms, and meters, with the unit of time—the second—a derived unit. Therefore, the choice of the most accurate standard units depends both on what is most accurately measurable and on the accuracy of physical law.

  4. Metabolomic analysis of three Mollicute species.

    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.

  5. FT-ICR/MS and GC-EI/MS Metabolomics Networking Unravels Global Potato Sprout's Responses to Rhizoctonia solani Infection

    Aliferis, Konstantinos A.; Jabaji, Suha

    2012-01-01

    The complexity of plant-pathogen interactions makes their dissection a challenging task for metabolomics studies. Here we are reporting on an integrated metabolomics networking approach combining gas chromatography/mass spectrometry (GC/MS) with Fourier transform ion cyclotron resonance/mass spectrometry (FT-ICR/MS) and bioinformatics analyses for the study of interactions in the potato sprout-Rhizoctonia solani pathosystem and the fluctuations in the global metabolome of sprouts. The develop...

  6. Metabolomics reveals positive acceleration(+Gz)-induced metabolic perturbations and the protective effect of Ginkgo biloba extract in a rat model based on ultra high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry.

    Yang, Zhihui; Zhao, Andong; Li, Zhongdong; Ge, Hua; Li, Tonghua; Zhang, Fucheng; Zhan, Hao; Wang, Jianchang

    2016-06-01

    Positive acceleration (+Gz) in the head-to-foot direction generated by modern high-performance fighter jets during flight maneuvers is characterized by high G values and a rapid rate of acceleration, and is often long in duration and a repeated occurrence. The acceleration overload far exceeds the pilot's physiological tolerance limits and causes considerable strain on several organ systems. Despite the importance of monitoring pathophysiological alterations related to +Gz exposure, we lack a complete explanation of the pathophysiology of +Gz exposure. Ginkgo biloba extract (GBE) is a classic traditional Chinese medicine (TCM) that might exert a protective effect against +Gz exposure. However, its mechanism remains unclear. Here, a metabolomics approach based on ultra high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOFMS) was used to characterize +Gz-induced metabolic fluctuations in a rat model and to evaluate the protective effect of GBE. Using partial least-squares discriminant analysis for the classification and selection of biomarkers, eighteen serum metabolites related to +Gz exposure were identified, and were found to primarily involve the fatty acid β-oxidation pathway, glycerophospholipid metabolism, phospholipid metabolism, bile acid metabolism, purine metabolism and lysine metabolism. Taking these potential biomarkers as screening indexes, we found that GBE could reverse the pathological process of +Gz exposure by partially regulating the perturbed fatty acid β-oxidation pathway, glycerophospholipid metabolism, purine metabolism and lysine metabolism. This indicates that UHPLC-Q-TOFMS-based metabolomics provides a powerful tool to reveal serum metabolic fluctuations in response to +Gz exposure and to study the mechanism underlying TCM. PMID:27010354

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

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

    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

  9. Impacts on the metabolome of down-regulating polyphenol oxidase in transgenic potato tubers

    Tubers of potato (Solanum tuberosum L. cv. Estima) genetically modified (GM) to reduce polyphenol oxidase (PPO) activity and enzymatic discolouration were assessed for changes in the metabolome using Liquid Chromatography-Mass Spectrometry (LC-MS) and Gas Chromatography (GC)-MS. Metabolome changes ...

  10. Mealtime, temporal, and daily variability of the human urinary and plasma metabolomes in a tightly controlled environment.

    Kyoungmi Kim

    Full Text Available While metabolomics has tremendous potential for diagnostic biomarker and therapeutic target discovery, its utility may be diminished by the variability that occurs due to environmental exposures including diet and the influences of the human circadian rhythm. For successful translation of metabolomics findings into the clinical setting, it is necessary to exhaustively define the sources of metabolome variation. To address these issues and to measure the variability of urinary and plasma metabolomes throughout the day, we have undertaken a comprehensive inpatient study in which we have performed non-targeted metabolomics analysis of blood and urine in 26 volunteers (13 healthy subjects with no known disease and 13 healthy subjects with autosomal dominant polycystic kidney disease not taking medication. These individuals were evaluated in a clinical research facility on two separate occasions, over three days, while on a standardized, weight-based diet. Subjects provided pre- and post-prandial blood and urine samples at the same time of day, and all samples were analyzed by "fast lane" LC-MS-based global metabolomics. The largest source of variability in blood and urine metabolomes was attributable to technical issues such as sample preparation and analysis, and less variability was due to biological variables, meals, and time of day. Higher metabolome variability was observed after the morning as compared to the evening meal, yet day-to-day variability was minimal and urine metabolome variability was greater than that of blood. Thus we suggest that blood and urine are suitable biofluids for metabolomics studies, though nontargeted mass spectrometry alone may not offer sufficient precision to reveal subtle changes in the metabolome. Additional targeted analyses may be needed to support the data from nontargeted mass spectrometric analyses. In light of these findings, future metabolomics studies should consider these sources of variability to allow

  11. Metabolomics and Its Application to Acute Lung Diseases.

    Stringer, Kathleen A; McKay, Ryan T; Karnovsky, Alla; Quémerais, Bernadette; Lacy, Paige

    2016-01-01

    Metabolomics is a rapidly expanding field of systems biology that is gaining significant attention in many areas of biomedical research. Also known as metabonomics, it comprises the analysis of all small molecules or metabolites that are present within an organism or a specific compartment of the body. Metabolite detection and quantification provide a valuable addition to genomics and proteomics and give unique insights into metabolic changes that occur in tangent to alterations in gene and protein activity that are associated with disease. As a novel approach to understanding disease, metabolomics provides a "snapshot" in time of all metabolites present in a biological sample such as whole blood, plasma, serum, urine, and many other specimens that may be obtained from either patients or experimental models. In this article, we review the burgeoning field of metabolomics in its application to acute lung diseases, specifically pneumonia and acute respiratory disease syndrome (ARDS). We also discuss the potential applications of metabolomics for monitoring exposure to aerosolized environmental toxins. Recent reports have suggested that metabolomics analysis using nuclear magnetic resonance (NMR) and mass spectrometry (MS) approaches may provide clinicians with the opportunity to identify new biomarkers that may predict progression to more severe disease, such as sepsis, which kills many patients each year. In addition, metabolomics may provide more detailed phenotyping of patient heterogeneity, which is needed to achieve the goal of precision medicine. However, although several experimental and clinical metabolomics studies have been conducted assessing the application of the science to acute lung diseases, only incremental progress has been made. Specifically, little is known about the metabolic phenotypes of these illnesses. These data are needed to substantiate metabolomics biomarker credentials so that clinicians can employ them for clinical decision-making and

  12. Metabolomics Research Group 2011 Study

    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...

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

    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,...

  14. Metabolomics for Quality and food security

    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.

  15. Negative electrospray ionisation of fluorotelomer alcohols (FTOH) and FTOH-derived acrylate surfactants by liquid chromatography coupled to accurate (tandem) mass spectrometry

    Trier, Xenia; Christensen, Jan H.; Niessen, Wilfried M. A.

    Fluorotelomer alcohols (FTOHs) are used to synthesize fluorinated surfactants, which form bioaccumulative perfluorinated degradation products, which are toxic to humans and the environment. To facilitate screening for FTOH-derived surfactants by LC-ESI–-MS, we identified product ions of FTOHs, an...... propose FTOH fragmentation pathways on two MS instruments. By extraction of FTOH basepeak ions from accurate mass spectra, homologues series of peaks showed up in an industrial blend of FTOH-derived fluoroacrylates used in food paper packaging....

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

    Storey, Michael; Rivera, Tiffany; Flude, Stephanie

    -Instruments multi-collector Noblesse noble gas mass spectrometer configured with a faraday detector and three ion-counting electron multipliers. The instrument has the capability to measure several noble gas isotopes simultaneously and to change measurement configurations instantaneously by the use of QUAD lenses......New generation, high resolution, multi-collector noble gas mass spectrometers equipped with ion-counting electron multipliers provide opportunities for improved accuracy and precision in 40Ar/39Ar dating. Here we report analytical protocols and age cross-calibration studies using a NU...... (zoom optics). The Noblesse offer several advantages over previous generation noble gas mass spectrometers and is particularly suited for single crystal 40Ar/39Ar dating because of: (i) improved source sensitivity (ii) ion-counting electron multipliers, which have much lower signal to noise ratios than...

  17. Metabolomics and Atherosclerosis

    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 ...

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

    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.

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

    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.

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

    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

  1. Metabolomics for Secondary Metabolite Research

    Eriko Takano

    2013-11-01

    Full Text Available Metabolomics, the global characterization of metabolite profiles, is becoming an increasingly powerful tool for research on secondary metabolite discovery and production. In this review we discuss examples of recent technological advances and biological applications of metabolomics in the search for chemical novelty and the engineered production of bioactive secondary metabolites.

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

    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.

  3. Accurate quantification of endogenous androgenic steroids in cattle's meat by gas chromatography mass spectrometry using a surrogate analyte approach

    Determination of endogenous steroids in complex matrices such as cattle's meat is a challenging task. Since endogenous steroids always exist in animal tissues, no analyte-free matrices for constructing the standard calibration line will be available, which is crucial for accurate quantification specially at trace level. Although some methods have been proposed to solve the problem, none has offered a complete solution. To this aim, a new quantification strategy was developed in this study, which is named 'surrogate analyte approach' and is based on using isotope-labeled standards instead of natural form of endogenous steroids for preparing the calibration line. In comparison with the other methods, which are currently in use for the quantitation of endogenous steroids, this approach provides improved simplicity and speed for analysis on a routine basis. The accuracy of this method is better than other methods at low concentration and comparable to the standard addition at medium and high concentrations. The method was also found to be valid according to the ICH criteria for bioanalytical methods. The developed method could be a promising approach in the field of compounds residue analysis

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

    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

  5. Metabolomic profiling of plant tissues.

    Rambla, José L; López-Gresa, M P; Bellés, J M; Granell, Antonio

    2015-01-01

    Metabolomics is a powerful discipline aimed at a comprehensive and global analysis of the metabolites present in a cell, tissue, or organism, and to which increasing attention has been paid in the last few years. Given the high diversity in physical and chemical properties of plant metabolites, not a single method is able to analyze them all.Here we describe two techniques for the profiling of two quite different groups of metabolites: polar and semi-polar secondary metabolites, including many of those involved in plant response to biotic and abiotic stress, and volatile compounds, which include those responsible of most of our perception of food flavor. According to these techniques, polar and semi-polar metabolites are extracted in methanol, separated by liquid chromatography (UPLC), and detected by a UV-VIS detector (PDA) and a time-of-flight (ToF) mass spectrometer. Volatile compounds, on the other hand, are extracted by headspace solid phase microextraction (HS-SPME), and separated and detected by gas chromatography coupled to mass spectrometry (GC-MS). PMID:25757775

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

    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

  7. 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.

    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

  8. 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

    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....

  9. Accurate determination of ⁴¹Ca concentrations in spent resins from the nuclear industry by accelerator mass spectrometry.

    Nottoli, Emmanuelle; Bourlès, Didier; Bienvenu, Philippe; Labet, Alexandre; Arnold, Maurice; Bertaux, Maité

    2013-12-01

    The radiological characterisation of nuclear waste is essential for managing storage sites. Determining the concentration of Long-Lived RadioNuclides (LLRN) is fundamental for their long-term management. This paper focuses on the measurement of low (41)Ca concentrations in ions exchange resins used for primary fluid purification in Pressurised Water Reactors (PWR). (41)Ca concentrations were successfully measured by Accelerator Mass Spectrometry (AMS) after the acid digestion of resin samples, followed by radioactive decontamination and isobaric suppression through successive hydroxide, carbonate, nitrate and final CaF2 precipitations. Measured (41)Ca concentrations ranged from 0.02 to 0.03 ng/g, i.e. from 0.06 to 0.09 Bq/g. The (41)Ca/(60)Co activity ratios obtained were remarkably reproducible and in good agreement with the current ratio used for resins management. PMID:24144617

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

    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

  11. 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.

    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. PMID:25160955

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

    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...

  13. Improved batch correction in untargeted MS-based metabolomics

    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

  14. Independent component analysis in non-hypothesis driven metabolomics

    Li, Xiang; Hansen, Jakob; Zhao, Xinjie;

    2012-01-01

    In a non-hypothesis driven metabolomics approach plasma samples collected at six different time points (before, during and after an exercise bout) were analyzed by gas chromatography-time of flight mass spectrometry (GC-TOF MS). Since independent component analysis (ICA) does not need a priori...

  15. Metabolomics for phytochemical discovery: development of statistical approaches using a cranberry model system.

    Turi, Christina E; Finley, Jamie; Shipley, Paul R; Murch, Susan J; Brown, Paula N

    2015-04-24

    Metabolomics is the qualitative and quantitative analysis of all of the small molecules in a biological sample at a specific time and influence. Technologies for metabolomics analysis have developed rapidly as new analytical tools for chemical separations, mass spectrometry, and NMR spectroscopy have emerged. Plants have one of the largest metabolomes, and it is estimated that the average plant leaf can contain upward of 30 000 phytochemicals. In the past decade, over 1200 papers on plant metabolomics have been published. A standard metabolomics data set contains vast amounts of information and can either investigate or generate hypotheses. The key factors in using plant metabolomics data most effectively are the experimental design, authentic standard availability, extract standardization, and statistical analysis. Using cranberry (Vaccinium macrocarpon) as a model system, this review will discuss and demonstrate strategies and tools for analysis and interpretation of metabolomics data sets including eliminating false discoveries and determining significance, metabolite clustering, and logical algorithms for discovery of new metabolites and pathways. Together these metabolomics tools represent an entirely new pipeline for phytochemical discovery. PMID:25751407

  16. Application of Metabolomics to Multiple Chemical Sensitivity Research.

    Katoh, Takahiko; Fujiwara, Yuki; Nakashita, Chihiro; Lu, Xi; Hisada, Aya; Miyazaki, Wataru; Azuma, Kenichi; Tanigawa, Mari; Uchiyama, Iwao; Kunugita, Naoki

    2016-01-01

    Multiple chemical sensitivity (MCS) is an acquired chronic disorder characterized by nonspecific symptoms in multiple organ systems associated with exposure to low-level chemicals. Diagnosis of MCS can be difficult because of the inability to assess the causal relationship between exposure and symptoms. No standardized objective measures for the identification of MCS and no precise definition of this disorder have been established. Recent technological advances in mass spectrometry have significantly improved our capacity to obtain more data from each biological sample. Metabolomics comprises the methods and techniques that are used to determine the small-level molecules in biofluids and tissues. The metabolomic profile-the metabolome-has multiple applications in many biological sciences, including the development of new diagnostic tools for medicine. We performed metabolomics to detect the difference between 9 patients with MCS and 9 controls. We identified 183 substances whose levels were beyond the normal detection limit. The most prominent differences included significant increases in the levels of both hexanoic acid and pelargonic acid, and also a significant decrease in the level of acetylcarnitine in patients with MCS. In conclusion, using metabolomics analysis, we uncovered a hitherto unrecognized alteration in the levels of metabolites in MCS. These changes may have important biological implications and may have a significant potential for use as biomarkers. PMID:26832623

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

    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...

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

    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

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

    Kiefer, F.; Halbwachs, J.-L.; Arenou, F.; Pourbaix, D.; Famaey, B.; Guillout, P.; Lebreton, Y.; Nebot Gómez-Morán, A.; Mazeh, T.; Salomon, J.-B.; Soubiran, C.; Tal-Or, L.

    2016-05-01

    In anticipation of the Gaia astrometric mission, a large sample of spectroscopic binaries has been observed since 2010 with the Spectrographe pour l'Observation des PHénomènes des Intérieurs Stellaires et des Exoplanètes 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 per cent 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 d. 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 per cent for the 10 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 per cent, respectively.

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

    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...

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

    Bengtström, Linda; Rosenmai, Anna Kjerstine; Trier, Xenia;

    2016-01-01

    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...... 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 identified in recycled low quality P&B....

  2. Metabolomics of genetically modified crops.

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

    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 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. PMID:25334064

  3. Metabolomics of Genetically Modified Crops

    Carolina Simó

    2014-10-01

    Full Text Available 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.

  4. Comprehensive analysis of transcriptome and metabolome analysis in Intrahepatic Cholangiocarcinoma and Hepatocellular Carcinoma.

    Murakami, Yoshiki; Kubo, Shoji; Tamori, Akihiro; Itami, Saori; Kawamura, Etsushi; Iwaisako, Keiko; Ikeda, Kazuo; Kawada, Norifumi; Ochiya, Takahiro; Taguchi, Y-h

    2015-01-01

    Intrahepatic cholangiocarcinoma (ICC) and hepatocellular carcinoma (HCC) are liver originated malignant tumors. Of the two, ICC has the worse prognosis because it has no reliable diagnostic markers and its carcinogenic mechanism is not fully understood. The aim of this study was to integrate metabolomics and transcriptomics datasets to identify variances if any in the carcinogenic mechanism of ICC and HCC. Ten ICC and 6 HCC who were resected surgically, were enrolled. miRNA and mRNA expression analysis were performed by microarray on ICC and HCC and their corresponding non-tumor tissues (ICC_NT and HCC_NT). Compound analysis was performed using capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS). Principle component analysis (PCA) revealed that among the four sample groups (ICC, ICC_NT, HCC, and HCC_NT) there were 14 compounds, 62 mRNAs and 17 miRNAs with two distinct patterns: tumor and non-tumor, and ICC and non-ICC. We accurately (84.38%) distinguished ICC by the distinct pattern of its compounds. Pathway analysis using transcriptome and metabolome showed that several pathways varied between tumor and non-tumor samples. Based on the results of the PCA, we believe that ICC and HCC have different carcinogenic mechanism therefore knowing the specific profile of genes and compounds can be useful in diagnosing ICC. PMID:26538415

  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.

    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. Target-based metabolomics for the quantitative measurement of 37 pathway metabolites in rat brain and serum using hydrophilic interaction ultra-high-performance liquid chromatography-tandem mass spectrometry.

    Chen, Jiahui; Hou, Waner; Han, Bo; Liu, Guanghui; Gong, Jin; Li, Yemeng; Zhong, Danmin; Liao, Qiongfeng; Xie, Zhiyong

    2016-04-01

    Amino acids, neurotransmitters, purines, and pyrimidines are bioactive molecules that play fundamental roles in maintaining various physiological functions. Their metabolism is closely related to the health, growth, development, reproduction, and homeostasis of organisms. Most recently, comprehensive measurements of these metabolites have shown their potential as innovative approaches in disease surveillance or drug intervention. However, simultaneous measurement of these metabolites presents great difficulties. Here, we report a novel quantitative method that uses hydrophilic interaction ultra-high-performance liquid chromatography-tandem mass spectrometry (HILIC-UPLC-MS/MS), which is highly selective, high throughput, and exhibits better chromatographic behavior than existing methods. The developed method enabled the rapid quantification of 37 metabolites, spanning amino acids, neurotransmitters, purines, and pyrimidines pathways, within 6.5 min. The compounds were separated on an ACQUITY UPLC® BEH Amide column. Serum and brain homogenate were extracted by protein precipitation. The intra- and interday precision of all of the analytes was less than 11.34 %, and the accuracy was between -11.74 and 11.51 % for all quality control (QC) levels. The extraction recoveries of serum ranged from 84.58 % to 116.43 % and those of brain samples from 80.80 % to 119.39 %, while the RSD was 14.61 % or less for all recoveries. This method was used to successfully characterize alterations in the rat brain and, in particular, their dynamics in serum. The following study was performed to simultaneously test global changes of these metabolites in a serotonin antagonist p-chlorophenylalanine (PCPA)-induced anxiety and insomnia rat model to understand the effect and mechanism of PCPA. Taken together, these results show that the method is able to simultaneously monitor a large panel of metabolites and that this protocol may represent a metabolomic method to diagnose

  7. Metabolomics of Genetically Modified Crops

    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...

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

    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

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

    Arnaudguilhem, C.; Bierla, K.; Ouerdane, L.; Preud' homme, H. [CNRS/UPPA, Laboratoire de Chimie Analytique Bio-inorganique et Environnement, UMR 5254, Helioparc, 2, Av. Pr. Angot, 64053 Pau (France); Yiannikouris, A. [Alltech Inc., 3031 Catnip Hill Pike, Nicholasville, KY (United States); Lobinski, R., E-mail: ryszard.lobinski@univ-pau.fr [CNRS/UPPA, Laboratoire de Chimie Analytique Bio-inorganique et Environnement, UMR 5254, Helioparc, 2, Av. Pr. Angot, 64053 Pau (France); Chair of Analytical Chemistry, Warsaw University of Technology, 00-664 Warszawa (Poland)

    2012-12-13

    Highlights: Black-Right-Pointing-Pointer The use of bimodal chromatographic separation enlarged amount of compounds identified. Black-Right-Pointing-Pointer The method allowed the largest scale ever (>60 compounds) speciation analysis of selenium metabolites in Se-rich yeast. Black-Right-Pointing-Pointer 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 MS{sup n}). 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.

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

    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.