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Sample records for plasma proteome project

  1. Low-molecular weight plasma proteome analysis using centrifugal ultrafiltration.

    Science.gov (United States)

    Greening, David W; Simpson, Richard J

    2011-01-01

    The low-molecular weight fraction (LMF) of the human plasma proteome is an invaluable source of biological information, especially in the context of identifying plasma-based biomarkers of disease. This protocol outlines a standardized procedure for the rapid/reproducible LMF profiling of human plasma samples using centrifugal ultrafiltration fractionation, followed by 1D-SDS-PAGE separation and nano-LC-MS/MS. Ultrafiltration is a convective process that uses anisotropic semipermeable membranes to separate macromolecular species on the basis of size. We have optimized centrifugal ultrafiltration for plasma fractionation with respect to buffer and solvent composition, centrifugal force, duration and temperature to facilitate >95% recovery, and enrichment of low-M (r) components from human plasma. Using this protocol, >260 unique peptides can be identified from a single plasma profiling experiment using 100 μL of plasma (Greening and Simpson, J Proteomics 73:637-648, 2010). The efficacy of this method is demonstrated by the identification, for the first time, of several plasma proteins (e.g., protein KIAA0649 (Q9Y4D3), rheumatoid factor D5, serine protease inhibitor A3, and transmembrane adapter protein PAG) previously not reported in extant high-confidence Human Proteome Organization Plasma Proteome Project datasets.

  2. Proteomics and the dynamic plasma membrane

    DEFF Research Database (Denmark)

    Sprenger, Richard R; Jensen, Ole Nørregaard

    2010-01-01

    plasma membrane is of particular interest, by not only serving as a barrier between the "cell interior" and the external environment, but moreover by organizing and clustering essential components to enable dynamic responses to internal and external stimuli. Defining and characterizing the dynamic plasma...... membrane proteome is crucial for understanding fundamental biological processes, disease mechanisms and for finding drug targets. Protein identification, characterization of dynamic PTMs and protein-ligand interactions, and determination of transient changes in protein expression and composition are among...... the challenges in functional proteomic studies of the plasma membrane. We review the recent progress in MS-based plasma membrane proteomics by presenting key examples from eukaryotic systems, including mammals, yeast and plants. We highlight the importance of enrichment and quantification technologies required...

  3. Analyzing large-scale proteomics projects with latent semantic indexing.

    Science.gov (United States)

    Klie, Sebastian; Martens, Lennart; Vizcaíno, Juan Antonio; Côté, Richard; Jones, Phil; Apweiler, Rolf; Hinneburg, Alexander; Hermjakob, Henning

    2008-01-01

    Since the advent of public data repositories for proteomics data, readily accessible results from high-throughput experiments have been accumulating steadily. Several large-scale projects in particular have contributed substantially to the amount of identifications available to the community. Despite the considerable body of information amassed, very few successful analyses have been performed and published on this data, leveling off the ultimate value of these projects far below their potential. A prominent reason published proteomics data is seldom reanalyzed lies in the heterogeneous nature of the original sample collection and the subsequent data recording and processing. To illustrate that at least part of this heterogeneity can be compensated for, we here apply a latent semantic analysis to the data contributed by the Human Proteome Organization's Plasma Proteome Project (HUPO PPP). Interestingly, despite the broad spectrum of instruments and methodologies applied in the HUPO PPP, our analysis reveals several obvious patterns that can be used to formulate concrete recommendations for optimizing proteomics project planning as well as the choice of technologies used in future experiments. It is clear from these results that the analysis of large bodies of publicly available proteomics data by noise-tolerant algorithms such as the latent semantic analysis holds great promise and is currently underexploited.

  4. Human maternal plasma proteomic changes with parturition

    Directory of Open Access Journals (Sweden)

    Robert J. Phillips

    2014-12-01

    Significance: Proteomic technology is constantly advancing, and the latest techniques enable gel-free analysis of minimally preprocessed, complex biological samples, enabling simultaneous identification and quantification of many hundreds of proteins. The technique of TMT labelling and Orbitrap mass spectrometry is applicable to the analysis of serial maternal plasma samples in order to identify potential markers of the onset of labour.

  5. Proteomics reveals the effects of sustained weight loss on the human plasma proteome

    DEFF Research Database (Denmark)

    Geyer, Philipp E; Wewer Albrechtsen, Nicolai J; Tyanova, Stefka;

    2016-01-01

    Sustained weight loss is a preferred intervention in a wide range of metabolic conditions, but the effects on an individual's health state remain ill-defined. Here, we investigate the plasma proteomes of a cohort of 43 obese individuals that had undergone 8 weeks of 12% body weight loss followed ...... evaluates and monitors intervention in metabolic diseases....... in the plasma proteome, and eight plasma proteins correlated better with insulin resistance than the known marker adiponectin. Nearly all study participants benefited from weight loss regarding a ten-protein inflammation panel defined from the proteomics data. We conclude that plasma proteome profiling broadly...

  6. Proteomics reveals the effects of sustained weight loss on the human plasma proteome

    DEFF Research Database (Denmark)

    Geyer, Philipp E; Wewer Albrechtsen, Nicolai J; Tyanova, Stefka

    2016-01-01

    Sustained weight loss is a preferred intervention in a wide range of metabolic conditions, but the effects on an individual's health state remain ill-defined. Here, we investigate the plasma proteomes of a cohort of 43 obese individuals that had undergone 8 weeks of 12% body weight loss followed...... by a year of weight maintenance. Using mass spectrometry-based plasma proteome profiling, we measured 1,294 plasma proteomes. Longitudinal monitoring of the cohort revealed individual-specific protein levels with wide-ranging effects of losing weight on the plasma proteome reflected in 93 significantly...... evaluates and monitors intervention in metabolic diseases....

  7. Proteomics reveals the effects of sustained weight loss on the human plasma proteome.

    Science.gov (United States)

    Geyer, Philipp E; Wewer Albrechtsen, Nicolai J; Tyanova, Stefka; Grassl, Niklas; Iepsen, Eva W; Lundgren, Julie; Madsbad, Sten; Holst, Jens J; Torekov, Signe S; Mann, Matthias

    2016-12-22

    Sustained weight loss is a preferred intervention in a wide range of metabolic conditions, but the effects on an individual's health state remain ill-defined. Here, we investigate the plasma proteomes of a cohort of 43 obese individuals that had undergone 8 weeks of 12% body weight loss followed by a year of weight maintenance. Using mass spectrometry-based plasma proteome profiling, we measured 1,294 plasma proteomes. Longitudinal monitoring of the cohort revealed individual-specific protein levels with wide-ranging effects of losing weight on the plasma proteome reflected in 93 significantly affected proteins. The adipocyte-secreted SERPINF1 and apolipoprotein APOF1 were most significantly regulated with fold changes of -16% and +37%, respectively (P plasma proteome, and eight plasma proteins correlated better with insulin resistance than the known marker adiponectin. Nearly all study participants benefited from weight loss regarding a ten-protein inflammation panel defined from the proteomics data. We conclude that plasma proteome profiling broadly evaluates and monitors intervention in metabolic diseases. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

  8. The Human Skeletal Muscle Proteome Project

    DEFF Research Database (Denmark)

    Gonzalez-Freire, Marta; Semba, Richard D.; Ubaida-Mohien, Ceereena

    2017-01-01

    Skeletal muscle is a large organ that accounts for up to half the total mass of the human body. A progressive decline in muscle mass and strength occurs with ageing and in some individuals configures the syndrome of ‘sarcopenia’, a condition that impairs mobility, challenges autonomy, and is a risk...... factor for mortality. The mechanisms leading to sarcopenia as well as myopathies are still little understood. The Human Skeletal Muscle Proteome Project was initiated with the aim to characterize muscle proteins and how they change with ageing and disease. We conducted an extensive review...... of the literature and analysed publically available protein databases. A systematic search of peer-reviewed studies was performed using PubMed. Search terms included ‘human’, ‘skeletal muscle’, ‘proteome’, ‘proteomic(s)’, and ‘mass spectrometry’, ‘liquid chromatography-mass spectrometry (LC-MS/MS)’. A catalogue...

  9. Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

    Energy Technology Data Exchange (ETDEWEB)

    Omenn, Gilbert; States, David J.; Adamski, Marcin; Blackwell, Thomas W.; Menon, Rajasree; Hermjakob, Henning; Apweiler, Rolf; Haab, Brian B.; Simpson, Richard; Eddes, James; Kapp, Eugene; Moritz, Rod; Chan, Daniel W.; Rai, Alex J.; Admon, Arie; Aebersold, Ruedi; Eng, Jimmy K.; Hancock, William S.; Hefta, Stanley A.; Meyer, Helmut; Paik, Young-Ki; Yoo, Jong-Shin; Ping, Peipei; Pounds, Joel G.; Adkins, Joshua N.; Qian, Xiaohong; Wang, Rong; Wasinger, Valerie; Wu, Chi Yue; Zhao, Xiaohang; Zeng, Rong; Archakov, Alexander; Tsugita, Akira; Beer, Ilan; Pandey, Akhilesh; Pisano, Michael; Andrews, Philip; Tammen, Harald; Speicher, David W.; Hanash, Samir M.

    2005-08-13

    HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics. med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan

  10. The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.

    Science.gov (United States)

    Schwenk, Jochen M; Omenn, Gilbert S; Sun, Zhi; Campbell, David S; Baker, Mark S; Overall, Christopher M; Aebersold, Ruedi; Moritz, Robert L; Deutsch, Eric W

    2017-09-22

    Human blood plasma provides a highly accessible window to the proteome of any individual in health and disease. Since its inception in 2002, the Human Proteome Organization's Human Plasma Proteome Project (HPPP) has been promoting advances in the study and understanding of the full protein complement of human plasma and on determining the abundance and modifications of its components. In 2017, we review the history of the HPPP and the advances of human plasma proteomics in general, including several recent achievements. We then present the latest 2017-04 build of Human Plasma PeptideAtlas, which yields ~43 million peptide-spectrum matches and 122,730 distinct peptide sequences from 178 individual experiments at a 1% protein-level FDR globally across all experiments. Applying the latest Human Proteome Project Data Interpretation Guidelines, we catalog 3509 proteins that have at least two non-nested uniquely-mapping peptides of 9 amino acids or more and >1300 additional proteins with ambiguous evidence. We apply the same two-peptide guideline to historical PeptideAtlas builds going back to 2006 and examine the progress made in the past ten years in plasma proteome coverage. We also compare the distribution of proteins in historical PeptideAtlas builds in various RNA-abundance and cellular localization categories. We then discuss advances in plasma proteomics based on targeted mass spectrometry as well as affinity assays, which during early 2017 target ~2000 proteins. Finally we describe considerations about sample handling and study design, concluding with an outlook for future advances in deciphering the human plasma proteome.

  11. Characterization of the porcine synovial fluid proteome and a comparison to the plasma proteome

    DEFF Research Database (Denmark)

    Bennike, Tue Bjerg; Barnaby, Omar; Steen, Hanno;

    2015-01-01

    Synovial fluid is present in all joint cavities, and protects the articular cartilage surfaces in large by lubricating the joint, thus reducing friction. Several studies have described changes in the protein composition of synovial fluid in patients with joint disease. However, the protein...... concentration, content, and synovial fluid volume change dramatically during active joint diseases and inflammation, and the proteome composition of healthy synovial fluid is incompletely characterized. We performed a normative proteomics analysis of porcine synovial fluid, and report data from optimizing...... data used in the method optimization, human plasma proteomics data, and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD000935....

  12. Experimental plasma research project summaries

    Energy Technology Data Exchange (ETDEWEB)

    1978-08-01

    This report contans descriptions of the activities supported by the Experimental Plasma Research Branch of APP. The individual project summaries were prepared by the principal investigators and include objectives and milestones for each project. The projects are arranged in six research categories: Plasma Properties; Plasma Heating; Plasma Measurements and Instrumentation; Atomic, Molecular and Nuclear Physics; Advanced Superconducting Materials; and the Fusion Plasma Research Facility (FPRF). Each category is introduced with a statement of objectives and recent progress and followed by descriptions of individual projects. An overall budget summary is provided at the beginning of the report.

  13. Experimental Plasma Research project summaries

    Energy Technology Data Exchange (ETDEWEB)

    None

    1980-09-01

    This report contains descriptions of the activities supported by the Experimental Plasma Research Branch of APP. The individual project summaries were prepared by the principal investigators and include objectives and milestones for each project. The projects are arranged in six research categories: Plasma Properties; Plasma Heating; Plasma Diagnostics; Atomic, Molecular and Nuclear Physics; Advanced Superconducting Materials; and the Fusion Plasma Research Facility (FPRF). Each category is introduced with a statement of objectives and recent progress and followed by descriptions of individual projects. An overall budget summary is provided at the beginning of the report.

  14. Statistical Analysis of Variation in the Human Plasma Proteome

    Directory of Open Access Journals (Sweden)

    Todd H. Corzett

    2010-01-01

    Full Text Available Quantifying the variation in the human plasma proteome is an essential prerequisite for disease-specific biomarker detection. We report here on the longitudinal and individual variation in human plasma characterized by two-dimensional difference gel electrophoresis (2-D DIGE using plasma samples from eleven healthy subjects collected three times over a two week period. Fixed-effects modeling was used to remove dye and gel variability. Mixed-effects modeling was then used to quantitate the sources of proteomic variation. The subject-to-subject variation represented the largest variance component, while the time-within-subject variation was comparable to the experimental variation found in a previous technical variability study where one human plasma sample was processed eight times in parallel and each was then analyzed by 2-D DIGE in triplicate. Here, 21 protein spots had larger than 50% CV, suggesting that these proteins may not be appropriate as biomarkers and should be carefully scrutinized in future studies. Seventy-eight protein spots showing differential protein levels between different individuals or individual collections were identified by mass spectrometry and further characterized using hierarchical clustering. The results present a first step toward understanding the complexity of longitudinal and individual variation in the human plasma proteome, and provide a baseline for improved biomarker discovery.

  15. The plasma membrane proteome of germinating barley embryos

    DEFF Research Database (Denmark)

    Hynek, Radovan; Svensson, Birte; Jensen, O.N.

    2009-01-01

    was used to reduce soluble protein contamination and enrich for hydrophobic proteins. Sixty-one proteins in 14 SDS-PAGE bands were identified by LC-MS/MS and database searches. The identifications provide new insight into the plasma membrane functions in seed germination.......Cereal seed germination involves a complex coordination between different seed tissues. Plasma membranes must play crucial roles in coordination and execution of germination; however, very little is known about seed plasma membrane proteomes due to limited tissue amounts combined...... with amphiphilicity and low abundance of membrane proteins. A fraction enriched in plasma membranes was prepared from embryos dissected from 18 h germinated barley seeds using aqueous two-phase partitioning. Reversed-phase chromatography on C-4 resin performed in micro-spin columns with stepwise elution by 2-propanol...

  16. Miniature Flat Plasma Spectrometer Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This phase I SBIR project will develop a micromachined charged particle energy collimator plate to be used as a principle component in a micromachined plasma...

  17. Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project.

    Science.gov (United States)

    Omenn, Gilbert S; Lane, Lydie; Lundberg, Emma K; Overall, Christopher M; Deutsch, Eric W

    2017-08-30

    The Human Proteome Organization (HUPO) Human Proteome Project (HPP) continues to make progress on its two overall goals: (1) completing the protein parts list, with an annual update of the HUPO draft human proteome, and (2) making proteomics an integrated complement to genomics and transcriptomics throughout biomedical and life sciences research. neXtProt version 2017-01-23 has 17,008 confident protein identifications (Protein Existence [PE] level 1) that are compliant with the HPP Guidelines v2.1 (https://hupo.org/Guidelines), up from 13,664 in 2012-12 and 16,518 in 2016-04. Remaining to be found by mass spectrometry and other methods are 2579 "missing proteins" (PE2+3+4), down from 2949 in 2016. PeptideAtlas 2017-01 has 15,173 canonical proteins, accounting for nearly all of the 15,290 PE1 proteins based on MS data. These resources have extensive data on PTMs, single amino acid variants, and splice isoforms. The Human Protein Atlas v16 has 10,492 highly-curated protein entries with tissue and subcellular spatial localization of proteins and transcript expression. Organ-specific popular protein lists have been generated for broad use in quantitative targeted proteomics using SRM-MS or DIA-SWATH-MS studies of biology and disease.

  18. Novel effects of hormonal contraceptive use on the plasma proteome.

    Directory of Open Access Journals (Sweden)

    Andrea R Josse

    Full Text Available BACKGROUND: Hormonal contraceptive (HC use may increase cardiometabolic risk; however, the effect of HC on emerging cardiometabolic and other disease risk factors is not clear. OBJECTIVES: To determine the association between HC use and plasma proteins involved in established and emerging disease risk pathways. METHOD: Concentrations of 54 high-abundance plasma proteins were measured simultaneously by LC-MRM/MS in 783 women from the Toronto Nutrigenomics and Health Study. C-reactive protein (CRP was measured separately. ANCOVA was used to test differences in protein concentrations between users and non-users, and among HC users depending on total hormone dose. Linear regression was used to test the association between duration (years of HC use and plasma protein concentrations. Principal components analysis (PCA was used to identify plasma proteomic profiles in users and non-users. RESULTS: After Bonferroni correction, 19 proteins involved in inflammation, innate immunity, coagulation and blood pressure regulation were significantly different between users and non-users (P<0.0009. These differences were replicated across three distinct ethnocultural groups. Traditional markers of glucose and lipid metabolism were also significantly higher among HC users. Neither hormone dose nor duration of use affected protein concentrations. PCA identified 4 distinct proteomic profiles in users and 3 in non-users. CONCLUSION: HC use was associated with different concentrations of plasma proteins along various disease-related pathways, and these differences were present across different ethnicities. Aside from the known effect of HC on traditional biomarkers of cardiometabolic risk, HC use also affects numerous proteins that may be biomarkers of dysregulation in inflammation, coagulation and blood pressure.

  19. Site specific modification of the human plasma proteome by methylglyoxal.

    Science.gov (United States)

    Kimzey, Michael J; Kinsky, Owen R; Yassine, Hussein N; Tsaprailis, George; Stump, Craig S; Monks, Terrence J; Lau, Serrine S

    2015-12-01

    Increasing evidence identifies dicarbonyl stress from reactive glucose metabolites, such as methylglyoxal (MG), as a major pathogenic link between hyperglycemia and complications of diabetes. MG covalently modifies arginine residues, yet the site specificity of this modification has not been thoroughly investigated. Sites of MG adduction in the plasma proteome were identified using LC-MS/MS analysis in vitro following incubation of plasma proteins with MG. Treatment of plasma proteins with MG yielded 14 putative MG hotspots from five plasma proteins (albumin [nine hotspots], serotransferrin, haptoglobin [2 hotspots], hemopexin, and Ig lambda-2 chain C regions). The search results revealed two versions of MG-arginine modification, dihydroxyimidazolidine (R+72) and hydroimidazolone (R+54) adducts. One of the sites identified was R257 in human serum albumin, which is a critical residue located in drug binding site I. This site was validated as a target for MG modification by a fluorescent probe displacement assay, which revealed significant drug dissociation at 300 μM MG from a prodan-HSA complex (75 μM). Moreover, twelve human plasma samples (six male, six female, with two type 2 diabetic subjects from both genders) were analyzed using multiple reaction monitoring (MRM) tandem mass spectrometry and revealed the presence of the MG-modified albumin R257 peptide. These data provide insights into the nature of the site-specificity of MG modification of arginine, which may be useful for therapeutic treatments that aim to prevent MG-mediated adverse responses in patients.

  20. Site Specific Modification of the Human Plasma Proteome by Methylglyoxal

    Science.gov (United States)

    Kimzey, Michael J.; Kinsky, Owen R.; Yassine, Hussein N.; Tsaprailis, George; Stump, Craig; Monks, Terrence J.; Lau, Serrine S.

    2015-01-01

    Increasing evidence identifies dicarbonyl stress from reactive glucose metabolites, such as methylglyoxal (MG), as a major pathogenic link between hyperglycemia and complications of diabetes. MG covalently modifies arginine residues, yet the site specificity of this modification has not been thoroughly investigated. Sites of MG adduction in the plasma proteome were identified using LC-MS/MS analysis in vitro following incubation of plasma proteins with MG. Treatment of plasma proteins with MG yielded 14 putative MG hotspots from five plasma proteins (albumin [nine hotspots], serotransferrin, haptoglobin [2 hotspots], hemopexin, and Ig lambda-2 chain C regions). The search results revealed two versions of MG-arginine modification, dihydroxyimidazolidine (R+72) and hydroimidazolone (R+54) adducts. One of the sites identified was R257 in human serum albumin, which is a critical residue located in drug binding site I. This site was validated as a target for MG modification by a fluorescent probe displacement assay, which revealed significant drug dissociation at 300 μM MG from a prodan-HSA complex (75 μM). Moreover, twelve human plasma samples (six male, six female, with two type 2 diabetic subjects from both genders) were analyzed using multiple reaction monitoring (MRM) tandem mass spectrometry and revealed the presence of the MG-modified albumin R257 peptide. These data provide insights into the nature of the site-specificity of MG modification of arginine, which may be useful for therapeutic treatments that aim to prevent MG-mediated adverse responses in patients. PMID:26435215

  1. Fusion Plasma Theory project summaries

    Energy Technology Data Exchange (ETDEWEB)

    1993-10-01

    This Project Summary book is a published compilation consisting of short descriptions of each project supported by the Fusion Plasma Theory and Computing Group of the Advanced Physics and Technology Division of the Department of Energy, Office of Fusion Energy. The summaries contained in this volume were written by the individual contractors with minimal editing by the Office of Fusion Energy. Previous summaries were published in February of 1982 and December of 1987. The Plasma Theory program is responsible for the development of concepts and models that describe and predict the behavior of a magnetically confined plasma. Emphasis is given to the modelling and understanding of the processes controlling transport of energy and particles in a toroidal plasma and supporting the design of the International Thermonuclear Experimental Reactor (ITER). A tokamak transport initiative was begun in 1989 to improve understanding of how energy and particles are lost from the plasma by mechanisms that transport them across field lines. The Plasma Theory program has actively-participated in this initiative. Recently, increased attention has been given to issues of importance to the proposed Tokamak Physics Experiment (TPX). Particular attention has been paid to containment and thermalization of fast alpha particles produced in a burning fusion plasma as well as control of sawteeth, current drive, impurity control, and design of improved auxiliary heating. In addition, general models of plasma behavior are developed from physics features common to different confinement geometries. This work uses both analytical and numerical techniques. The Fusion Theory program supports research projects at US government laboratories, universities and industrial contractors. Its support of theoretical work at universities contributes to the office of Fusion Energy mission of training scientific manpower for the US Fusion Energy Program.

  2. 2 D gel based analysis of biological variability of the human plasma proteome

    DEFF Research Database (Denmark)

    Rentsch, Maria Louise; Jessen, Flemming

    Human blood plasma is a valuable specimen for the biomarker discovery process, since it is easily accessible and contains proteins that are synthesised, secreted or lost from cells and tissue. In this way, changes in plasma proteome reflect the current state of the organism. The analysis of plasma...... by one-week interval. Blood samples were drawn before the meal intake and five times during 24 hours for proteome analysis. Plasma was fractionated by use of IgY-12 spin column depleting the 12 highly abundant proteins and further processed for two-dimensional gel electrophoresis. The plasma proteome...... proteome is yet challenging due to the huge dynamic range of protein abundance. When evaluating a potential biomarker, stable basal level of the protein is needed before it can be considered a functional biomarker. However, basal level differences of plasma proteins are naturally occurring between...

  3. WGM Resonators for Proteomic Analysis Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Due to the extensive amounts of data generated from the genome sequencing projects, the focus of genomics has shifted from elucidating DNA sequence to the...

  4. Dietary zinc depletion and repletion affects plasma proteins: an analysis of the plasma proteome.

    Science.gov (United States)

    Grider, Arthur; Wickwire, Kathie; Ho, Emily; Chung, Carolyn S; King, Janet

    2013-02-01

    Zinc (Zn) deficiency is a problem world-wide. Current methods for assessing Zn status are limited to measuring plasma or serum Zn within populations suspected of deficiency. Despite the high prevalence of Zn deficiency in the human population there are no methods currently available for sensitively assessing Zn status among individuals. The purpose of this research was to utilize a proteomic approach using two-dimensional gel electrophoresis (2DE) and mass spectrometry to identify protein biomarkers that were sensitive to changes in dietary Zn levels in humans. Proteomic analysis was performed in human plasma samples (n = 6) obtained from healthy adult male subjects that completed a dietary Zn depletion/repletion protocol, current dietary zinc intake has a greater effect on fractional zinc absorption than does longer term zinc consumption in healthy adult men. Chung et al. (Am J Clin Nutr 87 (5):1224-1229, 2008). After a 13 day Zn acclimatization period where subjects consumed a Zn-adequate diet, the male subjects consumed a marginal Zn-depleted diet for 42 days followed by consumption of a Zn-repleted diet for 28 days. The samples at baseline, end of depletion and end of repletion were pre-fractionated through immuno-affinity columns to remove 14 highly abundant proteins, and each fraction separated by 2DE. Following staining by colloidal Coomassie blue and densitometric analysis, three proteins were identified by mass spectrometry as affected by changes in dietary Zn. Fibrin β and chain E, fragment double D were observed in the plasma protein fraction that remained bound to the immunoaffinity column. An unnamed protein that was related to immunoglobulins was observed in the immunodepleted plasma fraction. Fibrin β increased two-fold following the Zn depletion period and decreased to baseline values following the Zn repletion period; this protein may serve as a viable biomarker for Zn status in the future.

  5. Plasma proteome analysis of patients with type 1 diabetes with diabetic nephropathy

    DEFF Research Database (Denmark)

    Overgaard, Anne Julie; Hansen, Henning Gram; Lajer, Maria

    2010-01-01

    -driven studies or urinary based investigations. To date only two studies have investigated the proteome of blood in search for new biomarkers, and these studies were conducted in sera from patients with type 2 diabetes. This is the first reported in depth proteomic study where plasma from type 1 diabetic......As part of a clinical proteomics program focused on diabetes and its complications we are looking for new and better protein biomarkers for diabetic nephropathy. The search for new and better biomarkers for diabetic nephropathy has, with a few exceptions, previously focused on either hypothesis...

  6. Additions to the Human Plasma Proteome via a Tandem MARS Depletion iTRAQ-Based Workflow

    Directory of Open Access Journals (Sweden)

    Zhiyun Cao

    2013-01-01

    Full Text Available Robust platforms for determining differentially expressed proteins in biomarker and discovery studies using human plasma are of great interest. While increased depth in proteome coverage is desirable, it is associated with costs of experimental time due to necessary sample fractionation. We evaluated a robust quantitative proteomics workflow for its ability (1 to provide increased depth in plasma proteome coverage and (2 to give statistical insight useful for establishing differentially expressed plasma proteins. The workflow involves dual-stage immunodepletion on a multiple affinity removal system (MARS column, iTRAQ tagging, offline strong-cation exchange chromatography, and liquid chromatography tandem mass spectrometry (LC-MS/MS. Independent workflow experiments were performed in triplicate on four plasma samples tagged with iTRAQ 4-plex reagents. After stringent criteria were applied to database searched results, 689 proteins with at least two spectral counts (SC were identified. Depth in proteome coverage was assessed by comparison to the 2010 Human Plasma Proteome Reference Database in which our studies reveal 399 additional proteins which have not been previously reported. Additionally, we report on the technical variation of this quantitative workflow which ranges from ±11 to 30%.

  7. Additions to the Human Plasma Proteome via a Tandem MARS Depletion iTRAQ-Based Workflow.

    Science.gov (United States)

    Cao, Zhiyun; Yende, Sachin; Kellum, John A; Robinson, Renã A S

    2013-01-01

    Robust platforms for determining differentially expressed proteins in biomarker and discovery studies using human plasma are of great interest. While increased depth in proteome coverage is desirable, it is associated with costs of experimental time due to necessary sample fractionation. We evaluated a robust quantitative proteomics workflow for its ability (1) to provide increased depth in plasma proteome coverage and (2) to give statistical insight useful for establishing differentially expressed plasma proteins. The workflow involves dual-stage immunodepletion on a multiple affinity removal system (MARS) column, iTRAQ tagging, offline strong-cation exchange chromatography, and liquid chromatography tandem mass spectrometry (LC-MS/MS). Independent workflow experiments were performed in triplicate on four plasma samples tagged with iTRAQ 4-plex reagents. After stringent criteria were applied to database searched results, 689 proteins with at least two spectral counts (SC) were identified. Depth in proteome coverage was assessed by comparison to the 2010 Human Plasma Proteome Reference Database in which our studies reveal 399 additional proteins which have not been previously reported. Additionally, we report on the technical variation of this quantitative workflow which ranges from ±11 to 30%.

  8. Plasma proteomics to identify biomarkers - Application to cardiovascular diseases

    DEFF Research Database (Denmark)

    Beck, Hans Christian; Overgaard, Martin; Melholt Rasmussen, Lars

    2015-01-01

    , this technology may therefore identify new biomarkers that previously have not been associated with cardiovascular diseases. In this review, we summarize the key challenges and considerations, including strategies, recent discoveries and clinical applications in cardiovascular proteomics that may lead...

  9. Differential proteomics of human seminal plasma: A potential target for searching male infertility marker proteins.

    Science.gov (United States)

    Tomar, Anil Kumar; Sooch, Balwinder Singh; Singh, Sarman; Yadav, Savita

    2012-04-01

    The clinical fertility tests, available in the market, fail to define the exact cause of male infertility in almost half of the cases and point toward a crucial need of developing better ways of infertility investigations. The protein biomarkers may help us toward better understanding of unknown cases of male infertility that, in turn, can guide us to find better therapeutic solutions. Many clinical attempts have been made to identify biomarkers of male infertility in sperm proteome but only few studies have targeted seminal plasma. Human seminal plasma is a rich source of proteins that are essentially required for development of sperm and successful fertilization. This viewpoint article highlights the importance of human seminal plasma proteome in reproductive physiology and suggests that differential proteomics integrated with functional analysis may help us in searching potential biomarkers of male infertility.

  10. GEC Plasma Data Exchange Project

    Science.gov (United States)

    Pitchford, L. C.

    2013-08-01

    In 2010 the Gaseous Electronics Conference (GEC), a major international conference for the low temperature plasma science (LTPS) community, initiated the Plasma Data Exchange Project (PDEP). The PDEP is an informal, community-based project that aims to address, at least in part, the well-recognized needs for the community to organize the means of collecting, evaluating and sharing data both for modelling and for interpretation of experiments. The emphasis to date in the PDEP has been on data related to the electron and ion components of these plasmas rather than on the plasma chemistry. At the heart of the PDEP is the open-access website, LXCat [1], developed by researchers at LAPLACE (Laboratoire Plasma et Conversion d'Energie, Toulouse, France). LXCat is a platform for archiving and manipulating collections of data related to electron scattering and transport in cold, neutral gases, organized in databases set-up by individual members or institutions of the LTPS community. At present, 15 databases of electron scattering data, contributed by groups around the world, can be accessed on LXCat. These databases include complete sets of electron cross sections, over an energy range from thermal to nominally 1 keV, for almost 40 ground-state neutral species and partial sets of data for about 30 other neutral, excited and ionized species. 'Complete' implies that all the major electron momentum and energy loss processes are well described in the dataset. Such 'complete' datasets can be used as input to a Boltzmann calculation of the electron energy distribution function (generally non-Maxwellian), and electron transport and rate coefficients can be obtained in pure gases or mixtures by averaging over the distribution function. Online tools enable importing and exporting data, plotting and comparing different sets of data. An online version of the Boltzmann equation solver BOLSIG+ [2] is also available on the LXCat site. Other members of the community have contributed their

  11. Single Electron Transistor Platform for Microgravity Proteomics Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Proteomic studies in microgravity are crucial to understanding the health effects of spaceflight on astronauts. Unfortunately, existing tools for measuring protein,...

  12. Proteomics

    DEFF Research Database (Denmark)

    Dam, Svend; Stougaard, Jens

    2014-01-01

    proteomics data. Two characteristics of legumes are the high seed protein level and the nitrogen fixing symbiosis. Thus, the majority of the proteomics studies in Lotus have been performed on seed/pod and nodule/root tissues in order to create proteome reference maps and to enable comparative analyses within...... Lotus tissues or toward similar tissues from other legume species. More recently, N-glycan structures and compositions have been determined from mature Lotus seeds using glycomics and glycoproteomics, and finally, phosphoproteomics has been employed...... and annotated Lotus japonicus (Lotus) genome has been essential for obtaining high-quality protein identifications from proteomics studies. Furthermore, additional genomics and transcriptomics studies from several Lotus species/ecotypes support putative gene structures and these can be further supported using...

  13. Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics.

    Science.gov (United States)

    Malmström, Erik; Kilsgård, Ola; Hauri, Simon; Smeds, Emanuel; Herwald, Heiko; Malmström, Lars; Malmström, Johan

    2016-01-06

    The plasma proteome is highly dynamic and variable, composed of proteins derived from surrounding tissues and cells. To investigate the complex processes that control the composition of the plasma proteome, we developed a mass spectrometry-based proteomics strategy to infer the origin of proteins detected in murine plasma. The strategy relies on the construction of a comprehensive protein tissue atlas from cells and highly vascularized organs using shotgun mass spectrometry. The protein tissue atlas was transformed to a spectral library for highly reproducible quantification of tissue-specific proteins directly in plasma using SWATH-like data-independent mass spectrometry analysis. We show that the method can determine drastic changes of tissue-specific protein profiles in blood plasma from mouse animal models with sepsis. The strategy can be extended to several other species advancing our understanding of the complex processes that contribute to the plasma proteome dynamics.

  14. Plasma membrane proteomics and its application in clinical cancer biomarker discovery

    DEFF Research Database (Denmark)

    Leth-Larsen, Rikke; Lund, Rikke; Ditzel, Henrik J

    2010-01-01

    Plasma membrane proteins that are exposed on the cell surface have important biological functions, such as signaling into and out of the cells, ion transport, and cell-cell and cell-matrix interactions. The expression level of many of the plasma membrane proteins involved in these key functions...... targeted by protein drugs, such as human antibodies, that have enhanced survival of several groups of cancer patients. The combination of novel analytical approaches and subcellular fractionation procedures has made it possible to study the plasma membrane proteome in more detail, which will elucidate...... cancer biology, particularly metastasis, and guide future development of novel drug targets. The technical advances in plasma membrane proteomics and the consequent biological revelations will be discussed herein. Many of the advances have been made using cancer cell lines, but because the main goal...

  15. Proteomic analysis of liver plasma membrane from hepatitis B surface antigen transgenic mice

    Institute of Scientific and Technical Information of China (English)

    贾小芳

    2012-01-01

    Objective To explore the differential liver plasma membrane( PM) proteins that may be related to the occurrence,development and reversal process of hepatitis and to understand the pathogenesis of hepatitis and the new drug targets by performing a comparative proteomics research of liver PM between

  16. Electron Kinetics in Hypersonic Plasmas Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The goal of this SBIR project is to advance the state-of-the-art in computations of hypersonic plasmas by adding high-fidelity kinetic models for electrons. Electron...

  17. Plasma proteome changes in cardiovascular disease patients: novel isoforms of apolipoprotein A1

    Directory of Open Access Journals (Sweden)

    Oravec Milan

    2011-06-01

    Full Text Available Abstract Background The aim of this proteomic study was to look for changes taking place in plasma proteomes of patients with acute myocardial infarction (AMI, unstable angina pectoris (UAP, and stable angina pectoris (SAP. Methods Depleted plasma proteins were separated by 2D SDS-PAGE (pI 4-7, and proteomes were compared using Progenesis SameSpots statistical software. Proteins were identified by nanoLC-MS/MS. Proteins were quantified using commercial kits. Apolipoprotein A1 was studied using 1D and 2D SDS-PAGE, together with western blotting. Results Reciprocal comparison revealed 46 unique, significantly different spots; proteins in 34 spots were successfully identified and corresponded to 38 different proteins. Discrete comparisons of patient groups showed 45, 41, and 8 significantly different spots when AMI, UAP, and SAP were compared with the control group. On the basis of our proteomic data, plasma levels of two of them, alpha-1 microglobulin and vitamin D-binding protein, were determined. The data, however, failed to prove the proteins to be suitable markers or risk factors in the studied groups. The plasma level and isoform representation of apolipoprotein A1 were also estimated. Using 1D and 2D SDS-PAGE, together with western blotting, we observed extra high-molecular weight apolipoprotein A1 fractions presented only in the patient groups, indicating that the novel high-molecular weight isoforms of apolipoprotein A1 may be potential new markers or possible risk factors of cardiovascular disease. Conclusion The reported data show plasma proteome changes in patients with AMI, UAP, and SAP. We propose some apolipoprotein A1 fractions as a possible new disease-associated marker of cardiovascular disorders.

  18. Plasma proteome response to severe burn injury revealed by 18O-labeled "universal" reference-based quantitative proteomics.

    Science.gov (United States)

    Qian, Wei-Jun; Petritis, Brianne O; Kaushal, Amit; Finnerty, Celeste C; Jeschke, Marc G; Monroe, Matthew E; Moore, Ronald J; Schepmoes, Athena A; Xiao, Wenzhong; Moldawer, Lyle L; Davis, Ronald W; Tompkins, Ronald G; Herndon, David N; Camp, David G; Smith, Richard D

    2010-09-01

    A burn injury represents one of the most severe forms of human trauma and is responsible for significant mortality worldwide. Here, we present the first quantitative proteomics investigation of the blood plasma proteome response to severe burn injury by comparing the plasma protein concentrations of 10 healthy control subjects with those of 15 severe burn patients at two time-points following the injury. The overall analytical strategy for this work integrated immunoaffinity depletion of the 12 most abundant plasma proteins with cysteinyl-peptide enrichment-based fractionation prior to LC-MS analyses of individual patient samples. Incorporation of an 18O-labeled "universal" reference among the sample sets enabled precise relative quantification across samples. In total, 313 plasma proteins confidently identified with two or more unique peptides were quantified. Following statistical analysis, 110 proteins exhibited significant abundance changes in response to the burn injury. The observed changes in protein concentrations suggest significant inflammatory and hypermetabolic response to the injury, which is supported by the fact that many of the identified proteins are associated with acute phase response signaling, the complement system, and coagulation system pathways. The regulation of approximately 35 proteins observed in this study is in agreement with previous results reported for inflammatory or burn response, but approximately 50 potentially novel proteins previously not known to be associated with burn response or inflammation are also found. Elucidating proteins involved in the response to severe burn injury may reveal novel targets for therapeutic interventions as well as potential predictive biomarkers for patient outcomes such as multiple organ failure.

  19. Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate.

    Science.gov (United States)

    Serra, Aida; Zhu, Hongbin; Gallart-Palau, Xavier; Park, Jung Eun; Ho, Hee Haw; Tam, James P; Sze, Siu Kwan

    2016-03-01

    The ionic detergent sodium deoxycholate (SDC) is compatible with in-solution tryptic digestion and LC-MS/MS-based shotgun proteomics by virtue of being easy to separate from the peptide products via precipitation in acidic buffers. However, it remains unclear whether unique human peptides co-precipitate with SDC during acid treatment of complex biological samples. In this study, we demonstrate for the first time that a large quantity of unique peptides in human blood plasma can be co-precipitated with SDC using an optimized sample preparation method prior to shotgun proteomic analysis. We show that the plasma peptides co-precipitated with SDC can be successfully recovered using a sequential re-solubilization and precipitation procedure, and that this approach is particularly efficient at the extraction of long peptides. Recovery of peptides from the SDC pellet dramatically increased overall proteome coverage (>60 %), thereby improving the identification of low-abundance proteins and enhancing the identification of protein components of membrane-bound organelles. In addition, when we analyzed the physiochemical properties of the co-precipitated peptides, we observed that SDC-based sample preparation improved the identification of mildly hydrophilic/hydrophobic proteins that would otherwise be lost upon discarding the pellet. These data demonstrate that the optimized SDC protocol is superior to sodium dodecyl sulfate (SDS)/urea treatment for identifying plasma biomarkers by shotgun proteomics.

  20. An update on medium- and low-abundant blood plasma proteome of horse.

    Science.gov (United States)

    Lepczyński, A; Ożgo, M; Dratwa-Chałupnik, A; Robak, P; Pyć, A; Zaborski, D; Herosimczyk, A

    2017-07-10

    The main objectives of the study were to: (1) deeply analyse the serum protein composition of Equus caballus, (2) assess the effectiveness of the high-abundant protein depletion and improve the concentration of medium- and low-abundant proteins. The analysis were performed on the blood plasma of three healthy part-Arabian mares. The implementation of two-dimensional electrophoresis and matrix-assisted laser desorption/ionisation - time of flight mass spectrometry allowed us to establish a horse plasma proteome map. Serum proteins were resolved at pH 4 to 7, followed by 12% SDS-PAGE. As a result 136 spots were successfully identified, representing the products of 46 unique genes. Of these, 22 gene products have not been previously identified in horse serum/plasma samples using proteomic tools. Gene ontology analysis showed that almost 30% of all identified gene products belong to the coagulation and complement cascades. These results can undoubtedly serve as a useful and prospective prerequisite for the future analysis of horse plasma proteome changes in different physiological and pathophysiological conditions. The use of the medium- and low-abundant protein enrichment tool increased their abundance and allowed us to identify a higher number of protein gene products. The highest depletion efficiency was observed for the most abundant plasma proteins, that is albumin, IgG heavy chains and serotransferrin.

  1. Automated Sample Preparation Platform for Mass Spectrometry-Based Plasma Proteomics and Biomarker Discovery

    Directory of Open Access Journals (Sweden)

    Vilém Guryča

    2014-03-01

    Full Text Available The identification of novel biomarkers from human plasma remains a critical need in order to develop and monitor drug therapies for nearly all disease areas. The discovery of novel plasma biomarkers is, however, significantly hampered by the complexity and dynamic range of proteins within plasma, as well as the inherent variability in composition from patient to patient. In addition, it is widely accepted that most soluble plasma biomarkers for diseases such as cancer will be represented by tissue leakage products, circulating in plasma at low levels. It is therefore necessary to find approaches with the prerequisite level of sensitivity in such a complex biological matrix. Strategies for fractionating the plasma proteome have been suggested, but improvements in sensitivity are often negated by the resultant process variability. Here we describe an approach using multidimensional chromatography and on-line protein derivatization, which allows for higher sensitivity, whilst minimizing the process variability. In order to evaluate this automated process fully, we demonstrate three levels of processing and compare sensitivity, throughput and reproducibility. We demonstrate that high sensitivity analysis of the human plasma proteome is possible down to the low ng/mL or even high pg/mL level with a high degree of technical reproducibility.

  2. Plasma proteomic alterations in non-human primates and humans after chronic alcohol self-administration.

    Science.gov (United States)

    Freeman, Willard M; Vanguilder, Heather D; Guidone, Elizabeth; Krystal, John H; Grant, Kathleen A; Vrana, Kent E

    2011-08-01

    Objective diagnostics of excessive alcohol use are valuable tools in the identification and monitoring of subjects with alcohol use disorders. A number of potential biomarkers of alcohol intake have been proposed, but none have reached widespread clinical usage, often due to limited diagnostic sensitivity and specificity. In order to identify novel potential biomarkers, we performed proteomic biomarker target discovery in plasma samples from non-human primates that chronically self-administer high levels of ethanol. Two-dimensional difference in-gel electrophoresis (2D-DIGE) was used to quantify plasma proteins from within-subject samples collected before exposure to ethanol and after 3 months of excessive ethanol self-administration. Highly abundant plasma proteins were depleted from plasma samples to increase proteomic coverage. Altered plasma levels of serum amyloid A4 (SAA4), retinol-binding protein, inter-alpha inhibitor H4, clusterin, and fibronectin, identified by 2D-DIGE analysis, were confirmed in unmanipulated, whole plasma from these animals by immunoblotting. Examination of these target plasma proteins in human subjects with excessive alcohol consumption (and control subjects) revealed increased levels of SAA4 and clusterin and decreased levels of fibronectin compared to controls. These proteins not only serve as targets for further development as biomarker candidates or components of biomarker panels, but also add to the growing understanding of dysregulated immune function and lipoprotein metabolism with chronic, excessive alcohol consumption.

  3. Method and platform standardization in MRM-based quantitative plasma proteomics.

    Science.gov (United States)

    Percy, Andrew J; Chambers, Andrew G; Yang, Juncong; Jackson, Angela M; Domanski, Dominik; Burkhart, Julia; Sickmann, Albert; Borchers, Christoph H

    2013-12-16

    There exists a growing demand in the proteomics community to standardize experimental methods and liquid chromatography-mass spectrometry (LC/MS) platforms in order to enable the acquisition of more precise and accurate quantitative data. This necessity is heightened by the evolving trend of verifying and validating candidate disease biomarkers in complex biofluids, such as blood plasma, through targeted multiple reaction monitoring (MRM)-based approaches with stable isotope-labeled standards (SIS). Considering the lack of performance standards for quantitative plasma proteomics, we previously developed two reference kits to evaluate the MRM with SIS peptide approach using undepleted and non-enriched human plasma. The first kit tests the effectiveness of the LC/MRM-MS platform (kit #1), while the second evaluates the performance of an entire analytical workflow (kit #2). Here, these kits have been refined for practical use and then evaluated through intra- and inter-laboratory testing on 6 common LC/MS platforms. For an identical panel of 22 plasma proteins, similar concentrations were determined, regardless of the kit, instrument platform, and laboratory of analysis. These results demonstrate the value of the kit and reinforce the utility of standardized methods and protocols. The proteomics community needs standardized experimental protocols and quality control methods in order to improve the reproducibility of MS-based quantitative data. This need is heightened by the evolving trend for MRM-based validation of proposed disease biomarkers in complex biofluids such as blood plasma. We have developed two kits to assist in the inter- and intra-laboratory quality control of MRM experiments: the first kit tests the effectiveness of the LC/MRM-MS platform (kit #1), while the second evaluates the performance of an entire analytical workflow (kit #2). In this paper, we report the use of these kits in intra- and inter-laboratory testing on 6 common LC/MS platforms. This

  4. Proteomic methodological recommendations for studies involving human plasma, platelets, and peripheral blood mononuclear cells.

    Science.gov (United States)

    de Roos, Baukje; Duthie, Susan J; Polley, Abigael C J; Mulholland, Francis; Bouwman, Freek G; Heim, Carolin; Rucklidge, Garry J; Johnson, Ian T; Mariman, Edwin C; Daniel, Hannelore; Elliott, Ruan M

    2008-06-01

    This study was designed to develop, optimize and validate protocols for blood processing prior to proteomic analysis of plasma, platelets and peripheral blood mononuclear cells (PBMC) and to determine analytical variation of a single sample of depleted plasma, platelet and PBMC proteins within and between four laboratories each using their own standard operating protocols for 2D gel electrophoresis. Plasma depleted either using the Beckman Coulter IgY-12 proteome partitioning kit or the Amersham albumin and IgG depletion columns gave good quality gels, but reproducibility appeared better with the single-use immuno-affinity column. The use of the Millipore Filter Device for protein concentration gave a 16% ( p appears as a single abundant spot. The average within-laboratory coefficient of variation (CV) for each of the matched spots after automatic matching using either PDQuest or ProteomWeaver software ranged between 18 and 69% for depleted plasma proteins, between 21 and 55% for platelet proteins, and between 22 and 38% for PBMC proteins. Subsequent manual matching improved the CV with on average between 1 and 16%. The average between laboratory CV for each of the matched spots after automatic matching ranged between 4 and 54% for depleted plasma proteins, between 5 and 60% for platelet proteins, and between 18 and 70% for PBMC proteins. This variation must be considered when designing sufficiently powered studies that use proteomics tools for biomarker discovery. The use of tricine in the running buffer for the second dimension appears to enhance the resolution of proteins especially in the high molecular weight range.

  5. Plasma proteomic profiling in HIV-1 infected methamphetamine abusers.

    Directory of Open Access Journals (Sweden)

    Gwenael Pottiez

    Full Text Available We wanted to determine whether methamphetamine use affects a subset of plasma proteins in HIV-infected persons. Plasma samples from two visits were identified for subjects from four groups: HIV+, ongoing, persistent METH use; HIV+, short-term METH abstinent; HIV+, long term METH abstinence; HIV negative, no history of METH use. Among 390 proteins identified, 28 showed significant changes in expression in the HIV+/persistent METH+ group over the two visits, which were not attributable to HIV itself. These proteins were involved in complement, coagulation pathways and oxidative stress. Continuous METH use is an unstable condition, altering levels of a number of plasma proteins.

  6. Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project.

    Science.gov (United States)

    Díez, Paula; Droste, Conrad; Dégano, Rosa M; González-Muñoz, María; Ibarrola, Nieves; Pérez-Andrés, Martín; Garin-Muga, Alba; Segura, Víctor; Marko-Varga, Gyorgy; LaBaer, Joshua; Orfao, Alberto; Corrales, Fernando J; De Las Rivas, Javier; Fuentes, Manuel

    2015-09-04

    A comprehensive study of the molecular active landscape of human cells can be undertaken to integrate two different but complementary perspectives: transcriptomics, and proteomics. After the genome era, proteomics has emerged as a powerful tool to simultaneously identify and characterize the compendium of thousands of different proteins active in a cell. Thus, the Chromosome-centric Human Proteome Project (C-HPP) is promoting a full characterization of the human proteome combining high-throughput proteomics with the data derived from genome-wide expression profiling of protein-coding genes. Here we present a full proteomic profiling of a human lymphoma B-cell line (Ramos) performed using a nanoUPLC-LTQ-Orbitrap Velos proteomic platform, combined to an in-depth transcriptomic profiling of the same cell type. Data are available via ProteomeXchange with identifier PXD001933. Integration of the proteomic and transcriptomic data sets revealed a 94% overlap in the proteins identified by both -omics approaches. Moreover, functional enrichment analysis of the proteomic profiles showed an enrichment of several functions directly related to the biological and morphological characteristics of B-cells. In turn, about 30% of all protein-coding genes present in the whole human genome were identified as being expressed by the Ramos cells (stable average of 30% genes along all the chromosomes), revealing the size of the protein expression-set present in one specific human cell type. Additionally, the identification of missing proteins in our data sets has been reported, highlighting the power of the approach. Also, a comparison between neXtProt and UniProt database searches has been performed. In summary, our transcriptomic and proteomic experimental profiling provided a high coverage report of the expressed proteome from a human lymphoma B-cell type with a clear insight into the biological processes that characterized these cells. In this way, we demonstrated the usefulness of

  7. Proteomics

    DEFF Research Database (Denmark)

    Tølbøll, Trine Højgaard; Danscher, Anne Mette; Andersen, Pia Haubro;

    2012-01-01

    different proteins were identified, with 146 proteins available for identification in C, 279 proteins in D and 269 proteins in L. A functional annotation of the identified proteins was obtained using the on-line Blast2GO tool. Three hundred and sixteen of the identified proteins could be subsequently...... grouped manually to one or more of five major functional groups related to metabolism, cell structure, immunity, apoptosis and angiogenesis. These were chosen to represent basic cell functions and biological processes potentially involved in the pathogenesis of CHD. The LC–MS/MS-based proteomic analysis...

  8. Proteomic profiling of human plasma exosomes identifies PPARgamma as an exosome-associated protein.

    Science.gov (United States)

    Looze, Christopher; Yui, David; Leung, Lester; Ingham, Matthew; Kaler, Maryann; Yao, Xianglan; Wu, Wells W; Shen, Rong-Fong; Daniels, Mathew P; Levine, Stewart J

    2009-01-16

    Exosomes are nanovesicles that are released from cells as a mechanism of cell-free intercellular communication. Only a limited number of proteins have been identified from the plasma exosome proteome. Here, we developed a multi-step fractionation scheme incorporating gel exclusion chromatography, rate zonal centrifugation through continuous sucrose gradients, and high-speed centrifugation to purify exosomes from human plasma. Exosome-associated proteins were separated by SDS-PAGE and 66 proteins were identified by LC-MS/MS, which included both cellular and extracellular proteins. Furthermore, we identified and characterized peroxisome proliferator-activated receptor-gamma (PPARgamma), a nuclear receptor that regulates adipocyte differentiation and proliferation, as well as immune and inflammatory cell functions, as a novel component of plasma-derived exosomes. Given the important role of exosomes as intercellular messengers, the discovery of PPARgamma as a component of human plasma exosomes identifies a potential new pathway for the paracrine transfer of nuclear receptors.

  9. A Quest for Missing Proteins : update 2015 on Chromosome-Centric Human Proteome Project

    NARCIS (Netherlands)

    Horvatovich, Péter; Lundberg, Emma K; Chen, Yu-Ju; Sung, Ting-Yi; He, Fuchu; Nice, Edouard C; Goode, Robert J A; Yu, Simon; Ranganathan, Shoba; Baker, Mark S; Domont, Gilberto B; Velasquez, Erika; Li, Dong; Liu, Siqi; Wang, Quanhui; He, Qing-Yu; Menon, Rajasree; Guan, Yuanfang; Corrales, Fernando Jose; Segura, Victor; Casal, José Ignacio; Pascual-Montano, Alberto; Albar, Juan Pablo; Fuentes, Manuel; Gonzalez-Gonzalez, Maria; Diez, Paula; Ibarrola, Nieves; Degano, Rosa M; Mohammed, Yassene; Borchers, Christoph H; Urbani, Andrea; Soggiu, Alessio; Yamamoto, Tadashi; Archakov, Alexander I; Ponomarenko, Elena; Lisitsa, Andrey V; Lichti, Cheryl F; Mostovenko, Ekaterina; Kroes, Roger A; Rezeli, Melinda; Vegvari, Akos; Fehniger, Thomas E; Bischoff, Rainer; Vizcaíno, Juan Antonio; Deutsch, Eric W; Lane, Lydie; Nilsson, Carol L; Marko-Varga, György; Omenn, Gilbert S; Jeong, Seul-Ki; Cho, Jin-Young; Paik, Young-Ki; Hancock, William S

    2015-01-01

    This paper summarizes the recent activities of the Chromosome-Centric Human Proteome Project (C-HPP) consortium, which develops new technologies to identify yet-to-be annotated proteins (termed "missing proteins") in biological samples that lack sufficient experimental evidence at the protein level

  10. A Quest for Missing Proteins : update 2015 on Chromosome-Centric Human Proteome Project

    NARCIS (Netherlands)

    Horvatovich, Péter; Lundberg, Emma K; Chen, Yu-Ju; Sung, Ting-Yi; He, Fuchu; Nice, Edouard C; Goode, Robert J A; Yu, Simon; Ranganathan, Shoba; Baker, Mark S; Domont, Gilberto B; Velasquez, Erika; Li, Dong; Liu, Siqi; Wang, Quanhui; He, Qing-Yu; Menon, Rajasree; Guan, Yuanfang; Corrales, Fernando Jose; Segura, Victor; Casal, José Ignacio; Pascual-Montano, Alberto; Albar, Juan Pablo; Fuentes, Manuel; Gonzalez-Gonzalez, Maria; Diez, Paula; Ibarrola, Nieves; Degano, Rosa M; Mohammed, Yassene; Borchers, Christoph H; Urbani, Andrea; Soggiu, Alessio; Yamamoto, Tadashi; Archakov, Alexander I; Ponomarenko, Elena; Lisitsa, Andrey V; Lichti, Cheryl F; Mostovenko, Ekaterina; Kroes, Roger A; Rezeli, Melinda; Vegvari, Akos; Fehniger, Thomas E; Bischoff, Rainer; Vizcaíno, Juan Antonio; Deutsch, Eric W; Lane, Lydie; Nilsson, Carol L; Marko-Varga, György; Omenn, Gilbert S; Jeong, Seul-Ki; Cho, Jin-Young; Paik, Young-Ki; Hancock, William S

    2015-01-01

    This paper summarizes the recent activities of the Chromosome-Centric Human Proteome Project (C-HPP) consortium, which develops new technologies to identify yet-to-be annotated proteins (termed "missing proteins") in biological samples that lack sufficient experimental evidence at the protein level

  11. Plasma proteome analysis in HTLV-1-associated myelopathy/tropical spastic paraparesis

    Directory of Open Access Journals (Sweden)

    Stumpf Michael PH

    2011-10-01

    Full Text Available Abstract Background Human T lymphotropic virus Type 1 (HTLV-1 causes a chronic inflammatory disease of the central nervous system known as HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM which resembles chronic spinal forms of multiple sclerosis (MS. The pathogenesis of HAM remains uncertain. To aid in the differential diagnosis of HAM and to identify pathogenetic mechanisms, we analysed the plasma proteome in asymptomatic HTLV-1 carriers (ACs, patients with HAM, uninfected controls, and patients with MS. We used surface-enhanced laser desorption-ionization (SELDI mass spectrometry to analyse the plasma proteome in 68 HTLV-1-infected individuals (in two non-overlapping sets, each comprising 17 patients with HAM and 17 ACs, 16 uninfected controls, and 11 patients with secondary progressive MS. Candidate biomarkers were identified by tandem Q-TOF mass spectrometry. Results The concentrations of three plasma proteins - high [β2-microglobulin], high [Calgranulin B], and low [apolipoprotein A2] - were specifically associated with HAM, independently of proviral load. The plasma [β2-microglobulin] was positively correlated with disease severity. Conclusions The results indicate that monocytes are activated by contact with activated endothelium in HAM. Using β2-microglobulin and Calgranulin B alone we derive a diagnostic algorithm that correctly classified the disease status (presence or absence of HAM in 81% of HTLV-1-infected subjects in the cohort.

  12. RNAi-mediated downregulation of poplar plasma membrane intrinsic proteins (PIPs) changes plasma membrane proteome composition and affects leaf physiology.

    Science.gov (United States)

    Bi, Zhen; Merl-Pham, Juliane; Uehlein, Norbert; Zimmer, Ina; Mühlhans, Stefanie; Aichler, Michaela; Walch, Axel Karl; Kaldenhoff, Ralf; Palme, Klaus; Schnitzler, Jörg-Peter; Block, Katja

    2015-10-14

    Plasma membrane intrinsic proteins (PIPs) are one subfamily of aquaporins that mediate the transmembrane transport of water. To reveal their function in poplar, we generated transgenic poplar plants in which the translation of PIP genes was downregulated by RNA interference investigated these plants with a comprehensive leaf plasma membrane proteome and physiome analysis. First, inhibition of PIP synthesis strongly altered the leaf plasma membrane protein composition. Strikingly, several signaling components and transporters involved in the regulation of stomatal movement were differentially regulated in transgenic poplars. Furthermore, hormonal crosstalk related to abscisic acid, auxin and brassinosteroids was altered, in addition to cell wall biosynthesis/cutinization, the organization of cellular structures and membrane trafficking. A physiological analysis confirmed the proteomic results. The leaves had wider opened stomata and higher net CO2 assimilation and transpiration rates as well as greater mesophyll conductance for CO2 (gm) and leaf hydraulic conductance (Kleaf). Based on these results, we conclude that PIP proteins not only play essential roles in whole leaf water and CO2 flux but have important roles in the regulation of stomatal movement.

  13. A workflow for peptide-based proteomics in a poorly sequenced plant: A case study on the plasma membrane proteome of banana

    DEFF Research Database (Denmark)

    Vertommen, A.; Laurell Blom Møller, Anders; Cordewener, J. H. G.

    2011-01-01

    Membrane proteins are an interesting class of proteins because of their functional importance. Unfortunately their analysis is hampered by low abundance and poor solubility in aqueous media. Since shotgun methods are high-throughput and partly overcome these problems, they are preferred......, integral plasma membrane proteins from banana leaves were successfully identified....... for membrane proteomics. However, their application in non-model plants demands special precautions to prevent false positive identification of proteins.In the current paper, a workflow for membrane proteomics in banana, a poorly sequenced plant, is proposed. The main steps of this workflow are (i...

  14. Plasma Proteomics Biomarkers in Alzheimer's Disease: Latest Advances and Challenges.

    Science.gov (United States)

    Perneczky, Robert; Guo, Liang-Hao

    2016-01-01

    The recent paradigm shift towards a more biologically oriented definition of Alzheimer's disease (AD) in clinical settings increases the need for sensitive biomarkers that can be applied in population-based settings. Blood plasma is easily accessible and contains a large number of proteins related to cerebral processes. It is therefore an ideal candidate for AD biomarker discovery. The present chapter provides an overview of the current research landscape in relation to blood-based AD biomarkers. Both clinical and methodological issues are covered. A brief summary is given on two relevant laboratory techniques to ascertain blood biomarker changes due to AD; methodological and clinical challenges in the field are also discussed.

  15. The identification of proteomic markers of sperm freezing resilience in ram seminal plasma.

    Science.gov (United States)

    Rickard, J P; Leahy, T; Soleilhavoup, C; Tsikis, G; Labas, V; Harichaux, G; Lynch, G W; Druart, X; de Graaf, S P

    2015-08-03

    The source and composition of seminal plasma has previously been shown to alter the ability of spermatozoa to survive cryopreservation. In the present study, the ionic and proteomic composition of seminal plasma from rams with high (HSP; n = 3) or low (LSP; n = 3) freezing resilient spermatozoa was assessed. 75 proteins were identified to be more abundant in HSP and 48 proteins were identified to be more abundant in LSP. Individual seminal plasma proteomes were established for each of the six rams examined. For each ram, correlations were conducted between previously recorded freezing resilience [1] and individual spectral counts in order to identify markers of freezing resilience. 26S proteasome complex, acylamino acid releasing enzyme, alpha mannosidase class 2C, heat shock protein 90, tripeptidyl-peptidase 2, TCP-1 complex, sorbitol dehydrogenase and transitional endoplasmic reticulum ATPase were found to be positively correlated (r(2) > 0.7) with freezing resilience. Cystatin, zinc-2-alpha glycoprotein, angiogenin-2-like protein, cartilage acidic protein-1, cathepsin B and ribonuclease 4 isoform 1 were found to be negatively correlated (r(2) > 0.7) with freezing resilience. Several negative markers were found to originate from the accessory sex glands, whereas many positive markers originated from spermatozoa and were part of or associated with the 26S proteasome or CCT complex.

  16. Studying Different Clinical Syndromes Of Paediatric Severe Malaria Using Plasma Proteomics

    KAUST Repository

    Ramaprasad, Abhinay

    2012-08-01

    Background- Severe Plasmodium falciparum malaria remains one of the major causes of childhood morbidity and mortality in Africa. Severe malaria manifests itself as three main clinical syndromes-impaired consciousness (cerebral malaria), respiratory distress and severe malarial anaemia. Cerebral malaria and respiratory distress are major contributors to malaria mortality but their pathophysiology remains unclear. Motivation/Objectives- Most children with severe malaria die within the first 24 hours of admission to a hospital because of their pathophysiological conditions. Thus, along with anti-malarial drugs, various adjuvant therapies such as fluid bolus (for hypovolaemia) and anticonvulsants (for seizures) are given to alleviate the sick child’s condition. But these therapies can sometimes have adverse effects. Hence, a clear understanding of severe malaria pathophysiology is essential for making an informed decision regarding adjuvant therapies. Methodology- We used mass spectrometry-based shotgun proteomics to study plasma samples from Gambian children with severe malaria. We compared the proteomic profiles of different severe malaria syndromes and generated hypotheses regarding the underlying disease mechanisms. Results/Conclusions- The main challenges of studying the severe malaria syndromes using proteomics were the high complexity and variability among the samples. We hypothesized that hepatic injury and nitric oxide play roles in the pathophysiology of cerebral malaria and respiratory distress.

  17. Proteomic analysis of plasma from rats following total parenteral nutrition-induced liver injury.

    Science.gov (United States)

    Tsai, Jai-Jen; Kuo, Hsing-Chun; Lee, Kam-Fai; Tsai, Tung-Hu

    2015-11-01

    Total parenteral nutrition (TPN) is provided as the primary nitrogen source to manage patients with intestinal failure who were not able to sustain themselves on enteral feeds. The most common complication of long-term TPN use is hepatitis. A proteomic approach was used to identify proteins that are differentially expressed in the plasma of rats following TPN-related acute liver injury. Six male rats were randomly assigned to either the saline infusion control group or the TPN infusion group. Our results demonstrate that TPN infusion in rats resulted in hepatic dysfunction and hepatocyte apoptosis. Five proteins that were differentially expressed between TPN infusion and normal rats were determined and validated in vivo. Fascinatingly, the proteomic differential displays, downregulated proteins included peroxiredoxin 2 (PRDX2), alpha-1-antiproteinase (A1AT), and fibrinogen gamma chain (FIBG), which were involved in oxidative stress, inflammatory respondence and cells apoptosis. After TPN infusion, two protein spots showed increased expression, namely, the glucagon receptor (GLR) protein and apolipoprotein A-1 (APOA1), which may mediate the effects of TPN administration on glycogen and lipid metabolism. In this study, proteomic analysis suggested TPN-related acute liver injury could be involved in limiting cellular protection mechanisms against oxidative stress-induced apoptosis. On the basis of the results, we also give molecular evidences replying TPN-related hepatitis.

  18. Proteomic analysis of white and yellow seminal plasma in turkeys (Meleagris gallopavo).

    Science.gov (United States)

    Słowińska, M; Kozłowski, K; Jankowski, J; Ciereszko, A

    2015-06-01

    Yellow semen syndrome (YSS) is endemic within domestic turkey populations. Yellow semen is of lower quality and, when used for insemination, results in reduced fertility and hatchability. Little is known about the etiology of YSS. The aim of this study was to compare the proteome of white and yellow seminal plasma of turkeys using 1) 2-dimensional difference gel electrophoresis (2D-DIGE) to quantify seminal plasma proteins and 2) matrix-assisted laser desorption/ionization mass spectrometry to identify the proteins that are differentially abundant in white and yellow seminal plasma. A total of 49 protein spots (30 upregulated and 19 downregulated) were differentially expressed in yellow seminal plasma compared with white seminal plasma. Transthyretin and serum albumin-like showed a 3-fold increase in seminal plasma from males with YSS, and the latter was validated using Western blot analysis. A 3-fold increase was observed for hemopexin-like and immunoglobulin light chain V-J-C region. Pantetheinase-like showed a 1.3-fold increase. Ovotransferrin, hepatocyte growth factor activator, cysteine-rich secretory protein 3-like, and ferritin heavy chain-like showed a significant decrease (at least a 1.3-fold decrease) in yellow semen. Further studies are necessary to evaluate the precise function of the above-mentioned proteins in YSS and to establish quality markers of turkey semen to predict the reproductive potential of individual turkeys.

  19. Characterization of the seminal plasma proteome in men with prostatitis by mass spectrometry

    Directory of Open Access Journals (Sweden)

    Kagedan Daniel

    2012-02-01

    Full Text Available Abstract Background Prostatitis is an inflammation of the prostate gland which affects approximately 10% of men. Despite its frequency, diagnosing prostatitis and monitoring patient response to treatment remains frustrating. As the prostate contributes a substantial percentage of proteins to seminal plasma, we hypothesized that a protein biomarker of prostatitis might be found by comparing the seminal plasma proteome of patients with and without prostatitis. Results Using mass spectrometry, we identified 1708 proteins in the pooled seminal plasma of 5 prostatitis patients. Comparing this list to a previously published list of seminal plasma proteins in the pooled seminal plasma of 5 healthy, fertile controls yielded 1464 proteins in common, 413 found only in the control group, and 254 found only in the prostatitis group. Applying a set of criteria to this dataset, we generated a high-confidence list of 59 candidate prostatitis biomarkers, 33 of which were significantly increased in prostatitis as compared to control, and 26 of which were decreased. The candidates were analyzed using Gene Ontology and Ingenuity Pathway analysis to delineate their subcellular localizations and functions. Conclusions Thus, in this study, we identified 59 putative biomarkers in seminal plasma that need further validation for diagnosis and monitoring of prostatitis.

  20. Proteomic identification of novel differentiation plasma protein markers in hypobaric hypoxia-induced rat model.

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    Yasmin Ahmad

    Full Text Available BACKGROUND: Hypobaric hypoxia causes complex changes in the expression of genes, including stress related genes and corresponding proteins that are necessary to maintain homeostasis. Whereas most prior studies focused on single proteins, newer methods allowing the simultaneous study of many proteins could lead to a better understanding of complex and dynamic changes that occur during the hypobaric hypoxia. METHODS: In this study we investigated the temporal plasma protein alterations of rat induced by hypobaric hypoxia at a simulated altitude of 7620 m (25,000 ft, 282 mm Hg in a hypobaric chamber. Total plasma proteins collected at different time points (0, 6, 12 and 24 h, separated by two-dimensional electrophoresis (2-DE and identified using matrix assisted laser desorption ionization time of flight (MALDI-TOF/TOF. Biological processes that were enriched in the plasma proteins during hypobaric hypoxia were identified using Gene Ontology (GO analysis. According to their properties and obvious alterations during hypobaric hypoxia, changes of plasma concentrations of Ttr, Prdx-2, Gpx -3, Apo A-I, Hp, Apo-E, Fetub and Nme were selected to be validated by Western blot analysis. RESULTS: Bioinformatics analysis of 25 differentially expressed proteins showed that 23 had corresponding candidates in the database. The expression patterns of the eight selected proteins observed by Western blot were in agreement with 2-DE results, thus confirming the reliability of the proteomic analysis. Most of the proteins identified are related to cellular defense mechanisms involving anti-inflammatory and antioxidant activity. Their presence reflects the consequence of serial cascades initiated by hypobaric hypoxia. CONCLUSION/SIGNIFICANCE: This study provides information about the plasma proteome changes induced in response to hypobaric hypoxia and thus identification of the candidate proteins which can act as novel biomarkers.

  1. Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery.

    Directory of Open Access Journals (Sweden)

    Sharon J Pitteri

    Full Text Available The complexity of the human plasma proteome represents a substantial challenge for biomarker discovery. Proteomic analysis of genetically engineered mouse models of cancer and isolated cancer cells and cell lines provide alternative methods for identification of potential cancer markers that would be detectable in human blood using sensitive assays. The goal of this work is to evaluate the utility of an integrative strategy using these two approaches for biomarker discovery.We investigated a strategy that combined quantitative plasma proteomics of an ovarian cancer mouse model with analysis of proteins secreted or shed by human ovarian cancer cells. Of 106 plasma proteins identified with increased levels in tumor bearing mice, 58 were also secreted or shed from ovarian cancer cells. The remainder consisted primarily of host-response proteins. Of 25 proteins identified in the study that were assayed, 8 mostly secreted proteins common to mouse plasma and human cancer cells were significantly upregulated in a set of plasmas from ovarian cancer patients. Five of the eight proteins were confirmed to be upregulated in a second independent set of ovarian cancer plasmas, including in early stage disease.Integrated proteomic analysis of cancer mouse models and human cancer cell populations provides an effective approach to identify potential circulating protein biomarkers.

  2. The Proteomics Stock Market Project. A Cross-Disciplinary Collaboration in Biochemistry and Business Education

    Science.gov (United States)

    Keller, Heath; Cox, James R.

    2004-04-01

    Students taking courses in different disciplines can work together to add unique elements to their educational experience. A model for this type of pedagogical approach has been established in the Proteomics Stock Market Project, a collaborative effort between instructors and students in the Department of Chemistry and Department of Management, Marketing, and Business Administration at Murray State University. Stage I involved biochemistry students investigating the topic of proteomics and choosing companies for potential investment based only on scientific investigation. Marketing and management students completed Stage II and provided an investment analysis on the companies selected in Stage I. In Stage III, the biochemistry students focused on a particular company and investigated a protein-based therapeutic product. Blackboard software was utilized in each stage of the project to facilitate the exchange of information and electronic documents. This project was designed to give biochemistry students an appreciation for the emerging field of proteomics and the marketing and management students a flavor for real-world applications of business principles. During the project, students were exposed to ideas and concepts not typically covered in their courses. With this involvement, the students had the opportunity to gain a broader perspective of course content compared to a more traditional curriculum.

  3. ProteomeCommons.org collaborative annotation and project management resource integrated with the Tranche repository.

    Science.gov (United States)

    Hill, James A; Smith, Bryan E; Papoulias, Panagiotis G; Andrews, Philip C

    2010-06-01

    ProteomeCommons.org has implemented a resource that incorporates concepts of Web 2.0 social networking for collaborative annotation of data sets placed in the Tranche repository. The annotation tools are part of a project management resource that is effective for individual laboratories or large distributed groups. The creation of the resource was motivated by the need for a way to encourage annotation of data sets with high accuracy and compliance rates. The system is designed to respond to the dynamic nature of research in an easy-to-use fashion through the use of a dynamic data model that does not inhibit the innovation that is important for basic research. Placing the annotation tool within a project manager allows annotation to occur over the life of the project and provides the security and monitoring capabilities needed for large or small collaborative projects. The resource effectively supports distributed groups of investigators working on common data sets and is available immediately at https://ProteomeCommons.org . In addition, a silver compliant data resource based on ProteomeCommons.org has been developed for cancer Biomedical Informatics Grid (caBIG) to allow much broader access to the annotations describing data sets in the Tranche repository.

  4. Effects of increased CO2 on fish gill and plasma proteome.

    Directory of Open Access Journals (Sweden)

    Karine Bresolin de Souza

    Full Text Available Ocean acidification and warming are both primarily caused by increased levels of atmospheric CO2, and marine organisms are exposed to these two stressors simultaneously. Although the effects of temperature on fish have been investigated over the last century, the long-term effects of moderate CO2 exposure and the combination of both stressors are almost entirely unknown. A proteomics approach was used to assess the adverse physiological and biochemical changes that may occur from the exposure to these two environmental stressors. We analysed gills and blood plasma of Atlantic halibut (Hippoglossus hippoglossus exposed to temperatures of 12 °C (control and 18 °C (impaired growth in combination with control (400 µatm or high-CO2 water (1000 µatm for 14 weeks. The proteomic analysis was performed using two-dimensional gel electrophoresis (2DE followed by Nanoflow LC-MS/MS using a LTQ-Orbitrap. The high-CO2 treatment induced the up-regulation of immune system-related proteins, as indicated by the up-regulation of the plasma proteins complement component C3 and fibrinogen β chain precursor in both temperature treatments. Changes in gill proteome in the high-CO2 (18 °C group were mostly related to increased energy metabolism proteins (ATP synthase, malate dehydrogenase, malate dehydrogenase thermostable, and fructose-1,6-bisphosphate aldolase, possibly coupled to a higher energy demand. Gills from fish exposed to high-CO2 at both temperature treatments showed changes in proteins associated with increased cellular turnover and apoptosis signalling (annexin 5, eukaryotic translation elongation factor 1γ, receptor for protein kinase C, and putative ribosomal protein S27. This study indicates that moderate CO2-driven acidification, alone and combined with high temperature, can elicit biochemical changes that may affect fish health.

  5. Proteomic Profiling of Nonenzymatically Glycated Proteins in Human Plasma and Erythrocyte Membrane

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qibin; Tang, Ning; Schepmoes, Athena A.; Phillips, Lawrence S.; Smith, Richard D.; Metz, Thomas O.

    2008-05-01

    Non-enzymatic glycation of peptides and proteins by D-glucose has important implications in the pathogenesis of diabetes mellitus, particularly in the development of diabetic complications. In this report, a thorough proteomic profiling of glycated proteins was attempted by using phenylboronate affinity chromatography to enrich glycated proteins and glycated, tryptic peptides from human plasma and erythrocyte membranes. Enriched peptides were subsequently analyzed by liquid chromatography coupled with electron transfer dissociation tandem mass spectrometry, and 76 and 31 proteins were confidently identified as glycated from human plasma and erythrocyte membrane, respectively. It was observed that most of the glycated proteins can be identified in samples from individuals with normal glucose tolerance, although samples from individuals with impaired glucose tolerance and type 2 diabetes mellitus have slightly higher numbers of glycated proteins and more glycation sites identified.

  6. Effect of increased testicular temperature on seminal plasma proteome of the ram.

    Science.gov (United States)

    Rocha, David R; Martins, Jorge André M; van Tilburg, Mauricio F; Oliveira, Rodrigo V; Moreno, Frederico B; Monteiro-Moreira, Ana Cristina O; Moreira, Renato A; Araújo, Airton A; Moura, Arlindo A

    2015-11-01

    The present study evaluated the effects of heat stress on the ram seminal plasma proteome. Six Morada Nova rams were scrotal insulated for 8 days. Scrotal circumference, sperm parameters, and seminal fluid proteins were evaluated before (Day 0) and twice during scrotal insulation (Days 4 and 8), and weekly until semen parameters returned to preinsulation values (normal). Seminal proteins were analyzed by two-dimensional SDS-PAGE and mass spectrometry. Scrotal circumference decreased from 30 ± 0.4 cm on Day 0 to 22.6 ± 0.6 cm on Day 36 (P Rams were azoospermic between Days 29 and 64, and sperm concentration came back to normal on Day 92. The number of spots/two-dimensional gel reduced from 256 ± 31 on Day 0 to 104 ± 14 on Day 29 (when rams were azoospermic) and then increased to 183 ± 9 on Day 113 (P rams, indicating alterations in both spermatogenesis and sperm maturation. Changes of seminal plasma proteome were coincidental with variations in semen parameters. Proteins affected by heat challenge are potentially involved in sperm protection, maturation, and fertilization.

  7. Automated platform for fractionation of human plasma glycoproteome in clinical proteomics.

    Science.gov (United States)

    Kullolli, Majlinda; Hancock, William S; Hincapie, Marina

    2010-01-01

    This publication describes the development of an automated platform for the study of the plasma glycoproteome. The method consists of targeted depletion in-line with glycoprotein fractionation. A key element of this platform is the enabling of high throughput sample processing in a manner that minimizes analytical bias in a clinical sample set. The system, named High Performance Multi-Lectin Affinity Chromatography (HP-MLAC), is composed of a serial configuration of depletion columns containing anti-albumin antibody and protein A with in-line multilectin affinity chromatography (M-LAC) which consists of three mixtures of lectins concanavalin A (ConA), jacalin (JAC), and wheat germ agglutinin (WGA). We have demonstrated that this platform gives high recoveries for the fractionation of the plasma proteome (> or = 95%) and excellent stability (over 200 runs). In addition, glycoproteomes isolated using the HP-MLAC platform were shown to be highly reproducible and glycan specific as demonstrated by rechromatography of selected fractions and proteomic analysis of the unbound (glycoproteome 1) and bound (glycoproteome 2) fractions.

  8. A Plasma Proteomic Approach in Rett Syndrome: Classical versus Preserved Speech Variant

    Directory of Open Access Journals (Sweden)

    Alessio Cortelazzo

    2013-01-01

    Full Text Available Rett syndrome (RTT is a progressive neurodevelopmental disorder mainly caused by mutations in the gene encoding the methyl-CpG-binding protein 2 (MeCP2. Although over 200 mutations types have been identified so far, nine of which the most frequent ones. A wide phenotypical heterogeneity is a well-known feature of the disease, with different clinical presentations, including the classical form and the preserved speech variant (PSV. Aim of the study was to unveil possible relationships between plasma proteome and phenotypic expression in two cases of familial RTT represented by two pairs of sisters, harbor the same MECP2 gene mutation while being dramatically discrepant in phenotype, that is, classical RTT versus PSV. Plasma proteome was analysed by 2-DE/MALDI-TOF MS. A significant overexpression of six proteins in the classical sisters was detected as compared to the PSV siblings. A total of five out of six (i.e., 83.3% of the overexpressed proteins were well-known acute phase response (APR proteins, including alpha-1-microglobulin, haptoglobin, fibrinogen beta chain, alpha-1-antitrypsin, and complement C3. Therefore, the examined RTT siblings pairs proved to be an important benchmark model to test the molecular basis of phenotypical expression variability and to identify potential therapeutic targets of the disease.

  9. Proteomic-Biostatistic Integrated Approach for Finding the Underlying Molecular Determinants of Hypertension in Human Plasma.

    Science.gov (United States)

    Gajjala, Prathibha R; Jankowski, Vera; Heinze, Georg; Bilo, Grzegorz; Zanchetti, Alberto; Noels, Heidi; Liehn, Elisa; Perco, Paul; Schulz, Anna; Delles, Christian; Kork, Felix; Biessen, Erik; Narkiewicz, Krzysztof; Kawecka-Jaszcz, Kalina; Floege, Juergen; Soranna, Davide; Zidek, Walter; Jankowski, Joachim

    2017-08-01

    Despite advancements in lowering blood pressure, the best approach to lower it remains controversial because of the lack of information on the molecular basis of hypertension. We, therefore, performed plasma proteomics of plasma from patients with hypertension to identify molecular determinants detectable in these subjects but not in controls and vice versa. Plasma samples from hypertensive subjects (cases; n=118) and controls (n=85) from the InGenious HyperCare cohort were used for this study and performed mass spectrometric analysis. Using biostatistical methods, plasma peptides specific for hypertension were identified, and a model was developed using least absolute shrinkage and selection operator logistic regression. The underlying peptides were identified and sequenced off-line using matrix-assisted laser desorption ionization orbitrap mass spectrometry. By comparison of the molecular composition of the plasma samples, 27 molecular determinants were identified differently expressed in cases from controls. Seventy percent of the molecular determinants selected were found to occur less likely in hypertensive patients. In cross-validation, the overall R(2) was 0.434, and the area under the curve was 0.891 with 95% confidence interval 0.8482 to 0.9349, Phypertensive patients were found to be -2.007±0.3568 and 3.383±0.2643, respectively, Phypertensives and normotensives. The identified molecular determinants may be the starting point for further studies to clarify the molecular causes of hypertension. © 2017 American Heart Association, Inc.

  10. Plasma proteomic study in patients with high altitude pulmonary edema (HAPE

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    Yong-jun LUO

    2012-01-01

    Full Text Available Objective  To investigate the differential expressions of protein in the plasma proteome in patients suffering from high altitude pulmonary edema (HAPE and their implications. Methods  The plasmas of six HAPE patients and six healthy controls were studied. The high-abundant proteins in the plasma were removed. The low-abundant proteins in the plasma/serum were segregated by 2-DE. MALDI-TOF/MS was adopted to measure the peptide fingerprints after the differential protein spots were digested by enzymes. Comparison and analysis were made in the GenBank. Results  The immunoglobulin K1 light chain, serum transferrin protein precursor, and α-trypsin inhibitor heavy chain-related protein expressions were upregulated in HAPE patients compared with the control group. However the human fibrin glue coagulation protein 3 was down-regulated. Conclusion  The differential expression of the above four proteins in the plasma of HAPE patients may be related to the occurrence of HAPE and can be used as the target point for the prediction of HAPE.

  11. Proteomic analysis of plasma membrane and secretory vesicles from human neutrophils

    Directory of Open Access Journals (Sweden)

    Campbell Kevin P

    2007-08-01

    Full Text Available Abstract Background Polymorphonuclear neutrophils (PMN constitute an essential cellular component of innate host defense against microbial invasion and exhibit a wide array of responses both to particulate and soluble stimuli. As the cells recruited earliest during acute inflammation, PMN respond rapidly and release a variety of potent cytotoxic agents within minutes of exposure to microbes or their products. PMN rely on the redistribution of functionally important proteins, from intracellular compartments to the plasma membrane and phagosome, as the means by which to respond quickly. To determine the range of membrane proteins available for rapid recruitment during PMN activation, we analyzed the proteins in subcellular fractions enriched for plasma membrane and secretory vesicles recovered from the light membrane fraction of resting PMN after Percoll gradient centrifugation and free-flow electrophoresis purification using mass spectrometry-based proteomics methods. Results To identify the proteins light membrane fractions enriched for plasma membrane vesicles and secretory vesicles, we employed a proteomic approach, first using MALDI-TOF (peptide mass fingerprinting and then by HPLC-MS/MS using a 3D ion trap mass spectrometer to analyze the two vesicle populations from resting PMN. We identified several proteins that are functionally important but had not previously been recovered in PMN secretory vesicles. Two such proteins, 5-lipoxygenase-activating protein (FLAP and dysferlin were further validated by immunoblot analysis. Conclusion Our data demonstrate the broad array of proteins present in secretory vesicles that provides the PMN with the capacity for remarkable and rapid reorganization of its plasma membrane after exposure to proinflammatory agents or stimuli.

  12. Immunodepletion Plasma Proteomics by TripleTOF 5600 and Orbitrap Elite/LTQ-Orbitrap Velos/Q Exactive Mass Spectrometers

    Science.gov (United States)

    Patel, Bhavinkumar B.; Kelsen, Steven G.; Braverman, Alan; Swinton, Derrick J.; Gafken, Philip R.; Jones, Lisa A.; Lane, William S.; Neveu, John M.; Leung, Hon-Chiu E.; Shaffer, Scott A.; Leszyk, John D.; Stanley, Bruce A.; Fox, Todd E.; Stanley, Anne; Hall, Michael J.; Hampel, Heather; South, Christopher D.; de la Chapelle, Albert; Burt, Randall W.; Jones, David A.; Kopelovich, Levy; Yeung, Anthony T.

    2013-01-01

    Plasma proteomic experiments performed rapidly and economically using several of the latest high-resolution mass spectrometers were compared. Four quantitative hyperfractionated plasma proteomics experiments were analyzed in replicates by two AB SCIEX TripleTOF 5600 and three Thermo Scientific Orbitrap (Elite/LTQ-Orbitrap Velos/Q Exactive) instruments. Each experiment compared two iTRAQ isobaric-labeled immunodepleted plasma proteomes, provided as 30 labeled peptide fractions. 480 LC-MS/MS runs delivered >250 GB of data in two months. Several analysis algorithms were compared. At 1 % false discovery rate, the relative comparative findings concluded that the Thermo Scientific Q Exactive Mass Spectrometer resulted in the highest number of identified proteins and unique sequences with iTRAQ quantitation. The confidence of iTRAQ fold-change for each protein is dependent on the overall ion statistics (Mascot Protein Score) attainable by each instrument. The benchmarking also suggested how to further improve the mass spectrometry parameters and HPLC conditions. Our findings highlight the special challenges presented by the low abundance peptide ions of iTRAQ plasma proteome because the dynamic range of plasma protein abundance is uniquely high compared with cell lysates, necessitating high instrument sensitivity. PMID:24004147

  13. Shotgun proteomics and network analysis between plasma membrane and extracellular matrix proteins from rat olfactory ensheathing cells.

    Science.gov (United States)

    Liu, Yisong; Teng, Xiaohua; Yang, Xiaoxu; Song, Qing; Lu, Rong; Xiong, Jixian; Liu, Bo; Zeng, Nianju; Zeng, Yu; Long, Jia; Cao, Rui; Lin, Yong; He, Quanze; Chen, Ping; Lu, Ming; Liang, Songping

    2010-01-01

    Olfactory ensheathing cells (OECs) are a special type of glial cells that have characteristics of both astrocytes and Schwann cells. Evidence suggests that the regenerative capacity of OECs is induced by soluble, secreted factors that influence their microenvironment. These factors may regulate OECs self-renewal and/or induce their capacity to augment spinal cord regeneration. Profiling of plasma membrane and extracellular matrix through a high-throughput expression proteomics approach was undertaken to identify plasma membrane and extracellular matrix proteins of OECs under serum-free conditions. 1D-shotgun proteomics followed with gene ontology (GO) analysis was used to screen proteins from primary culture rat OECs. Four hundred and seventy nonredundant plasma membrane proteins and 168 extracellular matrix proteins were identified, the majority of which were never before reported to be produced by OECs. Furthermore, plasma membrane and extracellular proteins were classified based on their protein-protein interaction predicted by STRING quantitatively integrates interaction data. The proteomic profiling of the OECs plasma membrane proteins and their connection with the secretome in serum-free culture conditions provides new insights into the nature of their in vivo microenvironmental niche. Proteomic analysis for the discovery of clinical biomarkers of OECs mechanism warrants further study.

  14. Comprehensive Analysis of Low-Molecular-Weight Human Plasma Proteome Using Top-Down Mass Spectrometry.

    Science.gov (United States)

    Cheon, Dong Huey; Nam, Eun Ji; Park, Kyu Hyung; Woo, Se Joon; Lee, Hye Jin; Kim, Hee Cheol; Yang, Eun Gyeong; Lee, Cheolju; Lee, Ji Eun

    2016-01-01

    While human plasma serves as a great source for disease diagnosis, low-molecular-weight (LMW) proteome (mass spectrometry to analyze the LMW proteoforms present in four types of human plasma samples pooled from three healthy controls (HCs) without immunoaffinity depletion and with depletion of the top two, six, and seven high-abundance proteins. The LMW proteoforms were first fractionated based on molecular weight using gel-eluted liquid fraction entrapment electrophoresis (GELFrEE). Then, the GELFrEE fractions containing up to 30 kDa were subjected to nanocapillary-LC-MS/MS, and the high-resolution MS and MS/MS data were processed using ProSightPC 3.0. As a result, a total of 442 LMW proteins and cleaved products, including those with post-translational modifications and single amino acid variations, were identified. From additional comparative analysis of plasma samples without immunoaffinity depletion between HCs and colorectal cancer (CRC) patients via top-down approach, tens of LMW proteoforms, including platelet factor 4, were found to show >1.5-fold changes between the plasma samples of HCs and CRC patients, and six of the LMW proteins were verified by Western blot analysis.

  15. Plasma Fairings for Quieting Aircraft Landing Gear Noise Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This Phase II SBIR project deals with the design, development, and testing of a "Plasma Fairing" to reduce noise on the Gulfstream G550 landing gear. The plasma...

  16. Plasma proteomics classifiers improve risk prediction for renal disease in patients with hypertension or type 2 diabetes

    NARCIS (Netherlands)

    Pena, Michelle J.; Jankowski, Joachim; Heinze, Georg; Kohl, Maria; Heinzel, Andreas; Bakker, Stephan J. L.; Gansevoort, Ron T.; Rossing, Peter; de Zeeuw, Dick; Heerspink, Hiddo J. Lambers; Jankowski, Vera

    2015-01-01

    OBJECTIVE: Micro and macroalbuminuria are strong risk factors for progression of nephropathy in patients with hypertension or type 2 diabetes. Early detection of progression to micro and macroalbuminuria may facilitate prevention and treatment of renal diseases. We aimed to develop plasma proteomics

  17. Plasma proteomics classifiers improve risk prediction for renal disease in patients with hypertension or type 2 diabetes

    NARCIS (Netherlands)

    Pena, Michelle J.; Jankowski, Joachim; Heinze, Georg; Kohl, Maria; Heinzel, Andreas; Bakker, Stephan J. L.; Gansevoort, Ron T.; Rossing, Peter; de Zeeuw, Dick; Heerspink, Hiddo J. Lambers; Jankowski, Vera

    2015-01-01

    OBJECTIVE: Micro and macroalbuminuria are strong risk factors for progression of nephropathy in patients with hypertension or type 2 diabetes. Early detection of progression to micro and macroalbuminuria may facilitate prevention and treatment of renal diseases. We aimed to develop plasma proteomics

  18. Proteomic characterization of freeze-dried human plasma: providing treatment of bleeding disorders without the need for a cold chain.

    Science.gov (United States)

    Steil, Leif; Thiele, Thomas; Hammer, Elke; Bux, Jürgen; Kalus, Monika; Völker, Uwe; Greinacher, Andreas

    2008-11-01

    Transfusion of human plasma is a basic treatment for severe coagulopathies, especially in major bleeding. The required logistics to provide plasma is challenging because of the need to maintain a cold chain. This disadvantage could be overcome by lyophilized plasma. However, it is unknown to what extent lyophilization alters plasma proteins. Quantitative proteomic technologies were applied to monitor protein changes during production of lyophilized, solvent/detergent (S/D)-treated plasma. The impact of S/D treatment and lyophilization on the plasma proteome was evaluated by differential in-gel electrophoresis (2D-DIGE), and proteins were characterized by mass spectrometry. Clotting factor activities were determined in lyophilized S/D-treated plasma after 24 months of storage at room temperature. By 2D-DIGE, 600 individual protein spots were compared. Lyophilization did not change any of the 600 spots, whereas pathogen inactivation caused significant changes of 38 spots including alpha1-antitrypsin, alpha1-antichymotrypsin, and alpha2-antiplasmin. Clotting factor activities remained stable over 24 months of storage. Lyophilization of human plasma neither alters its protein composition nor impairs its clotting capacity. It does not require cost-intensive logistics for storage and transport and can be quickly reconstituted. It is suggested that lyophilized, pathogen-inactivated plasma is an attractive option to provide the most important basic treatment for severe coagulopathies in areas without cold chain and to provide plasma with reduced time delay in emergency situations.

  19. A high intake of industrial or ruminant trans fatty acids does not affect the plasma proteome in healthy men.

    Science.gov (United States)

    de Roos, Baukje; Wanders, Anne J; Wood, Sharon; Horgan, Graham; Rucklige, Garry; Reid, Martin; Siebelink, Els; Brouwer, Ingeborg A

    2011-10-01

    Consumption of industrial trans fat raises the risk of cardiovascular disease, but it is unclear whether cis9,trans11-conjugated linoleic acid (CLA)--a trans fatty acid in dairy products--modulates disease development. We investigated the effects of complete diets providing 7% of energy as industrial trans fat or cis9, trans11 CLA, compared with oleic acid, on regulation of plasma proteins in 12 healthy men. Diets were provided for 3 wk each, in random order. Plasma was collected at the end of each 3 wk intervention period, depleted of its 12 most abundant proteins and analyzed by 2-DE. Principal component analysis of protein spot intensity values revealed that the nature of the dietary intervention did not significantly affect the plasma proteome. The intervention provided in the 1st period produced a significant treatment effect compared with the interventions provided in the other two periods, and there was a significant subject effect. In conclusion, the nature of an extreme dietary intervention, i.e. 7% of energy provided by industrial trans fat or cis9,trans11 CLA, did not markedly affect the plasma proteome. Thus plasma proteomics using 2-DE appears, by and large, an unsuitable approach to detect regulation of plasma proteins due to changes in the diet.

  20. iTRAQ quantitative analysis of plasma proteome changes of cow from pregnancy to lactation

    Institute of Scientific and Technical Information of China (English)

    MA Lu; BU Deng-pan; YANG Yong-xing; YAN Su-mei; WANG Jia-qi

    2015-01-01

    Dairy cows undergo tremendous changes in physiological, metabolism and the immune function from pregnancy to lac-tation that are associated with cows being susceptible to metabolic and infectious diseases. The objective of this study is to investigate the changes of plasma proteome on 21 d before expected calving and 1 d after calving from dairy cows using an integrated proteomic approach consisting of minor abundance protein enrichment by ProteoMiner beads, protein labeling by isobaric tags for relative and absolute quantiifcation, and protein identiifcation by liquid chromatography coupled with tandem mass spectrometry. Nineteen proteins were changed around the time of calving. These proteins were asso-ciated with response to stress, including acute-phase response and defense response, based on the proteins annotation. In particular, three up-regulated proteins after calving including factor V,α2-antiplasmin and prothrombin were assigned into the complement and coagulation pathway. These results may provide new information in elucidating host response to lactation and parturition stress, and inlfammatory-like conditions at the protein level. Differential proteins may serve as potential markers to regulate the lactation and parturition stress in periparturient dairy cows.

  1. The plasma membrane proteome of maize roots grown under low and high iron conditions.

    Science.gov (United States)

    Hopff, David; Wienkoop, Stefanie; Lüthje, Sabine

    2013-10-08

    Iron (Fe) homeostasis is essential for life and has been intensively investigated for dicots, while our knowledge for species in the Poaceae is fragmentary. This study presents the first proteome analysis (LC-MS/MS) of plasma membranes isolated from roots of 18-day old maize (Zea mays L.). Plants were grown under low and high Fe conditions in hydroponic culture. In total, 227 proteins were identified in control plants, whereas 204 proteins were identified in Fe deficient plants and 251 proteins in plants grown under high Fe conditions. Proteins were sorted by functional classes, and most of the identified proteins were classified as signaling proteins. A significant number of PM-bound redox proteins could be identified including quinone reductases, heme and copper-containing proteins. Most of these components were constitutive, and others could hint at an involvement of redox signaling and redox homeostasis by change in abundance. Energy metabolism and translation seem to be crucial in Fe homeostasis. The response to Fe deficiency includes proteins involved in development, whereas membrane remodeling and assembly and/or repair of Fe-S clusters is discussed for Fe toxicity. The general stress response appears to involve proteins related to oxidative stress, growth regulation, an increased rigidity and synthesis of cell walls and adaption of nutrient uptake and/or translocation. This article is part of a Special Issue entitled: Plant Proteomics in Europe.

  2. Proteomic analysis identifies interleukin 11 regulated plasma membrane proteins in human endometrial epithelial cells in vitro

    Directory of Open Access Journals (Sweden)

    Stanton Peter G

    2011-05-01

    Full Text Available Abstract Background During the peri-implantation period, the embryo adheres to an adequately prepared or receptive endometrial surface epithelium. Abnormal embryo adhesion to the endometrium results in embryo implantation failure and infertility. Endometrial epithelial cell plasma membrane proteins critical in regulating adhesion may potentially be infertility biomarkers or targets for treating infertility. Interleukin (IL 11 regulates human endometrial epithelial cells (hEEC adhesion. Its production is abnormal in women with infertility. The objective of the study was to identify IL11 regulated plasma membrane proteins in hEEC in vitro using a proteomic approach. Methods Using a 2D-differential in-gel electrophoresis (DIGE electrophoresis combined with LCMS/MS mass spectrometry approach, we identified 20 unique plasma membrane proteins differentially regulated by IL11 in ECC-1 cells, a hEEC derived cell line. Two IL11 regulated proteins with known roles in cell adhesion, annexin A2 (ANXA2 and flotillin-1 (FLOT1, were validated by Western blot and immunocytochemistry in hEEC lines (ECC-1 and an additional cell line, Ishikawa and primary hEEC. Flotilin-1 was further validated by immunohistochemistry in human endometrium throughout the menstrual cycle (n = 6-8/cycle. Results 2D-DIGE analysis identified 4 spots that were significantly different between control and IL11 treated group. Of these 4 spots, there were 20 proteins that were identified with LCMS/MS. Two proteins; ANXA2 and FLOT1 were chosen for further analyses and have found to be significantly up-regulated following IL11 treatment. Western blot analysis showed a 2-fold and a 2.5-fold increase of ANXA2 in hEEC membrane fraction of ECC-1 and Ishikawa cells respectively. Similarly, a 1.8-fold and a 2.3/2.4-fold increase was also observed for FLOT1 in hEEC membrane fraction of ECC-1 and Ishikawa cells respectively. In vitro, IL11 induced stronger ANXA2 expression on cell surface of primary h

  3. Plasma proteome analysis of cervical intraepithelial neoplasia and cervical squamous cell carcinoma

    Indian Academy of Sciences (India)

    Mee Lee Looi; Saiful Anuar Karsani; Mariati Abdul Rahman; Ahmad Zailani Hatta Mohd Dali; Siti Aishah Md Ali; Wan Zurinah Wan Ngah; Yasmin Anum Mohd Yusof

    2009-12-01

    Although cervical cancer is preventable with early detection, it remains the second most common malignancy among women. An understanding of how proteins change in their expression during a particular diseased state such as cervical cancer will contribute to an understanding of how the disease develops and progresses. Potentially, it may also lead to the ability to predict the occurrence of the disease. With this in mind, we aimed to identify differentially expressed proteins in the plasma of cervical cancer patients. Plasma from control, cervical intraepithelial neoplasia (CIN) grade 3 and squamous cell carcinoma (SCC) stage IV subjects was resolved by two-dimensional gel electrophoresis and the resulting proteome profiles compared. Differentially expressed protein spots were then identified by mass spectrometry. Eighteen proteins were found to be differentially expressed in the plasma of CIN 3 and SCC stage IV samples when compared with that of controls. Competitive ELISA further validated the expression of cytokeratin 19 and tetranectin. Functional analyses of these differentially expressed proteins will provide further insight into their potential role(s) in cervical cancer-specific monitoring and therapeutics.

  4. Enrichment and proteomic analysis of plasma membrane from rat dorsal root ganglions

    Directory of Open Access Journals (Sweden)

    Lin Yong

    2009-11-01

    Full Text Available Abstract Background Dorsal root ganglion (DRG neurons are primary sensory neurons that conduct neuronal impulses related to pain, touch and temperature senses. Plasma membrane (PM of DRG cells plays important roles in their functions. PM proteins are main performers of the functions. However, mainly due to the very low amount of DRG that leads to the difficulties in PM sample collection, few proteomic analyses on the PM have been reported and it is a subject that demands further investigation. Results By using aqueous polymer two-phase partition in combination with high salt and high pH washing, PMs were efficiently enriched, demonstrated by western blot analysis. A total of 954 non-redundant proteins were identified from the plasma membrane-enriched preparation with CapLC-MS/MS analysis subsequent to protein separation by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE or shotgun digestion. 205 (21.5% of the identified proteins were unambiguously assigned as PM proteins, including a large number of signal proteins, receptors, ion channel and transporters. Conclusion The aqueous polymer two-phase partition is a simple, rapid and relatively inexpensive method. It is well suitable for the purification of PMs from small amount of tissues. Therefore, it is reasonable for the DRG PM to be enriched by using aqueous two-phase partition as a preferred method. Proteomic analysis showed that DRG PM was rich in proteins involved in the fundamental biological processes including material exchange, energy transformation and information transmission, etc. These data would help to our further understanding of the fundamental DRG functions.

  5. Assessment of Two Immunodepletion Methods: Off-Target Effects and Variations in Immunodepletion Efficiency May Confound Plasma Proteomics

    Science.gov (United States)

    Patel, Bhavinkumar B.; Barrero, Carlos A.; Braverman, Alan; Kim, Phillip D.; Jones, Kelly A.; Chen, Dian Er; Bowler, Russell P.; Merali, Salim; Kelsen, Steven G.; Yeung, Anthony T.

    2012-01-01

    Immunodepletion of abundant plasma proteins increases the depth of proteome penetration by mass spectrometry. However, the nature and extent of immunodepletion and the effect of off-target depletion on the quantitative comparison of the residual proteins have not been critically addressed. We performed mass spectrometry label-free quantitation to determine which proteins were immunodepleted and by how much. Two immunodepletion resins were compared: Qproteome (Qiagen) which removes albumin+immunoglobulins and Seppro IgY14+SuperMix (Sigma-Aldrich) which removes 14 target proteins plus a number of unidentified proteins. Plasma collected by P100 proteomic plasma collection tubes (BD) from 20 human subjects was individually immunodepleted to minimize potential variability, prior to pooling. The abundant proteins were quantified better when using only albumin+immunoglobulins removal (Qproteome) while lower abundance proteins were evaluated better using exhaustive immunodepletion (Seppro IgY14+SuperMix). The latter resin removed at least 155 proteins, 38% of the plasma proteome in protein number and 94% of plasma protein in mass. The depth of immunodepletion likely accounts for the effectiveness of this resin in revealing low abundance proteins. However, the more profound immunodepletion achieved with the IgY14+SuperMix may lead to false-positive fold-changes between comparison groups if the reproducibility and efficiency of the depletion of a given protein is not considered. PMID:23082855

  6. Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016.

    Science.gov (United States)

    Van Eyk, Jennifer E; Corrales, Fernando J; Aebersold, Ruedi; Cerciello, Ferdinando; Deutsch, Eric W; Roncada, Paola; Sanchez, Jean-Charles; Yamamoto, Tadashi; Yang, Pengyuan; Zhang, Hui; Omenn, Gilbert S

    2016-11-04

    The Biology and Disease-driven Human Proteome Project (B/D-HPP) is aimed at supporting and enhancing the broad use of state-of-the-art proteomic methods to characterize and quantify proteins for in-depth understanding of the molecular mechanisms of biological processes and human disease. Based on a foundation of the pre-existing HUPO initiatives begun in 2002, the B/D-HPP is designed to provide standardized methods and resources for mass spectrometry and specific protein affinity reagents and facilitate accessibility of these resources to the broader life sciences research and clinical communities. Currently there are 22 B/D-HPP initiatives and 3 closely related HPP resource pillars. The B/D-HPP groups are working to define sets of protein targets that are highly relevant to each particular field to deliver relevant assays for the measurement of these selected targets and to disseminate and make publicly accessible the information and tools generated. Major developments are the 2016 publications of the Human SRM Atlas and of "popular protein sets" for six organ systems. Here we present the current activities and plans of the BD-HPP initiatives as highlighted in numerous B/D-HPP workshops at the 14th annual HUPO 2015 World Congress of Proteomics in Vancouver, Canada.

  7. Integrated Cellular and Plasma Proteomics of Contrasting B-cell Cancers Reveals Common, Unique and Systemic Signatures.

    Science.gov (United States)

    Johnston, Harvey E; Carter, Matthew J; Cox, Kerry L; Dunscombe, Melanie; Manousopoulou, Antigoni; Townsend, Paul A; Garbis, Spiros D; Cragg, Mark S

    2017-03-01

    Approximately 800,000 leukemia and lymphoma cases are diagnosed worldwide each year. Burkitt's lymphoma (BL) and chronic lymphocytic leukemia (CLL) are examples of contrasting B-cell cancers; BL is a highly aggressive lymphoid tumor, frequently affecting children, whereas CLL typically presents as an indolent, slow-progressing leukemia affecting the elderly. The B-cell-specific overexpression of the myc and TCL1 oncogenes in mice induce spontaneous malignancies modeling BL and CLL, respectively. Quantitative mass spectrometry proteomics and isobaric labeling were employed to examine the biology underpinning contrasting Eμ-myc and Eμ-TCL1 B-cell tumors. Additionally, the plasma proteome was evaluated using subproteome enrichment to interrogate biomarker emergence and the systemic effects of tumor burden. Over 10,000 proteins were identified (qIL5) receptor. IL5 treatment promoted Eμ-TCL1 tumor proliferation, suggesting an amplification of IL5-induced AKT signaling by TCL1. Tumor plasma contained a substantial tumor lysis signature, most prominent in Eμ-myc plasma, whereas Eμ-TCL1 plasma contained signatures of immune-response, inflammation and microenvironment interactions, with putative biomarkers in early-stage cancer. These findings provide a detailed characterization of contrasting B-cell tumor models, identifying common and specific tumor mechanisms. Integrated plasma proteomics allowed the dissection of a systemic response and a tumor lysis signature present in early- and late-stage cancers, respectively. Overall, this study suggests common B-cell cancer signatures exist and illustrates the potential of the further evaluation of B-cell cancer subtypes by integrative proteomics.

  8. Proteome changes in the plasma of Pieris rapae parasitized by the endoparasitoid wasp Pteromalus puparum

    Institute of Scientific and Technical Information of China (English)

    Jia-ying ZHU; Qi FANG; Gong-yin YE; Cui HU

    2011-01-01

    Parasitism by the endoparasitoid wasp Pteromalus puparum causes alterations in the plasma proteins of Pieris rapae. Analysis of plasma proteins using a proteomic approach showed that seven proteins were differentially expressed in the host pupae after 24-h parasitism. They were masquerade-like serine proteinase homolog (MSPH),enolase (Eno), bilin-binding protein (BBP), imaginal disc growth factor (IDGF), ornithine decarboxylase (ODC), cellular retinoic acid binding protein (CRABP), and one unknown function protein. The full length cDNA sequences of MSPH,Eno, and BBP were successfully cloned using rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR). Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis indicated that the transcript levels of MSPH and BBP in the fat bodies of host pupae were inducible in response to the parasitism and their variations were consistent with translational changes of these genes after parasitism, while the transcript levels of Eno and IDGF were not affected by parasitism. This study will contribute to the better understanding of the molecular bases of parasitoid-induced host alterations associated with innate immune responses, detoxification, and energy metabolism.

  9. Plasma Air Decontamination System (PADS) Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed Plasma Air Decontamination System (PADS) is a trace contaminant control device based on non-thermal atmospheric pressure plasma technology that operates...

  10. Plasma Air Decontamination System (PADS) Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed Plasma Air Decontamination System (PADS) is a trace contaminant control device based on non-thermal atmospheric-pressure plasma technology. Compared to...

  11. Quantitative iTRAQ-Based Proteomic Identification of Candidate Biomarkers for Diabetic Nephropathy in Plasma of Type 1 Diabetic Patients

    DEFF Research Database (Denmark)

    Overgaard, Anne Julie; Thingholm, Tine Engberg; Larsen, Martin R

    2010-01-01

    INTRODUCTION: As part of a clinical proteomics programme focused on diabetes and its complications, it was our goal to investigate the proteome of plasma in order to find improved candidate biomarkers to predict diabetic nephropathy. METHODS: Proteins derived from plasma from a cross...... immunoassay confirmed the overall protein expression patterns observed by the iTRAQ analysis. CONCLUSION: The candidate biomarkers discovered in this cross-sectional cohort may turn out to be progression biomarkers and might have several clinical applications in the treatment and monitoring of diabetic......-sectional cohort of 123 type 1 diabetic patients previously diagnosed as normoalbuminuric, microalbuminuric or macroalbuminuric were enriched with hexapeptide library beads and subsequently pooled within three groups. Proteins from the three groups were compared by online liquid chromatography and tandem mass...

  12. Towards a membrane proteome in Drosophila: a method for the isolation of plasma membrane

    Directory of Open Access Journals (Sweden)

    Thomas Graham H

    2010-05-01

    Full Text Available Abstract Background The plasma membrane (PM is a compartment of significant interest because cell surface proteins influence the way in which a cell interacts with its neighbours and its extracellular environment. However, PM is hard to isolate because of its low abundance. Aqueous two-phase affinity purification (2PAP, based on PEG/Dextran two-phase fractionation and lectin affinity for PM-derived microsomes, is an emerging method for the isolation of high purity plasma membranes from several vertebrate sources. In contrast, PM isolation techniques in important invertebrate genetic model systems, such as Drosophila melanogaster, have relied upon enrichment by density gradient centrifugation. To facilitate genetic investigation of activities contributing to the content of the PM sub-proteome, we sought to adapt 2PAP to this invertebrate model to provide a robust PM isolation technique for Drosophila. Results We show that 2PAP alone does not completely remove contaminating endoplasmic reticulum and mitochondrial membrane. However, a novel combination of density gradient centrifugation plus 2PAP results in a robust PM preparation. To demonstrate the utility of this technique we isolated PM from fly heads and successfully identified 432 proteins using MudPIT, of which 37% are integral membrane proteins from all compartments. Of the 432 proteins, 22% have been previously assigned to the PM compartment, and a further 34% are currently unassigned to any compartment and represent candidates for assignment to the PM. The remainder have previous assignments to other compartments. Conclusion A combination of density gradient centrifugation and 2PAP results in a robust, high purity PM preparation from Drosophila, something neither technique can achieve on its own. This novel preparation should lay the groundwork for the proteomic investigation of the PM in different genetic backgrounds in Drosophila. Our results also identify two key steps in this

  13. The effects of eating marine- or vegetable-fed farmed trout on the human plasma proteome profiles of healthy men.

    Science.gov (United States)

    Rentsch, Maria L; Lametsch, René; Bügel, Susanne; Jessen, Flemming; Lauritzen, Lotte

    2015-02-28

    Most human intervention studies have examined the effects on a subset of risk factors, some of which may require long-term exposure. The plasma proteome may reflect the underlying changes in protein expression and activation, and this could be used to identify early risk markers. The aim of the present study was to evaluate the impact of regular fish intake on the plasma proteome. We recruited thirty healthy men aged 40 to 70 years, who were randomly allocated to a daily meal of chicken or trout raised on vegetable or marine feeds. Blood samples were collected before and after 8 weeks of intervention, and after the removal of the twelve most abundant proteins, plasma proteins were separated by two-dimensional gel electrophoresis. Protein spots 4·3 visualised by silver staining were matched by two-dimensional imaging software. Within-subject changes in spots were compared between the treatment groups. Differentially affected spots were identified by matrix-assisted laser desorption ionisation-time of flight/time of flight MS and the human Swiss-Prot database. We found 23/681 abundant plasma protein spots, which were up- or down-regulated by the dietary treatment (P spots differed from those in subjects given the chicken meal, but only three of these were common, and only one spot differed between the two trout groups. In both groups, the affected plasma proteins were involved in biological processes such as regulation of vitamin A and haem transport, blood fibrinolysis and oxidative defence. Thus, regular fish intake affects the plasma proteome, and the changes may indicate novel mechanisms of effect.

  14. HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy.

    Science.gov (United States)

    Hamacher, Michael; Apweiler, Rolf; Arnold, Georg; Becker, Albert; Blüggel, Martin; Carrette, Odile; Colvis, Christine; Dunn, Michael J; Fröhlich, Thomas; Fountoulakis, Michael; van Hall, André; Herberg, Friedrich; Ji, Jianguo; Ji, Juango; Kretzschmar, Hans; Lewczuk, Piotr; Lubec, Gert; Marcus, Katrin; Martens, Lennart; Palacios Bustamante, Nadine; Park, Young Mok; Pennington, Stephen R; Robben, Johan; Stühler, Kai; Reidegeld, Kai A; Riederer, Peter; Rossier, Jean; Sanchez, Jean-Charles; Schrader, Michael; Stephan, Christian; Tagle, Danilo; Thiele, Herbert; Wang, Jing; Wiltfang, Jens; Yoo, Jong Shin; Zhang, Chenggang; Klose, Joachim; Meyer, Helmut E

    2006-09-01

    The Human Proteome Organisation (HUPO) initiated several projects focusing on the proteome analysis of distinct human organs. The Brain Proteome Project (BPP) is the initiative dedicated to the brain, its development and correlated diseases. Two pilot studies have been performed aiming at the comparison of techniques, laboratories and approaches. With the help of the results gained, objective data submission, storage and reprocessing workflow have been established. The biological relevance of the data will be drawn from the inter-laboratory comparisons as well as from the re-calculation of all data sets submitted by the different groups. In the following, results of the single groups as well as the centralised reprocessing effort will be summarised and compared, showing the added value of this concerted work.

  15. Long-term heat stress induces the inflammatory response in dairy cows revealed by plasma proteome analysis.

    Science.gov (United States)

    Min, Li; Zheng, Nan; Zhao, Shengguo; Cheng, Jianbo; Yang, Yongxin; Zhang, Yangdong; Yang, Hongjian; Wang, Jiaqi

    2016-03-04

    In this work we employed a comparative proteomic approach to evaluate seasonal heat stress and investigate proteomic alterations in plasma of dairy cows. Twelve lactating Holstein dairy cows were used and the treatments were: heat stress (n = 6) in hot summer (at the beginning of the moderate heat stress) and no heat stress (n = 6) in spring natural ambient environment, respectively. Subsequently, heat stress treatment lasted 23 days (at the end of the moderate heat stress) to investigate the alterations of plasma proteins, which might be employed as long-term moderate heat stress response in dairy cows. Changes in plasma proteins were analyzed by two-dimensional electrophoresis (2-DE) combined with mass spectrometry. Analysis of the properties of the identified proteins revealed that the alterations of plasma proteins were related to inflammation in long-term moderate heat stress. Furthermore, the increase in plasma tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) directly demonstrated that long-term moderate heat stress caused an inflammatory response in dairy cows.

  16. Effects of ω-3 Polyunsaturated Fatty Acids on Plasma Proteome in Rett Syndrome

    Directory of Open Access Journals (Sweden)

    Claudio De Felice

    2013-01-01

    Full Text Available The mechanism of action of omega-3 polyunsaturated fatty acids (ω-3 PUFAs is only partially known. Prior reports suggest a partial rescue of clinical symptoms and oxidative stress (OS alterations following ω-3 PUFAs supplementation in patients with Rett syndrome (RTT, a devastating neurodevelopmental disorder with transient autistic features, affecting almost exclusively females and mainly caused by sporadic mutations in the gene encoding the methyl CpG binding protein 2 (MeCP2 protein. Here, we tested the hypothesis that ω-3 PUFAs may modify the plasma proteome profile in typical RTT patients with MECP2 mutations and classic phenotype. A total of 24 RTT girls at different clinical stages were supplemented with ω-3 PUFAs as fish oil for 12 months and compared to matched healthy controls. The expression of 16 proteins, mainly related to acute phase response (APR, was changed at the baseline in the untreated patients. Following ω-3 PUFAs supplementation, the detected APR was partially rescued, with the expression of 10 out of 16 (62% proteins being normalized. ω-3 PUFAs have a major impact on the modulation of the APR in RTT, thus providing new insights into the role of inflammation in autistic disorders and paving the way for novel therapeutic strategies.

  17. Proteomic Analysis of Rice Plasma Membrane-associated Proteins in Response to Chitooligosaccharide Elicitors

    Institute of Scientific and Technical Information of China (English)

    Fang Chen; Qun Li; Zuhua He

    2007-01-01

    Chitooligomers or chitooligosaccharides (COS) are elicitors that bind to the plasma membrane (PM) and elicit various defense responses. However, the PM-bound proteins involved in elicitor-mediated plant defense responses still remain widely unknown. In order to get more information about PM proteins involved in rice defense responses, we conducted PM proteomic analysis of the rice suspension cells elicited by COS. A total of 14 up- or down-regulated protein spots were observed on 2-D gels of PM fractions at 12 h and 24 h after COS incubation. Of them, eight protein spots were successfully identified by MS (mass spectrography) and predicted to be associated to the PM and function in plant defense, including a putative PKN/PRK1 protein kinase, a putative pyruvate kinase isozyme G, a putative zinc finger protein, a putative MAR-binding protein MFP1, and a putative calcium-dependent protein kinase. Interestingly, a COS-induced pM5-like protein was identified for the first time in plants, which is a trans-membrane nodal modulator in transforming growth factor-β(TGFβ) signaling in vertebrates. We also identified two members of a rice polyprotein family, which were up-regulated by COS. Our study would provide a starting point for functionality of PM proteins in the rice basal defense.

  18. Inductively Coupled Plasma Mass Spectrometry (ICP-MS) Applications in Quantitative Proteomics.

    Science.gov (United States)

    Chahrour, Osama; Malone, John

    2017-01-01

    Recent advances in inductively coupled plasma mass spectrometry (ICP-MS) hyphenated to different separation techniques have promoted it as a valuable tool in protein/peptide quantification. These emerging ICP-MS applications allow absolute quantification by measuring specific elemental responses. One approach quantifies elements already present in the structure of the target peptide (e.g. phosphorus and sulphur) as natural tags. Quantification of these natural tags allows the elucidation of the degree of protein phosphorylation in addition to absolute protein quantification. A separate approach is based on utilising bi-functional labelling substances (those containing ICP-MS detectable elements), that form a covalent chemical bond with the protein thus creating analogs which are detectable by ICP-MS. Based on the previously established stoichiometries of the labelling reagents, quantification can be achieved. This technique is very useful for the design of precise multiplexed quantitation schemes to address the challenges of biomarker screening and discovery. This review discusses the capabilities and different strategies to implement ICP-MS in the field of quantitative proteomics. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  19. Effects of Fuzheng Huayu Decoction on plasma proteome in cirrhosis: preliminary experimental study with rats

    Institute of Scientific and Technical Information of China (English)

    Jie LIU; Jiyao WANG; Liming WEI; Ye LU; Hong JIN

    2008-01-01

    The aim of this paper is to study the effects of Fuzheng Huayu Decoction on the plasma proteome in cirrhotic rats. Twenty-six male Sprague-Dawley (SD) rats were randomly divided into three groups: cirrhotic model group (n=10), treated with CCl4 (CCl4/olive oil: v/v=1:1); Fuzheng Huayu Decoction intervention group (n=10), treated with CCl4 + Fuzheng Huayu Decoction; and normal control group (n=6), treated with olive oil only. After 8 weeks, blood samples were collected from the inferior vena cava to undergo bi-dimensional electrophoresis (2DE) and analysis by PDQuest 7.3 software. Differential protein spots were cut, enzyme hydrolysis was conducted, and peptide fragments extracted from the mixture underwent mass spectrometry (MS) with MALDI-TOF-TOF-MS. The liver fibrogenesis was assessed using a digital image analysis instrument of Masson's trichrome stained sections. The fibrosis area of the Fuzheng Huayu Decoction was (8.9±3.7)%, significantly smaller than that of the cirrhotic model group [(12.4±4.7)%, P<0.05]. Ten markedly changed protein spots were identified by MALDI-TOF-TOF-MS. Eight of the 10 proteins, including plasma glutathione peroxidase, plasma glutathione peroxidase precursor, prealbumin, haptoglobin, apolipoprotein A-Ⅳ precursor, complement C4, inter-alpha-inhibitor H4 heavy chain, and serine/threonine-protein kinase microtubule-affinity regulating kinase 1 (MARK1) were expressed very lowly in the cirrhotic model group while they were expressed highly in the Fuzheng Huayu Decoction group. The expression of liver regeneration-related protein LRRG03 and vimentin increased in the cirrhotic model group, and reduced in the Fuzheng Huayu Decoction group. Some proteins related to oxidative stress, cell proliferation and transformation have changed in the plasma of cirrhosis induced by CCl4. Fuzheng Huayu Decoction promotes protein synthesis and plays an anti-fibrotic role by anti-oxidation and accommodation of cell proliferation and transformation.

  20. Role of DHA in aging-related changes in mouse brain synaptic plasma membrane proteome.

    Science.gov (United States)

    Sidhu, Vishaldeep K; Huang, Bill X; Desai, Abhishek; Kevala, Karl; Kim, Hee-Yong

    2016-05-01

    Aging has been related to diminished cognitive function, which could be a result of ineffective synaptic function. We have previously shown that synaptic plasma membrane proteins supporting synaptic integrity and neurotransmission were downregulated in docosahexaenoic acid (DHA)-deprived brains, suggesting an important role of DHA in synaptic function. In this study, we demonstrate aging-induced synaptic proteome changes and DHA-dependent mitigation of such changes using mass spectrometry-based protein quantitation combined with western blot or messenger RNA analysis. We found significant reduction of 15 synaptic plasma membrane proteins in aging brains including fodrin-α, synaptopodin, postsynaptic density protein 95, synaptic vesicle glycoprotein 2B, synaptosomal-associated protein 25, synaptosomal-associated protein-α, N-methyl-D-aspartate receptor subunit epsilon-2 precursor, AMPA2, AP2, VGluT1, munc18-1, dynamin-1, vesicle-associated membrane protein 2, rab3A, and EAAT1, most of which are involved in synaptic transmission. Notably, the first 9 proteins were further reduced when brain DHA was depleted by diet, indicating that DHA plays an important role in sustaining these synaptic proteins downregulated during aging. Reduction of 2 of these proteins was reversed by raising the brain DHA level by supplementing aged animals with an omega-3 fatty acid sufficient diet for 2 months. The recognition memory compromised in DHA-depleted animals was also improved. Our results suggest a potential role of DHA in alleviating aging-associated cognitive decline by offsetting the loss of neurotransmission-regulating synaptic proteins involved in synaptic function.

  1. The differential plasma proteome of obese and overweight individuals undergoing a nutritional weight loss and maintenance intervention

    DEFF Research Database (Denmark)

    Oller Moreno, Sergio; Cominetti, Ornella; Núñez Galindo, Antonio

    2017-01-01

    PURPOSE: The nutritional intervention program "DiOGenes" focuses on how obesity can be prevented and treated from a dietary perspective. We generated differential plasma proteome profiles in the DiOGenes cohort to identify proteins associated with weight loss and maintenance and explore their rel......PURPOSE: The nutritional intervention program "DiOGenes" focuses on how obesity can be prevented and treated from a dietary perspective. We generated differential plasma proteome profiles in the DiOGenes cohort to identify proteins associated with weight loss and maintenance and explore...... intervention. Protein relationships with clinical variables were explored using univariate linear models, considering collection center, gender and age as confounding factors. RESULTS: 473 subjects were measured at baseline and end of the intervention; 39 proteins were longitudinally differential. Proteins......-rich acidic protein 1 (PRAP1) variation and Matsuda insulin sensitivity increment was showed. CONCLUSIONS AND CLINICAL RELEVANCE: MS-based proteomic analysis of a large cohort of non-diabetic overweight and obese individuals concomitantly identified known and novel proteins associated with weight loss...

  2. Proteomics and aging : studying the influence of aging on endothelial cells and human plasma

    NARCIS (Netherlands)

    Eman, M.R.

    2007-01-01

    In general, human aging is considered one of the most complex and less-well understood process in biology. In this thesis the possibilities of proteomics technology in the field of aging were explored. The complexity of the aging process was supposed to accompanied by relatively subtle proteome vari

  3. High Power Helicon Plasma Propulsion Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed work seeks to develop and optimize an electrode-less plasma propulsion system that is based on a high power helicon (HPH) that is being developed...

  4. High Power Helicon Plasma Propulsion Project

    Data.gov (United States)

    National Aeronautics and Space Administration — A new thruster has been conceived and tested that is based on a high power helicon (HPH) plasma wave. In this new method of propulsion, an antenna generates and...

  5. Plasma proteome profiles of White Sucker (Catostomus commersonii) from the Athabasca River within the oil sands deposit.

    Science.gov (United States)

    Simmons, Denina B D; Sherry, James P

    2016-09-01

    There are questions about the potential for oil sands related chemicals to enter the Athabasca River, whether from tailing ponds, atmospheric deposition, precipitation, or transport of mining dust, at concentrations sufficient to negatively impact the health of biota. We applied shotgun proteomics to generate protein profiles of mature male and female White Sucker (Catostomus commersonii) that were collected from various sites along the main stem of the Athabasca River in 2011 and 2012. On average, 399±131 (standard deviation) proteins were identified in fish plasma from each location in both years. Ingenuity Pathway Analysis software was used to determine the proteins' core functions and to compare the datasets by location, year, and sex. Principal component analysis (PCA) was used to determine if variation in the number of proteins related to a core function among all male and female individuals from both sampling years was affected by location. The core biological functions of plasma proteins that were common to both sampling years for males and females from each location were also estimated separately (based on Ingenuity's Knowledge Base). PCA revealed site-specific differences in the functional characteristics of the plasma proteome from white sucker sampled from downstream of oil sands extraction facilities compared with fish from upstream. Plasma proteins that were unique to fish downstream of oil sands extraction were related to lipid metabolism, small molecule biochemistry, vitamin and mineral metabolism, endocrine system disorders, skeletal and muscular development and function, neoplasia, carcinomas, and gastrointestinal disease.

  6. IgY14 and SuperMix immunoaffinity separations coupled with liquid chromatography-mass spectrometry for human plasma proteomic biomarker discovery

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Tujin; Zhou, Jianying; Gritsenko, Marina A.; Hossain, Mahmud; Camp, David G.; Smith, Richard D.; Qian, Weijun

    2012-02-01

    Interest in the application of advanced proteomics technologies to human blood plasma- or serum-based clinical samples for the purpose of discovering disease biomarkers continues to grow; however, the enormous dynamic range of protein concentrations in these types of samples (often >10 orders of magnitude) represents a significant analytical challenge, particularly for detecting low-abundance candidate biomarkers. In response, immunoaffinity separation methods for depleting multiple high- and moderate-abundance proteins have become key tools for enriching low-abundance proteins and enhancing detection of these proteins in plasma proteomics. Herein, we describe IgY14 and tandem IgY14-Supermix separation methods for removing 14 high-abundance and up to 60 moderate-abundance proteins, respectively, from human blood plasma and highlight their utility when combined with liquid chromatography-tandem mass spectrometry for interrogating the human plasma proteome.

  7. IgY14 and SuperMix immunoaffinity separations coupled with liquid chromatography-mass spectrometry for human plasma proteomics biomarker discovery.

    Science.gov (United States)

    Shi, Tujin; Zhou, Jian-Ying; Gritsenko, Marina A; Hossain, Mahmud; Camp, David G; Smith, Richard D; Qian, Wei-Jun

    2012-02-01

    Interest in the application of advanced proteomics technologies to human blood plasma- or serum-based clinical samples for the purpose of discovering disease biomarkers continues to grow; however, the enormous dynamic range of protein concentrations in these types of samples (often >10 orders of magnitude) represents a significant analytical challenge, particularly for detecting low-abundance candidate biomarkers. In response, immunoaffinity separation methods for depleting multiple high- and moderate-abundance proteins have become key tools for enriching low-abundance proteins and enhancing detection of these proteins in plasma proteomics. Herein, we describe IgY14 and tandem IgY14-Supermix separation methods for removing 14 high-abundance and up to 60 moderate-abundance proteins, respectively, from human blood plasma and highlight their utility when combined with liquid chromatography-tandem mass spectrometry for interrogating the human plasma proteome.

  8. Free-flow electrophoresis of plasma membrane vesicles enriched by two-phase partitioning enhances the quality of the proteome from Arabidopsis seedlings

    DEFF Research Database (Denmark)

    de Michele, Roberto; McFarlane, Heather E; Parsons, Harriet Tempé

    2016-01-01

    The plant plasma membrane is the interface between the cell and its environment undertaking a range of important functions related to transport, signaling, cell wall biosynthesis, and secretion. Multiple proteomic studies have attempted to capture the diversity of proteins in the plasma membrane ...

  9. The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community.

    Science.gov (United States)

    Aebersold, Ruedi; Bader, Gary D; Edwards, Aled M; van Eyk, Jennifer E; Kussmann, Martin; Qin, Jun; Omenn, Gilbert S

    2013-01-04

    The biology and disease oriented branch of the Human Proteome Project (B/D-HPP) was established by the Human Proteome Organization (HUPO) with the main goal of supporting the broad application of state-of the-art measurements of proteins and proteomes by life scientists studying the molecular mechanisms of biological processes and human disease. This will be accomplished through the generation of research and informational resources that will support the routine and definitive measurement of the process or disease relevant proteins. The B/D-HPP is highly complementary to the C-HPP and will provide datasets and biological characterization useful to the C-HPP teams. In this manuscript we describe the goals, the plans, and the current status of the of the B/D-HPP.

  10. Nonequilibrium plasma generator (NPG) project - experimental program

    Energy Technology Data Exchange (ETDEWEB)

    Lineberry, J.T.; Wu, Y.C.L.; Lin, B.C. [and others

    1995-12-31

    This paper summarizes research conducted under a DOE MHD SBIR entitled: {open_quotes}A Light Metal Fueled Non-equilibrium Plasma Generator (NPG){close_quotes}. It is a summary paper presenting the idea of the NPG and activities of the NPG SBIR research program along with experimental results from NPG Proof-of-Principle tests. The NPG is an innovative concept for a combustion device that can produce a nonequilibrium plasma. This device bums powdered metal fuel, and it can be used to drive an MHD disk generator pulse power unit or a similar nonequilibrium MHD device or system. The NPG research program was concluded over the past two years under sponsorship of a DOE Phase II SBIR grant. This program focused on addressing fundamental and practical aspects of the NPG concept and its system design. The research included investigation of the physics of the NPG concept through theoretical and experimental studies on the quality of the plasma that it can produce, theoretical evaluations of the nonequilibrium ionization processes in an MHD disk generator driven by an NPG, and experimental validation of the NPG concept in Proof-of-Principle tests. At the conclusion of this research it was determined that the NPG is indeed a viable concept. Results from combustion tests using powdered aluminum fuel reveal that the NPG can produce an extremely hot argon plasma clean enough to support nonequilibrium ionization in an MHD device.

  11. Functional and proteomic alterations of plasma high density lipoproteins in type 1 diabetes mellitus.

    Science.gov (United States)

    Manjunatha, Shankarappa; Distelmaier, Klaus; Dasari, Surendra; Carter, Rickey E; Kudva, Yogish C; Nair, K Sreekumaran

    2016-09-01

    Higher HDL-cholesterol (HDL-C) is linked to lower cardiovascular risk but individuals with type 1 diabetes mellitus (T1DM) with normal or high HDL-C have higher cardiovascular events compared to age matched non-diabetic controls (ND). We determined whether altered HDL functions despite having normal HDL-C concentration may explain increased cardiovascular risk in T1DM individuals. We also determined whether irreversible posttranslational modifications (PTMs) of HDL bound proteins occur in T1DM individuals with altered HDL functions. T1DM with poor glycemic control (T1D-PC, HbA1c≥8.5%, n=15) and T1DM with good glycemic control (T1D-GC, HbA1c≤6.6%, n=15) were compared with equal numbers of NDs, ND-PC and ND-GC respectively, matched for age, sex and body mass index (BMI). We measured cholesterol efflux capacity (CEC) of HDL in the serum using J774 macrophages, antioxidant function of HDL as the ability to reverse the oxidative damage of LDL and PON1 activity using commercially available kit. For proteomic analysis, HDL was isolated by density gradient ultracentrifugation and was analyzed by mass spectrometry and shotgun proteomics method. Plasma HDL-C concentrations in both T1DM groups were similar to their ND. However, CEC (%) of T1D-PC (16.9±0.8) and T1D-GC (17.1±1) were lower than their respective ND (17.9±1, p=0.01 and 18.2±1.4, p=0.02). HDL antioxidative function also was lower (p<0.05). The abundance of oxidative PTMs of apolipoproteins involved in CEC and antioxidative functions of HDL were higher in T1D-PC (ApoA4, p=0.041) and T1D-GC (ApoA4, p=0.025 and ApoE, p=0.041) in comparison with ND. Both T1D-PC and T1D-GC groups had higher abundance of amadori modification of ApoD (p=0.002 and p=0.041 respectively) and deamidation modification of ApoA4 was higher in T1D-PC (p=0.025). Compromised functions of HDL particles in T1DM individuals, irrespective of glycemic control, could be explained by higher abundance of irreversible PTMs of HDL proteins. These

  12. Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project.

    Science.gov (United States)

    Horvatovich, Péter; Lundberg, Emma K; Chen, Yu-Ju; Sung, Ting-Yi; He, Fuchu; Nice, Edouard C; Goode, Robert J; Yu, Simon; Ranganathan, Shoba; Baker, Mark S; Domont, Gilberto B; Velasquez, Erika; Li, Dong; Liu, Siqi; Wang, Quanhui; He, Qing-Yu; Menon, Rajasree; Guan, Yuanfang; Corrales, Fernando J; Segura, Victor; Casal, J Ignacio; Pascual-Montano, Alberto; Albar, Juan P; Fuentes, Manuel; Gonzalez-Gonzalez, Maria; Diez, Paula; Ibarrola, Nieves; Degano, Rosa M; Mohammed, Yassene; Borchers, Christoph H; Urbani, Andrea; Soggiu, Alessio; Yamamoto, Tadashi; Salekdeh, Ghasem Hosseini; Archakov, Alexander; Ponomarenko, Elena; Lisitsa, Andrey; Lichti, Cheryl F; Mostovenko, Ekaterina; Kroes, Roger A; Rezeli, Melinda; Végvári, Ákos; Fehniger, Thomas E; Bischoff, Rainer; Vizcaíno, Juan Antonio; Deutsch, Eric W; Lane, Lydie; Nilsson, Carol L; Marko-Varga, György; Omenn, Gilbert S; Jeong, Seul-Ki; Lim, Jong-Sun; Paik, Young-Ki; Hancock, William S

    2015-09-04

    This paper summarizes the recent activities of the Chromosome-Centric Human Proteome Project (C-HPP) consortium, which develops new technologies to identify yet-to-be annotated proteins (termed "missing proteins") in biological samples that lack sufficient experimental evidence at the protein level for confident protein identification. The C-HPP also aims to identify new protein forms that may be caused by genetic variability, post-translational modifications, and alternative splicing. Proteogenomic data integration forms the basis of the C-HPP's activities; therefore, we have summarized some of the key approaches and their roles in the project. We present new analytical technologies that improve the chemical space and lower detection limits coupled to bioinformatics tools and some publicly available resources that can be used to improve data analysis or support the development of analytical assays. Most of this paper's content has been compiled from posters, slides, and discussions presented in the series of C-HPP workshops held during 2014. All data (posters, presentations) used are available at the C-HPP Wiki (http://c-hpp.webhosting.rug.nl/) and in the Supporting Information.

  13. The first pilot project of the consortium for top-down proteomics: A status report

    Energy Technology Data Exchange (ETDEWEB)

    Dang, Xibei [Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee FL USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee FL USA; Scotcher, Jenna [Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee FL USA; Wu, Si [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA USA; Chu, Rosalie K. [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA USA; Tolić, Nikola [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA USA; Ntai, Ioanna [Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston IL USA; Thomas, Paul M. [Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston IL USA; Fellers, Ryan T. [Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston IL USA; Early, Bryan P. [Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston IL USA; Zheng, Yupeng [Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston IL USA; Durbin, Kenneth R. [Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston IL USA; LeDuc, Richard D. [NIH/NCRR Mass Spectrometry Resource, Washington University in St. Louis, St. Louis MO USA; Wolff, Jeremy J. [Bruker Daltonics, Billerica MA USA; Thompson, Christopher J. [Bruker Daltonics, Billerica MA USA; Pan, Jingxi [UVic-Genome BC Proteomics Centre, Department of Biochemistry and Microbiology, University of Victoria, Victoria BC Canada; Han, Jun [UVic-Genome BC Proteomics Centre, Department of Biochemistry and Microbiology, University of Victoria, Victoria BC Canada; Shaw, Jared B. [Department of Chemistry, University of Texas, Austin TX USA; Salisbury, Joseph P. [Departments of Chemistry and Pharm. Sci., Barnett Institute, Northeastern University, Boston MA USA; Easterling, Michael [Bruker Daltonics, Billerica MA USA; Borchers, Christoph H. [UVic-Genome BC Proteomics Centre, Department of Biochemistry and Microbiology, University of Victoria, Victoria BC Canada; Brodbelt, Jennifer S. [Department of Chemistry, University of Texas, Austin TX USA; Agar, Jeffery N. [Departments of Chemistry and Pharm. Sci., Barnett Institute, Northeastern University, Boston MA USA; Paša-Tolić, Ljiljana [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA USA; Kelleher, Neil L. [Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston IL USA; Young, Nicolas L. [Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee FL USA

    2014-04-14

    Pilot Project #1—the identification and characterization of human histone H4 proteoforms by top-down MS—is the first project launched by the Consortium for Top-Down Proteomics (CTDP) to refine and validate top-down MS. Within the initial results from seven participating laboratories, all reported the probability-based identification of human histone H4 (UniProt accession P62805) with expectation values ranging from 10-13 to 10-105. Regarding characterization, a total of 74 proteoforms were reported, with 21 done so unambiguously; one new PTM, K79ac, was identified. Inter-laboratory comparison reveals aspects of the results that are consistent, such as the localization of individual PTMs and binary combinations, while other aspects are more variable, such as the accurate characterization of low-abundance proteoforms harboring >2 PTMs. An open-access tool and discussion of proteoform scoring are included, along with a description of general challenges that lie ahead including improved proteoform separations prior to mass spectrometric analysis, better instrumentation performance, and software development.

  14. Proteomic identification of plasma protein tyrosine phosphatase alpha and fibronectin associated with liver fluke, Opisthorchis viverrini, infection.

    Directory of Open Access Journals (Sweden)

    Jarinya Khoontawad

    Full Text Available Opisthorchiasis caused by Opisthorchis viverrini induces periductal fibrosis via host immune/inflammatory responses. Plasma protein alteration during host-parasite interaction-mediated inflammation may provide potential diagnostic and/or prognostic biomarkers. To search for target protein changes in O. viverrini-infected hamsters, a 1-D PAGE gel band was trypsin-digested and analyzed by a LC-MS/MS-based proteomics approach in the plasma profile of infected hamsters, and applied to humans. Sixty seven proteins were selected for further analysis based on at least two unique tryptic peptides with protein ID score >10 and increased expression at least two times across time points. These proteins have not been previously identified in O. viverrini-associated infection. Among those, proteins involved in structural (19%, immune response (13%, cell cycle (10% and transcription (10% were highly expressed. Western blots revealed an expression level of protein tyrosine phosphatase alpha (PTPα which reached a peak at 1 month and subsequently tended to decrease. Fibronectin significantly increased at 1 month and tended to increase with time, supporting proteomic analysis. PTPα was expressed in the cytoplasm of inflammatory cells, while fibronectin was observed mainly in the cytoplasm of fibroblasts and the extracellular matrix at periductal fibrosis areas. In addition, these protein levels significantly increased in the plasma of O. viverrini-infected patients compared to healthy individuals, and significantly decreased at 2-months post-treatment, indicating their potential as disease markers. In conclusion, our results suggest that plasma PTPα and fibronectin may be associated with opisthorchiasis and the hamster model provides the basis for development of novel diagnostic markers in the future.

  15. Analysis of the plasma proteome in COPD: Novel low abundance proteins reflect the severity of lung remodeling.

    Science.gov (United States)

    Merali, Salim; Barrero, Carlos A; Bowler, Russell P; Chen, Diane Er; Criner, Gerard; Braverman, Alan; Litwin, Samuel; Yeung, Anthony; Kelsen, Steven G

    2014-04-01

    The search for COPD biomarkers has largely employed a targeted approach that focuses on plasma proteins involved in the systemic inflammatory response and in lung injury and repair. This proof of concept study was designed to test the idea that an open, unbiased, in-depth proteomics approach could identify novel, low abundance plasma proteins i.e., ng/mL concentration, which could serve as potential biomarkers. Differentially expressed proteins were identified in a discovery group with severe COPD (FEV1 <45% predicted; n = 10). Subjects with normal lung function matched for age, sex, ethnicity and smoking history served as controls (n = 10). Pooled plasma from each group was exhaustively immunodepleted of abundant proteins, d separated by 1-D gel electrophoresis and extensively fractionated prior to LC-tandem mass spectroscopy (GeLC-MS). Thirty one differentially expressed proteins were identified in the discovery group including markers of lung defense against oxidant stress, alveolar macrophage activation, and lung tissue injury and repair. Four of the 31 proteins (i.e., GRP78, soluble CD163, IL1AP and MSPT9) were measured in a separate verification group of 80 subjects with varying COPD severity by immunoassay. All 4 were significantly altered in COPD and 2 (GRP78 and soluble CD163) correlated with both FEV1 and the extent of emphysema. In-depth, plasma proteomic analysis identified a group of novel, differentially expressed, low abundance proteins that reflect known pathogenic mechanisms and the severity of lung remodeling in COPD. These proteins may also prove useful as COPD biomarkers.

  16. Identification of altered plasma proteins by proteomic study in valvular heart diseases and the potential clinical significance.

    Directory of Open Access Journals (Sweden)

    Ge Gao

    Full Text Available BACKGROUND: Little is known about genetic basis and proteomics in valvular heart disease (VHD including rheumatic (RVD and degenerative (DVD valvular disease. The present proteomic study examined the hypothesis that certain proteins may be associated with the pathological changes in the plasma of VHD patients. METHODS AND RESULTS: Differential protein analysis in the plasma identified 18 differentially expressed protein spots and 14 corresponding proteins or polypeptides by two-dimensional electrophoresis and mass spectrometry in 120 subjects. Two up-regulated (complement C4A and carbonic anhydrase 1 and three down-regulated proteins (serotransferrin, alpha-1-antichymotrypsin, and vitronectin were validated by ELISA in enlarging samples. The plasma levels (n = 40 for each of complement C4A in RVD (715.8±35.6 vs. 594.7±28.2 ng/ml, P = 0.009 and carbonic anhydrase 1 (237.70±15.7 vs. 184.7±10.8 U/L, P = 0.007 in DVD patients were significantly higher and that of serotransferrin (2.36±0.20 vs. 2.93±0.16 mg/ml, P = 0.025 and alpha-1-antichymotrypsin (370.0±13.7 vs. 413.0±11.6 µg/ml, P = 0.019 in RVD patients were significantly lower than those in controls. The plasma vitronectin level in both RVD (281.3±11.0 vs. 323.2±10.0 µg/ml, P = 0.006 and DVD (283.6±11.4 vs. 323.2±10.0 µg/ml, P = 0.011 was significantly lower than those in normal controls. CONCLUSIONS: We have for the first time identified alterations of 14 differential proteins or polypeptides in the plasma of patients with various VHD. The elevation of plasma complement C4A in RVD and carbonic anhydrase 1 in DVD and the decrease of serotransferrin and alpha-1-antichymotrypsin in RVD patients may be useful biomarkers for these valvular diseases. The decreased plasma level of vitronectin - a protein related to the formation of valvular structure - in both RVD and DVD patients might indicate the possible genetic deficiency in these patients.

  17. M3D project for simulation studies of plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Park, W.; Belova, E.V.; Fu, G.Y. [Princeton Univ., NJ (United States). Plasma Physics Lab.; Strauss, H.R. [New York Univ., NY (United States); Sugiyama, L.E. [Massachusetts Inst. of Tech., Cambridge, MA (United States)

    1998-12-31

    The M3D (Multi-level 3D) project carries out simulation studies of plasmas of various regimes using multi-levels of physics, geometry, and mesh schemes in one code package. This paper and papers by Strauss, Sugiyama, and Belova in this workshop describe the project, and present examples of current applications. The currently available physics models of the M3D project are MHD, two-fluids, gyrokinetic hot particle/MHD hybrid, and gyrokinetic particle ion/two-fluid hybrid models. The code can be run with both structured and unstructured meshes.

  18. Confinement projections for the Burning Plasma Experiment (BPX)

    Energy Technology Data Exchange (ETDEWEB)

    Goldston, R.J.; Bateman, G.; Kaye, S.M.; Perkins, F.W.; Pomphrey, N.; Stotler, D.P.; Zarnstorff, M.C. (Princeton Univ., NJ (USA). Plasma Physics Lab.); Houlberg, W.A.; Neilson, G.H. (Oak Ridge National Lab., TN (USA)); Porkolab, M. (Massachusetts Inst. of Tech., Cambridge, MA (USA)); Reidel, K.S. (New York Univ., NY (USA)); Stambaugh, R.D.; Waltz, R.E. (General Atomics, San Diego, CA (USA))

    1991-01-01

    The mission of the Burning Plasma Experiment (BPX, formerly CIT) is to study the physics of self-heated fusion plasmas (Q = 5 to ignition), and to demonstrate the production of substantial amounts of fusion power (P{sub fus} = 100 to 500 MW). Confinement projections for BPX have been made on the basis of (1) dimensional extrapolation (2) theory-based modeling calibrated to experiment, and (3) statistical scaling from the available empirical data base. The results of all three approaches, discussed in this paper, roughly coincide. We presently view the third approach, statistical scaling, as the most reliable means for projecting the confinement performance of BPX, and especially for assessing the uncertainty in the projection. 11 refs., 2 figs., 1 tab.

  19. Plasma membrane proteomics in the maize primary root growth zone: novel insights into root growth adaptation to water stress.

    Science.gov (United States)

    Voothuluru, Priyamvada; Anderson, Jeffrey C; Sharp, Robert E; Peck, Scott C

    2016-09-01

    Previous work on maize (Zea mays L.) primary root growth under water stress showed that cell elongation is maintained in the apical region of the growth zone but progressively inhibited further from the apex. These responses involve spatially differential and coordinated regulation of osmotic adjustment, modification of cell wall extensibility, and other cellular growth processes that are required for root growth under water-stressed conditions. As the interface between the cytoplasm and the apoplast (including the cell wall), the plasma membrane likely plays critical roles in these responses. Using a simplified method for enrichment of plasma membrane proteins, the developmental distribution of plasma membrane proteins was analysed in the growth zone of well-watered and water-stressed maize primary roots. The results identified 432 proteins with differential abundances in well-watered and water-stressed roots. The majority of changes involved region-specific patterns of response, and the identities of the water stress-responsive proteins suggest involvement in diverse biological processes including modification of sugar and nutrient transport, ion homeostasis, lipid metabolism, and cell wall composition. Integration of the distinct, region-specific plasma membrane protein abundance patterns with results from previous physiological, transcriptomic and cell wall proteomic studies reveals novel insights into root growth adaptation to water stress.

  20. Plasma proteomics classifiers improve risk prediction for renal disease in patients with hypertension or type 2 diabetes

    DEFF Research Database (Denmark)

    Pena, Michelle J; Jankowski, Joachim; Heinze, Georg

    2015-01-01

    OBJECTIVE: Micro and macroalbuminuria are strong risk factors for progression of nephropathy in patients with hypertension or type 2 diabetes. Early detection of progression to micro and macroalbuminuria may facilitate prevention and treatment of renal diseases. We aimed to develop plasma...... proteomics classifiers to predict the development of micro or macroalbuminuria in hypertension or type 2 diabetes. METHODS: Patients with hypertension (n = 125) and type 2 diabetes (n = 82) were selected for this case-control study from the Prevention of REnal and Vascular ENd-stage Disease cohort....... RESULTS: In hypertensive patients, the classifier improved risk prediction for transition in albuminuria stage on top of the reference model (C-index from 0.69 to 0.78; P diabetes, the classifier improved risk prediction for transition from micro to macroalbuminuria (C-index from 0...

  1. Comparative analysis of boar seminal plasma proteome from different freezability ejaculates and identification of Fibronectin 1 as sperm freezability marker.

    Science.gov (United States)

    Vilagran, I; Yeste, M; Sancho, S; Castillo, J; Oliva, R; Bonet, S

    2015-03-01

    Variation in boar sperm freezability (i.e. capacity to withstand cryopreservation) between ejaculates is a limitation largely reported in the literature. Prediction of sperm freezability and classification of boar ejaculates into good (GFEs) and poor freezability ejaculates (PFEs) before cryopreservation takes place may increase the use of frozen-thawed spermatozoa. While markers of boar sperm freezability have been found from sperm cell extracts, little attention has been paid to seminal plasma. On this basis, the present study compared the fresh seminal plasma proteome of 9 GFEs and 9 PFEs through two-dimensional difference gel electrophoresis (2D-DIGE) and liquid chromatography mass spectrometry (LC-MS/MS). The ejaculates were previously classified as GFE or PFE upon their sperm viability and progressive motility assessments at 30 and 240 min post thawing. From a total of 51 spots, four were found to significantly (p sperm quality parameters. Results confirmed that FN1 is a reliable marker of boar sperm freezability, because GFEs presented significantly (p boar sperm freezability marker. We can thus conclude that levels of FN1 in fresh seminal plasma from boar semen may be used as a sperm freezability marker, thereby facilitating the use of frozen-thawed boar spermatozoa.

  2. Proteome Changes in the Plasma of Myelodysplastic Syndrome Patients with Refractory Anemia with Excess Blasts Subtype 2

    Directory of Open Access Journals (Sweden)

    Pavel Majek

    2014-01-01

    Full Text Available The goal of this study was to explore the plasma proteome of myelodysplastic syndrome (MDS patients with refractory anemia with excess blasts subtype 2 (RAEB-2 in comparison to healthy controls. 20 plasma samples were separated with 2D electrophoresis and statistically processed with Progenesis SameSpots software. 47 significantly differing (P<0.05 spots were observed, and 27 different proteins were identified by nano-LC-MS/MS. Mass spectrometry-based relative label-free quantification showed a 2-fold increase of the leucine-rich alpha-2-glycoprotein (LRAG peptide levels in the RAEB-2 group. Changes in the fragments of the inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4 protein were observed. Western blot analysis showed no differences in albumin and ITIH4 levels, while increased expression was observed for LRAG in the RAEB-2 group. Quantification using ELISA showed decreased plasma level of alpha-2-HS glycoprotein in the RAEB-2 group. In conclusion, this is the first time that alpha-2-HS glycoprotein and LRAG were proposed as new biomarkers of RAEB-2 and advanced MDS, respectively. Alpha-2-HS glycoprotein, a protein involved in the bone marrow development and previously proposed as a MDS biomarker candidate, was significantly decreased in RAEB-2. Increased expression and changes in modification(s were observed for LRAG, a protein involved in granulocytic and neutrophil differentiation, and angiogenesis.

  3. Label-Free Proteome Analysis of Plasma from Patients with Breast Cancer: Stage-Specific Protein Expression

    Science.gov (United States)

    Lobo, Marina Duarte Pinto; Moreno, Frederico Bruno Mendes Batista; Souza, Gustavo Henrique Martins Ferreira; Verde, Sara Maria Moreira Lima; Moreira, Renato de Azevedo; Monteiro-Moreira, Ana Cristina de Oliveira

    2017-01-01

    Breast cancer is one of the most commonly diagnosed types of cancer among women. Breast cancer mortality rates remain high probably because its diagnosis is hampered by inaccurate detection methods. Since changes in protein expression as well as modifications in protein glycosylation have been frequently reported in cancer development, the aim of this work was to study the differential expression as well as modifications of glycosylation of proteins from plasma of women with breast cancer at different stages of disease (n = 30) compared to healthy women (n = 10). A proteomics approach was used that depleted albumin and IgG from plasma followed by glycoprotein enrichment using immobilized Moraceae lectin (frutalin)-affinity chromatography and data-independent label-free mass spectrometric analysis. Data are available via ProteomeXchange with identifier PXD003106. As result, 57,016 peptides and 4,175 proteins among all samples were identified. From this, 40 proteins present in unbound (PI—proteins that did not interact with lectin) and bound (PII—proteins that interacted with lectin) fractions were differentially expressed. High levels of apolipoprotein A-II were detected here that were elevated significantly in the early and advanced stages of the disease. Apolipoprotein C-III was detected in both fractions, and its level was increased slightly in the PI fraction of patients with early-stage breast cancer and expressed at higher levels in the PII fraction of patients with early and intermediate stages. Clusterin was present at higher levels in both fractions of patients with early and intermediate stages of breast cancer. Our findings reveal a correlation between alterations in protein glycosylation, lipid metabolism, and the progression of breast cancer. PMID:28210565

  4. Differential proteomic analysis of virus-enriched fractions obtained from plasma pools of patients with dengue fever or severe dengue.

    Science.gov (United States)

    Fragnoud, Romain; Flamand, Marie; Reynier, Frederic; Buchy, Philippe; Duong, Vasna; Pachot, Alexandre; Paranhos-Baccala, Glaucia; Bedin, Frederic

    2015-11-14

    Dengue is the most widespread mosquito-borne viral disease of public health concern. In some patients, endothelial cell and platelet dysfunction lead to life-threatening hemorrhagic dengue fever or dengue shock syndrome. Prognostication of disease severity is urgently required to improve patient management. The pathogenesis of severe dengue has not been fully elucidated, and the role of host proteins associated with viral particles has received little exploration. The proteomes of virion-enriched fractions purified from plasma pools of patients with dengue fever or severe dengue were compared. Virions were purified by ultracentrifugation combined with a water-insoluble polyelectrolyte-based technique. Following in-gel hydrolysis, peptides were analyzed by nano-liquid chromatography coupled to ion trap mass spectrometry and identified using data libraries. Both dengue fever and severe dengue viral-enriched fractions contained identifiable viral envelope proteins and host cellular proteins. Canonical pathway analysis revealed the identified host proteins are mainly involved in the coagulation cascade, complement pathway or acute phase response signaling pathway. Some host proteins were over- or under-represented in plasma from patients with severe dengue compared to patients with dengue fever. ELISAs were used to validate differential expression of a selection of identified host proteins in individual plasma samples of patients with dengue fever compared to patients with severe dengue. Among 22 host proteins tested, two could differentiate between dengue fever and severe dengue in two independent cohorts (olfactomedin-4: area under the curve (AUC), 0.958; and platelet factor-4: AUC, 0.836). A novel technique of virion-enrichment from plasma has allowed to identify two host proteins that have prognostic value for classifying patients with acute dengue who are more likely to develop a severe dengue. The impact of these host proteins on pathogenicity and disease outcome

  5. Proteomics Core

    Data.gov (United States)

    Federal Laboratory Consortium — Proteomics Core is the central resource for mass spectrometry based proteomics within the NHLBI. The Core staff help collaborators design proteomics experiments in a...

  6. Proteomics Core

    Data.gov (United States)

    Federal Laboratory Consortium — Proteomics Core is the central resource for mass spectrometry based proteomics within the NHLBI. The Core staff help collaborators design proteomics experiments in...

  7. Connecting genetic risk to disease end points through the human blood plasma proteome

    Science.gov (United States)

    Suhre, Karsten; Arnold, Matthias; Bhagwat, Aditya Mukund; Cotton, Richard J.; Engelke, Rudolf; Raffler, Johannes; Sarwath, Hina; Thareja, Gaurav; Wahl, Annika; DeLisle, Robert Kirk; Gold, Larry; Pezer, Marija; Lauc, Gordan; El-Din Selim, Mohammed A.; Mook-Kanamori, Dennis O.; Al-Dous, Eman K.; Mohamoud, Yasmin A.; Malek, Joel; Strauch, Konstantin; Grallert, Harald; Peters, Annette; Kastenmüller, Gabi; Gieger, Christian; Graumann, Johannes

    2017-01-01

    Genome-wide association studies (GWAS) with intermediate phenotypes, like changes in metabolite and protein levels, provide functional evidence to map disease associations and translate them into clinical applications. However, although hundreds of genetic variants have been associated with complex disorders, the underlying molecular pathways often remain elusive. Associations with intermediate traits are key in establishing functional links between GWAS-identified risk-variants and disease end points. Here we describe a GWAS using a highly multiplexed aptamer-based affinity proteomics platform. We quantify 539 associations between protein levels and gene variants (pQTLs) in a German cohort and replicate over half of them in an Arab and Asian cohort. Fifty-five of the replicated pQTLs are located in trans. Our associations overlap with 57 genetic risk loci for 42 unique disease end points. We integrate this information into a genome-proteome network and provide an interactive web-tool for interrogations. Our results provide a basis for novel approaches to pharmaceutical and diagnostic applications. PMID:28240269

  8. Comparative proteomics evaluation of plasma exosome isolation techniques and assessment of the stability of exosomes in normal human blood plasma.

    Science.gov (United States)

    Kalra, Hina; Adda, Christopher G; Liem, Michael; Ang, Ching-Seng; Mechler, Adam; Simpson, Richard J; Hulett, Mark D; Mathivanan, Suresh

    2013-11-01

    Exosomes are nanovesicles released by a variety of cells and are detected in body fluids including blood. Recent studies have highlighted the critical application of exosomes as personalized targeted drug delivery vehicles and as reservoirs of disease biomarkers. While these research applications have created significant interest and can be translated into practice, the stability of exosomes needs to be assessed and exosome isolation protocols from blood plasma need to be optimized. To optimize methods to isolate exosomes from blood plasma, we performed a comparative evaluation of three exosome isolation techniques (differential centrifugation coupled with ultracentrifugation, epithelial cell adhesion molecule immunoaffinity pull-down, and OptiPrep(TM) density gradient separation) using normal human plasma. Based on MS, Western blotting and microscopy results, we found that the OptiPrep(TM) density gradient method was superior in isolating pure exosomal populations, devoid of highly abundant plasma proteins. In addition, we assessed the stability of exosomes in plasma over 90 days under various storage conditions. Western blotting analysis using the exosomal marker, TSG101, revealed that exosomes are stable for 90 days. Interestingly, in the context of cellular uptake, the isolated exosomes were able to fuse with target cells revealing that they were indeed biologically active.

  9. Plasma membrane proteome analysis of the early effect of alcohol on liver:implications for alcoholic liver disease

    Institute of Scientific and Technical Information of China (English)

    Lijun Zhang; Ye Zheng; Pengyuan Yang; Zhenghong Yuan; Xiaofang Jia; Yanling Feng; Xia Peng; Zhiyong Zhang; Wenjiang Zhou; Zhanqing Zhang; Fang Ma; Xiaohui Liu

    2011-01-01

    In humans, the over-consumption of alcohol can lead to serious liver disease. To examine the early effects of alcohol on liver disease, rats were given sufficient ethanol to develop liver cirrhosis. Rats before the onset of fibrosis were studied in this work. Plasma membranes (PM) of liver were extracted by twice sucrose density gradient centrifugation. The proteome profiles of PM from ethanol-treated rats and the controls were analyzed using two-dimensional gel electrophoresis (2-DE) and isobaric tag for relative and absolute quantitation (iTRAQ) tech-nology. Ethanol treatment altered the amount of 15 differ-ent liver proteins: 10 of them were detected by 2-DE and 5 by iTRAQ. Keratin 8 was detected by both methods.Gene ontology analysis of these differentially detected proteins indicated that most of them were involved in important cell functions such as binding activity (includ-ing ion, DNA, ATP binding, etc.), cell structure, or enzyme activity. Among these, annexin A2, keratin 8, and keratin 18 were further verified using western blot analy-sis and annexin A2 was verified by immunohistochemis-try. Our results suggested that alcohol has the potential to affect cell structure, adhesion and enzyme activity by altering expression levels of several relevant proteins in the PM. To the best of our knowledge, this is the first time to study the effect of alcohol on the liver PM pro-teome and it might be helpful for understanding the poss-ible mechanisms of alcohol-induced liver disease.

  10. Randomized trial of glucosamine and chondroitin supplementation on inflammation and oxidative stress biomarkers and plasma proteomics profiles in healthy humans.

    Directory of Open Access Journals (Sweden)

    Sandi L Navarro

    Full Text Available Glucosamine and chondroitin are popular non-vitamin dietary supplements used for osteoarthritis. Long-term use is associated with lower incidence of colorectal and lung cancers and with lower mortality; however, the mechanism underlying these observations is unknown. In vitro and animal studies show that glucosamine and chondroitin inhibit NF-kB, a central mediator of inflammation, but no definitive trials have been done in healthy humans.We conducted a randomized, double-blind, placebo-controlled, cross-over study to assess the effects of glucosamine hydrochloride (1500 mg/d plus chondroitin sulfate (1200 mg/d for 28 days compared to placebo in 18 (9 men, 9 women healthy, overweight (body mass index 25.0-32.5 kg/m2 adults, aged 20-55 y. We examined 4 serum inflammatory biomarkers: C-reactive protein (CRP, interleukin 6, and soluble tumor necrosis factor receptors I and II; a urinary inflammation biomarker: prostaglandin E2-metabolite; and a urinary oxidative stress biomarker: F2-isoprostane. Plasma proteomics on an antibody array was performed to explore other pathways modulated by glucosamine and chondroitin.Serum CRP concentrations were 23% lower after glucosamine and chondroitin compared to placebo (P = 0.048. There were no significant differences in other biomarkers. In the proteomics analyses, several pathways were significantly different between the interventions after Bonferroni correction, the most significant being a reduction in the "cytokine activity" pathway (P = 2.6 x 10-16, after glucosamine and chondroitin compared to placebo.Glucosamine and chondroitin supplementation may lower systemic inflammation and alter other pathways in healthy, overweight individuals. This study adds evidence for potential mechanisms supporting epidemiologic findings that glucosamine and chondroitin are associated with reduced risk of lung and colorectal cancer.ClinicalTrials.gov NCT01682694.

  11. Identification of plasma biomarker candidates in glioblastoma using an antibody-array-based proteomic approach

    Directory of Open Access Journals (Sweden)

    Zupancic Klemen

    2014-09-01

    Full Text Available Background. Glioblastoma multiforme (GBM is a brain tumour with a very high patient mortality rate, with a median survival of 47 weeks. This might be improved by the identification of novel diagnostic, prognostic and predictive therapy-response biomarkers, preferentially through the monitoring of the patient blood. The aim of this study was to define the impact of GBM in terms of alterations of the plasma protein levels in these patients. Materials and methods. We used a commercially available antibody array that includes 656 antibodies to analyse blood plasma samples from 17 healthy volunteers in comparison with 17 blood plasma samples from patients with GBM.

  12. Proteomic biomarker discovery in 1000 human plasma samples with mass spectrometry

    DEFF Research Database (Denmark)

    Cominetti, Ornella; Núñez Galindo, Antonio; Corthésy, John

    2016-01-01

    the quality of the MS data and provided descriptive statistics. The data set was interrogated for proteins with most stable expression levels in that set of plasma samples. We evaluated standard clinical variables that typically impact forthcoming results and assessed body mass index-associated and gender......-specific proteins at two time points. We demonstrate that analyzing a large number of human plasma samples for biomarker discovery with MS using isobaric tagging is feasible, providing robust and consistent biological results....

  13. Identification of plasma biomarker candidates in glioblastoma using an antibody-array-based proteomic approach.

    Science.gov (United States)

    Zupancic, Klemen; Blejec, Andrej; Herman, Ana; Veber, Matija; Verbovsek, Urska; Korsic, Marjan; Knezevic, Miomir; Rozman, Primoz; Turnsek, Tamara Lah; Gruden, Kristina; Motaln, Helena

    2014-09-01

    Glioblastoma multiforme (GBM) is a brain tumour with a very high patient mortality rate, with a median survival of 47 weeks. This might be improved by the identification of novel diagnostic, prognostic and predictive therapy-response biomarkers, preferentially through the monitoring of the patient blood. The aim of this study was to define the impact of GBM in terms of alterations of the plasma protein levels in these patients. We used a commercially available antibody array that includes 656 antibodies to analyse blood plasma samples from 17 healthy volunteers in comparison with 17 blood plasma samples from patients with GBM. We identified 11 plasma proteins that are statistically most strongly associated with the presence of GBM. These proteins belong to three functional signalling pathways: T-cell signalling and immune responses; cell adhesion and migration; and cell-cycle control and apoptosis. Thus, we can consider this identified set of proteins as potential diagnostic biomarker candidates for GBM. In addition, a set of 16 plasma proteins were significantly associated with the overall survival of these patients with GBM. Guanine nucleotide binding protein alpha (GNAO1) was associated with both GBM presence and survival of patients with GBM. Antibody array analysis represents a useful tool for the screening of plasma samples for potential cancer biomarker candidates in small-scale exploratory experiments; however, clinical validation of these candidates requires their further evaluation in a larger study on an independent cohort of patients.

  14. Oocyte proteomics: localisation of mouse zona pellucida protein 3 to the plasma membrane of ovulated mouse eggs.

    Science.gov (United States)

    Coonrod, S A; Calvert, M E; Reddi, P P; Kasper, E N; Digilio, L C; Herr, J C

    2004-01-01

    In order to gain a deeper understanding of the molecular underpinnings of sperm-egg interaction and early development, we have used two-dimensional (2D) electrophoresis, avidin blotting and tandem mass spectrometry to identify, clone and characterise abundant molecules from the mouse egg proteome. Two-dimensional avidin blots of biotinylated zona-free eggs revealed an abundant approximately 75-kDa surface-labelled heterogeneous protein possessing a staining pattern similar to that of the zona pellucida glycoprotein, mouse ZP3 (mZP3). In light of this observation, we investigated whether mZP3 specifically localises to the plasma membrane of mature eggs. Zona pellucidae of immature mouse oocytes and mature eggs were removed using acid Tyrode's solution, chymotrypsin or mechanical shearing. Indirect immunofluorescence using the mZP3 monoclonal antibody (mAb) IE-10 demonstrated strong continuous staining over the entire surface of immature oocytes and weak microvillar staining on ovulated eggs, regardless of the method of zona removal. Interestingly, in mature eggs, increased fluorescence intensity was observed following artificial activation and fertilisation, whereas little to no fluorescence was observed in degenerated eggs. The surface localisation of ZP3 on mature eggs was supported by the finding that the IE-10 mAb immunoprecipitated an approximate 75-kDa protein from lysates of biotinylated zona-free eggs. To further investigate the specificity of the localisation of mZP3 to the oolemma, indirect immunofluorescence was performed using the IE-10 mAb on both CV-1 and CHO cells transfected with full-length recombinant mZP3 (re-mZP3). Plasma membrane targeting of the expressed re-mZP3 protein was observed in both cell lines. The membrane association of re-mZP3 was confirmed by the finding that biotinylated re-mZP3 (approximately 75 kDa) is immunoprecipitated from the hydrophobic phase of Triton X-114 extracts of transfected cells following phase partitioning

  15. Proteomics tools reveal startlingly high amounts of oxytocin in plasma and serum

    Science.gov (United States)

    Brandtzaeg, Ole Kristian; Johnsen, Elin; Roberg-Larsen, Hanne; Seip, Knut Fredrik; Maclean, Evan L.; Gesquiere, Laurence R.; Leknes, Siri; Lundanes, Elsa; Wilson, Steven Ray

    2016-08-01

    The neuropeptide oxytocin (OT) is associated with a plethora of social behaviors, and is a key topic at the intersection of psychology and biology. However, tools for measuring OT are still not fully developed. We describe a robust nano liquid chromatography-mass spectrometry (nanoLC-MS) platform for measuring the total amount of OT in human plasma/serum. OT binds strongly to plasma proteins, but a reduction/alkylation (R/A) procedure breaks this bond, enabling ample detection of total OT. The method (R/A + robust nanoLC-MS) was used to determine total OT plasma/serum levels to startlingly high concentrations (high pg/mL-ng/mL). Similar results were obtained when combining R/A and ELISA. Compared to measuring free OT, measuring total OT can have advantages in e.g. biomarker studies.

  16. Proteomic Characterization of Zinc-Binding Proteins of Canine Seminal Plasma.

    Science.gov (United States)

    Mogielnicka-Brzozowska, M; Kowalska, N; Fraser, L; Kordan, W

    2015-12-01

    The zinc-binding proteins (ZnBPs) of the seminal plasma are implicated in different processes related to sperm-egg fusion. The aim of this study was to characterize the ZnBPs of canine seminal plasma using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry. The ZnBPs were isolated from the ejaculates of five dogs by affinity chromatography and subjected to 2D-PAGE analysis. The acquired spots, detected across the gels, were analysed by mass spectrometry. Using 2D-PAGE analysis, it was shown that canine seminal plasma comprised about 46-57 zinc-binding polypeptides, with molecular mass ranging from 9.3 to 138.7 kDa and pI at pH 5.2-10.0. It was found that zinc-binding polypeptides of low molecular masses (9.3-19.0 kDa and pI at pH 6.1-10.0) were predominant in the seminal plasma, and seven polypeptides, with molecular masses ranging from 11.7 to 15.4 kDa and pI at pH 6.8-8.7, were characterized by high optical density values. In addition, analysis with mass spectrometry (LC-MS-MS/MS) revealed that the identified seven polypeptides are canine prostate-specific esterase (CPSE), which is the main proteolytic enzyme of the seminal plasma. The findings of this study indicate an important regulatory role of seminal plasma zinc ions in the functional activity of CPSE, which is of great significance for maintaining the normal function of canine prostate and the spermatozoa functions.

  17. Proteomic Profiling of Plasma and Serum in Elderly Patients With Delirium

    NARCIS (Netherlands)

    B.C. van Munster; M.J. van Breemen; P.D. Moerland; D. Speijer; S.E. de Rooij; C.J. Pfrommer; M. Levi; M.W. Hollmann; J.M. Aerts; A.H. Zwinderman; J.C. Korevaar

    2009-01-01

    The aim of this study was to compare plasma and serum protein profiles in elderly acute hip fracture patients with and without delirium. The spectra from surface-enhanced laser desorption ionization (SELDI) using time-of-flight (TOF) mass spectrometry of 16 patients without and 16 patients with deli

  18. High-throughput proteomic characterization of plasma rich in growth factors (PRGF-Endoret)-derived fibrin clot interactome.

    Science.gov (United States)

    Anitua, Eduardo; Prado, Roberto; Azkargorta, Mikel; Rodriguez-Suárez, Eva; Iloro, Ibon; Casado-Vela, Juan; Elortza, Felix; Orive, Gorka

    2015-11-01

    Plasma rich in growth factors (PRGF®-Endoret®) is an autologous technology that contains a set of proteins specifically addressed to wound healing and tissue regeneration. The scaffold formed by using this technology is a clot mainly composed of fibrin protein, forming a three-dimensional (3D) macroscopic network. This biomaterial is easily obtained by biotechnological means from blood and can be used in a range of situations to help wound healing and tissue regeneration. Although the main constituent of this clot is the fibrin scaffold, little is known about other proteins interacting in this clot that may act as adjuvants in the healing process. The aim of this study was to characterize the proteins enclosed by PRGF-Endoret scaffold, using a double-proteomic approach that combines 1D-SDS-PAGE approach followed by LC-MS/MS, and 2-DE followed by MALDI-TOF/TOF. The results presented here provide a description of the catalogue of key proteins in close contact with the fibrin scaffold. The obtained lists of proteins were grouped into families and networks according to gene ontology. Taken together, an enrichment of both proteins and protein families specifically involved in tissue regeneration and wound healing has been found.

  19. Plasma proteomics shows an elevation of the anti-inflammatory protein APOA-IV in chronic equine laminitis

    Directory of Open Access Journals (Sweden)

    Steelman Samantha M

    2012-09-01

    Full Text Available Abstract Background Equine laminitis is a devastating disease that causes severe pain in afflicted horses and places a major economic burden on the horse industry. In acute laminitis, the disintegration of the dermal-epidermal junction can cause the third phalanx to detach from the hoof wall, leaving the horse unable to bear weight on the affected limbs. Horses that survive the acute phase transition into a chronic form of laminitis, which is often termed “founder”. Some evidence suggests that chronic laminar inflammation might be associated with alterations in the endocrine and immune systems. We investigated this broad hypothesis by using DIGE to assess global differences in the plasma proteome between horses with chronic laminitis and controls. Results We identified 16 differentially expressed proteins; the majority of these were involved in the interrelated coagulation, clotting, and kininogen cascades. Clinical testing of functional coagulation parameters in foundered horses revealed a slight delay in prothrombin (PT clotting time, although most other indices were within normal ranges. Upregulation of the intestinal apolipoprotein APOA-IV in horses with chronic laminitis was confirmed by western blot. Conclusions Our results support the hypothesis that localized laminar inflammation may be linked to systemic alterations in immune regulation, particularly in the gastrointestinal system. Gastrointestinal inflammation has been implicated in the development of acute laminitis but has not previously been associated with chronic laminitis.

  20. Comparative Proteomic Analysis of Plasma from Clinical Healthy Cows and Mastitic Cows

    Institute of Scientific and Technical Information of China (English)

    YANG Yong-xin; ZHAO Xing-xu; ZHANG Yong

    2009-01-01

    The current research presents the protein changes in plasma from healthy dairy cows and clinical mastitic cows using two-dimensional gel electrophoresis (2-DE). After staining with silver nitrate and Coomassie Blue, differential expression proteins were detected by PDQuest 7.4 software, and then subjected to ion trap mass spectrometer equipped with a Surveyor HPLC System, differential spots of protein were identified. Three protein spots that originated from preparation gels were identified to be two proteins. Overall, haptoglobin precursor was up-regulated in cows infected with clinical mastitis and could be a mastitis-associated diagnostic marker, whereas SCGB 2A1 (secretoglobin, family 2A, member 1) was down-regulated protein. Plasma protein expression patterns were changed when cows were infected with mammary gland inflammation; it suggests that analysis of differential expression protein might be useful to clarify the mechanisms involved in the pathophysiology, and find new diagnostic markers of mastitis and potential protein targets for treatment.

  1. Statistical considerations of optimal study design for human plasma proteomics and biomarker discovery.

    Science.gov (United States)

    Zhou, Cong; Simpson, Kathryn L; Lancashire, Lee J; Walker, Michael J; Dawson, Martin J; Unwin, Richard D; Rembielak, Agata; Price, Patricia; West, Catharine; Dive, Caroline; Whetton, Anthony D

    2012-04-01

    A mass spectrometry-based plasma biomarker discovery workflow was developed to facilitate biomarker discovery. Plasma from either healthy volunteers or patients with pancreatic cancer was 8-plex iTRAQ labeled, fractionated by 2-dimensional reversed phase chromatography and subjected to MALDI ToF/ToF mass spectrometry. Data were processed using a q-value based statistical approach to maximize protein quantification and identification. Technical (between duplicate samples) and biological variance (between and within individuals) were calculated and power analysis was thereby enabled. An a priori power analysis was carried out using samples from healthy volunteers to define sample sizes required for robust biomarker identification. The result was subsequently validated with a post hoc power analysis using a real clinical setting involving pancreatic cancer patients. This demonstrated that six samples per group (e.g., pre- vs post-treatment) may provide sufficient statistical power for most proteins with changes>2 fold. A reference standard allowed direct comparison of protein expression changes between multiple experiments. Analysis of patient plasma prior to treatment identified 29 proteins with significant changes within individual patient. Changes in Peroxiredoxin II levels were confirmed by Western blot. This q-value based statistical approach in combination with reference standard samples can be applied with confidence in the design and execution of clinical studies for predictive, prognostic, and/or pharmacodynamic biomarker discovery. The power analysis provides information required prior to study initiation.

  2. Plasma proteome profiles associated with diet-induced metabolic syndrome and the early onset of metabolic syndrome in a pig model.

    Science.gov (United States)

    te Pas, Marinus F W; Koopmans, Sietse-Jan; Kruijt, Leo; Calus, Mario P L; Smits, Mari A

    2013-01-01

    Obesity and related diabetes are important health threatening multifactorial metabolic diseases and it has been suggested that 25% of all diabetic patients are unaware of their patho-physiological condition. Biomarkers for monitoring and control are available, but early stage predictive biomarkers enabling prevention of these diseases are still lacking. We used the pig as a model to study metabolic disease because humans and pigs share a multitude of metabolic similarities. Diabetes was chemically induced and control and diabetic pigs were either fed a high unsaturated fat (Mediterranean) diet or a high saturated fat/cholesterol/sugar (cafeteria) diet. Physiological parameters related to fat metabolism and diabetes were measured. Diabetic pigs' plasma proteome profiles differed more between the two diets than control pigs plasma proteome profiles. The expression levels of several proteins correlated well with (patho)physiological parameters related to the fat metabolism (cholesterol, VLDL, LDL, NEFA) and diabetes (Glucose) and to the diet fed to the animals. Studying only the control pigs as a model for metabolic syndrome when fed the two diets showed correlations to the same parameters but now more focused on insulin, glucose and abdominal fat depot parameters. We conclude that proteomic profiles can be used as a biomarker to identify pigs with developing metabolic syndrome (prediabetes) and diabetes when fed a cafeteria diet. It could be developed into a potential biomarkers for the early recognition of metabolic diseases.

  3. Plasma proteome profiles associated with diet-induced metabolic syndrome and the early onset of metabolic syndrome in a pig model.

    Directory of Open Access Journals (Sweden)

    Marinus F W te Pas

    Full Text Available Obesity and related diabetes are important health threatening multifactorial metabolic diseases and it has been suggested that 25% of all diabetic patients are unaware of their patho-physiological condition. Biomarkers for monitoring and control are available, but early stage predictive biomarkers enabling prevention of these diseases are still lacking. We used the pig as a model to study metabolic disease because humans and pigs share a multitude of metabolic similarities. Diabetes was chemically induced and control and diabetic pigs were either fed a high unsaturated fat (Mediterranean diet or a high saturated fat/cholesterol/sugar (cafeteria diet. Physiological parameters related to fat metabolism and diabetes were measured. Diabetic pigs' plasma proteome profiles differed more between the two diets than control pigs plasma proteome profiles. The expression levels of several proteins correlated well with (pathophysiological parameters related to the fat metabolism (cholesterol, VLDL, LDL, NEFA and diabetes (Glucose and to the diet fed to the animals. Studying only the control pigs as a model for metabolic syndrome when fed the two diets showed correlations to the same parameters but now more focused on insulin, glucose and abdominal fat depot parameters. We conclude that proteomic profiles can be used as a biomarker to identify pigs with developing metabolic syndrome (prediabetes and diabetes when fed a cafeteria diet. It could be developed into a potential biomarkers for the early recognition of metabolic diseases.

  4. Screening of plasma biomarkers in patients with unstable angina pectoris with proteomics analysis

    Directory of Open Access Journals (Sweden)

    Shui-wang HU

    2017-08-01

    Full Text Available Objective To analyze and compare the differentially expressed plasma proteins between patients with stable angina pectoris (SAP and unstable angina pectoris (UAP, and search for the biomarkers that maybe used for early diagnosis of UAP. Methods Sixty plasma samples were collected respectively from normal controls group (N group, SAP group and UAP group during Jun. 2014 to Apr. 2015 from the Third Affiliated Hospital of Southern Medical University. Ten samples (100μl of each group were selected randomly to pool into 3 groups severally. After removing high-abundance proteins from plasma, two- dimensional difference gel electrophoresis (DIGE was used to isolate the total proteins, and then the protein spots with more than 2-fold changes between UAP and SAP were picked up after the differential software analysis. Afterward, the varied proteins were identified by matrix assisted laser desorption ionization-time of flight/time of flight (MALDI-TOF/TOF mass spectrometry (MS. Finally, 40 plasma samples were collected respectively from N, SAP and UAP group, and the UAP specific differential proteins were selected to be verified by ELISA. Results A total of 10 varied protein spots with more than 2-fold changes in UAP and SAP were found including 9 up-regulated proteins and 1 down-regulated one. MS identification indicated that the up-regulated proteins included fibrinogen gamma chain (FGG, complement C4-B (C4B, immunoglobulin (Ig kappa chain C region (IGKC and hemoglobin subunit alpha (HBA1, whereas the down-regulated one was haptoglobin (HP. After comparing the varied proteins with that in N group, 2 specifically UAP-related proteins, IGKC and HP, were detected totally. IGKC was selected to validate by ELISA, and the corresponding results showed that IGKC was increased specifically in UAP plasma (P<0.05 when compared with N and SAP group, which was consistent with DIGE. Conclusion IGKC and HP have been detected as specifically related proteins to UAP

  5. Identifying cytotoxic T cell epitopes from genomic and proteomic information: "The human MHC project."

    DEFF Research Database (Denmark)

    Lauemøller, S L; Kesmir, C; Corbet, S L

    2000-01-01

    processing, as these become available. The ability to translate the accumulating primary sequence databases in terms of immune recognition should enable scientists and clinicians to analyze any protein of interest for the presence of potentially immunogenic epitopes. The computational tools to scan entire...... discrimination, even at the peptide level. It is not surprising that peptides are key targets of the immune system. It follows that proteomes can be translated into immunogens once it is known how the immune system generates and handles peptides. Recent advances have identified many of the basic principles...

  6. Isobaric Tags for Relative and Absolute Quantification-based Comparative Proteomics Reveals the Features of Plasma Membrane-Associated Proteomes of Pollen Grains and Pollen Tubes from Lilium davidii

    Institute of Scientific and Technical Information of China (English)

    Bing Han; Sixue Chen; Shaojun Dai; Ning Yang; Tai Wang

    2010-01-01

    Mature pollen grains (PGs) from most plant species are metabolically quiescent. However, once pollinated onto stigma, they quickly hydrate and germinate. APG can give rise to a vegetative cell-derived polarized pollen tube (PT), which represents a specialized polar cell. The polarized PT grows by the tip and requires interaction of different signaling molecules localized in the apical plasma membrane and active membrane trafficking. The mechanisms underlying the interaction and membrane trafficking are not well understood. In this work, we purified PG and PT plasma-membrane vesicles from Lilium davidii Duch. using the aqueous two-phase partition technique, then enriched plasma membrane proteins by using Brij58 and KCl to remove loosely bound contaminants. We identified 223 integral and membrane-associated proteins in the plasma membrane of PGs and PTs by using isobaric tags for relative and absolute quantification (iTRAQ) and 2-D high-performance liquid chromatography-tandem mass spectrometry. More than 68% of the proteins have putative transmembrane domains and/or lipid-modified motifs. Proteins involved in signal transduction, membrane trafficking and transport are predominant in the plasma-membrane proteome. We revealed most components of the clathrin-dependent endocytosis pathway. Statistical analysis revealed 14 proteins differentially expressed in the two development stages: in PTs, six upregulated and eight downregulated are mainly involved in signaling, transport and membrane trafficking. These results provide novel insights into polarized PT growth.

  7. Proteomic identification of protein targets for 15-deoxy-Δ(12,14-prostaglandin J2 in neuronal plasma membrane.

    Directory of Open Access Journals (Sweden)

    Yasuhiro Yamamoto

    Full Text Available 15-deoxy-Δ(12,14-prostaglandin J(2 (15d-PGJ(2 is one of factors contributed to the neurotoxicity of amyloid β (Aβ, a causative protein of Alzheimer's disease. Type 2 receptor for prostaglandin D(2 (DP2 and peroxysome-proliferator activated receptorγ (PPARγ are identified as the membrane receptor and the nuclear receptor for 15d-PGJ(2, respectively. Previously, we reported that the cytotoxicity of 15d-PGJ(2 was independent of DP2 and PPARγ, and suggested that 15d-PGJ(2 induced apoptosis through the novel specific binding sites of 15d-PGJ(2 different from DP2 and PPARγ. To relate the cytotoxicity of 15d-PGJ(2 to amyloidoses, we performed binding assay [(3H]15d-PGJ(2 and specified targets for 15d-PGJ(2 associated with cytotoxicity. In the various cell lines, there was a close correlation between the susceptibilities to 15d-PGJ(2 and fibrillar Aβ. Specific binding sites of [(3H]15d-PGJ(2 were detected in rat cortical neurons and human bronchial smooth muscle cells. When the binding assay was performed in subcellular fractions of neurons, the specific binding sites of [(3H]15d-PGJ(2 were detected in plasma membrane, nuclear and cytosol, but not in microsome. A proteomic approach was used to identify protein targets for 15d-PGJ(2 in the plasma membrane. By using biotinylated 15d-PGJ(2, eleven proteins were identified as biotin-positive spots and classified into three different functional proteins: glycolytic enzymes (Enolase2, pyruvate kinase M1 (PKM1 and glyceraldehyde 3-phosphate dehydrogenase (GAPDH, molecular chaperones (heat shock protein 8 and T-complex protein 1 subunit α, cytoskeletal proteins (Actin β, F-actin-capping protein, Tubulin β and Internexin α. GAPDH, PKM1 and Tubulin β are Aβ-interacting proteins. Thus, the present study suggested that 15d-PGJ(2 plays an important role in amyloidoses not only in the central nervous system but also in the peripheral tissues.

  8. Proteomics Technologies and Challenges

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Proteomics is the study of proteins and their interactions in a cell. With the completion of the Human Genome Project, the emphasis is shifting to the protein compliment of the human organism. Because proteome reflects more accurately on the dynamic state of a cell, tissue, or organism, much is expected from proteomics to yield better disease markers for diagnosis and therapy monitoring. The advent of proteomics technologies for global detection and quantitation of proteins creates new opportunities and challenges for those seeking to gain greater understanding of diseases. High-throughput proteomics technologies combining with advanced bioinformatics are extensively used to identify molecular signatures of diseases based on protein pathways and signaling cascades. Mass spectrometry plays a vital role in proteomics and has become an indispensable tool for molecular and cellular biology. While the potential is great, many challenges and issues remain to be solved, such as mining low abundant proteins and integration of proteomics with genomics and metabolomics data. Nevertheless, proteomics is the foundation for constructing and extracting useful knowledge to biomedical research. In this review, a snapshot of contemporary issues in proteomics technologies is discussed.

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

    Science.gov (United States)

    Mounicou, Sandra; Szpunar, Joanna; Lobinski, Ryszard

    2010-01-01

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

  10. Differential profiling of breast cancer plasma proteome by isotope-coded affinity tagging method reveals biotinidase as a breast cancer biomarker

    Directory of Open Access Journals (Sweden)

    Yu Myeong-Hee

    2010-03-01

    Full Text Available Abstract Background Breast cancer is one of the leading causes of women's death worldwide. It is important to discover a reliable biomarker for the detection of breast cancer. Plasma is the most ideal source for cancer biomarker discovery since many cells cross-communicate through the secretion of soluble proteins into blood. Methods Plasma proteomes obtained from 6 breast cancer patients and 6 normal healthy women were analyzed by using the isotope-coded affinity tag (ICAT labeling approach and tandem mass spectrometry. All the plasma samples used were depleted of highly abundant 6 plasma proteins by immune-affinity column chromatography before ICAT labeling. Several proteins showing differential abundance level were selected based on literature searches and their specificity to the commercially available antibodies, and then verified by immunoblot assays. Results A total of 155 proteins were identified and quantified by ICAT method. Among them, 33 proteins showed abundance changes by more than 1.5-fold between the plasmas of breast cancer patients and healthy women. We chose 5 proteins for the follow-up confirmation in the individual plasma samples using immunoblot assay. Four proteins, α1-acid glycoprotein 2, monocyte differentiation antigen CD14, biotinidase (BTD, and glutathione peroxidase 3, showed similar abundance ratio to ICAT result. Using a blind set of plasmas obtained from 21 breast cancer patients and 21 normal healthy controls, we confirmed that BTD was significantly down-regulated in breast cancer plasma (Wilcoxon rank-sum test, p = 0.002. BTD levels were lowered in all cancer grades (I-IV except cancer grade zero. The area under the receiver operating characteristic curve of BTD was 0.78. Estrogen receptor status (p = 0.940 and progesterone receptor status (p = 0.440 were not associated with the plasma BTD levels. Conclusions Our study suggests that BTD is a potential serological biomarker for the detection of breast cancer.

  11. Assessment of violations of the proteomic profile in blood plasma in children being under inhalation exposure to fine dust containing vanadium

    Directory of Open Access Journals (Sweden)

    N.V. Zaitseva

    2016-03-01

    Full Text Available The results of research and evaluation of the protein profile in blood plasma in children, that have been exposed to long-term effect of fine dust containing vanadium in the zone of influence of metallurgical production sources, are demonstrated. It was established that under conditions of poor air quality in the residential area due to vanadium pentoxide dust content at the level up to 1.2 mean daily MAC (34 RfC chr , by the suspended solids – up to 0.6 mean daily MAC (1.2 RfC chr , there is vanadium concentration in blood of the exposed 4–7 aged children, that exceeds up to 6 times the reference level. The technology of the proteomic analysis showed that children with high content of vanadium in blood have changes in proteomic profile in blood plasma in the type of increase of the relative volume of acid glycoprotein alpha-1; reduction of clusterin, apolipoprotein A-IV, alpha-2-HS-glycoprotein, that are associated with vanadium concentration in blood. In the absence of timely primary and secondary prevention and the preservation of vanadium sustained exposure the revealed cell-molecular abnormalities allow us to predict further development of functional disturbances on tissue and organ levels as the early development of osteoporosis and osteoarticular pathology, atherosclerotic vascular changes, autoimmune allergic processes on the background of disorders of immune regulation, oncology diseases.

  12. A high confidence, manually validated human blood plasma protein reference set

    DEFF Research Database (Denmark)

    Schenk, Susann; Schoenhals, Gary J; de Souza, Gustavo

    2008-01-01

    sources, including the HUPO PPP dataset. CONCLUSION: Superior instrumentation combined with rigorous validation criteria gave rise to a set of 697 plasma proteins in which we have very high confidence, demonstrated by an exceptionally low false peptide identification rate of 0.29%.......BACKGROUND: The immense diagnostic potential of human plasma has prompted great interest and effort in cataloging its contents, exemplified by the Human Proteome Organization (HUPO) Plasma Proteome Project (PPP) pilot project. Due to challenges in obtaining a reliable blood plasma protein list...

  13. Peroxiredoxin 2: a potential biomarker for early diagnosis of Hepatitis B Virus related liver fibrosis identified by proteomic analysis of the plasma

    Directory of Open Access Journals (Sweden)

    Wang Haijian

    2010-10-01

    Full Text Available Abstract Background Liver fibrosis is a middle stage in the course of chronic Hepatitis B virus (HBV infection, which will develop into cirrhosis and eventually hepatocellular carcinoma (HCC if not treated at the early stage. Considering the limitations and patients' reluctance to undergo liver biopsy, a reliable, noninvasive diagnostic system to predict and assess treatment and prognosis of liver fibrosis is needed. The aim of this study was to identify biomarkers for early diagnosis of HBV related liver fibrosis. Method Plasma samples from 7 healthy volunteers and 27 HBV infected patients with different stages of fibrosis were selected for 2-DIGE proteomic screening. One-way ANOVA analysis was used to assess differences in protein expression among all groups. The alteration was further confirmed by western blotting. Plasma levels of 25 serological variables in 42 healthy volunteers and 68 patients were measured to establish a decision tree for the detection of various stages fibrosis. Result The up-regulated proteins along with fibrosis progress included fibrinogen, collagen, macroglobulin, hemopexin, antitrypsin, prealbumin and thioredoxin peroxidase. The down-regulated proteins included haptoglobin, serotransferrin, CD5 antigen like protein, clusterin, apolipoprotein and leucine-rich alpha-2-glycoprotein. For the discrimination of milder stage fibrosis, the area under curve for Prx II was the highest. Four variables (PT, Pre, HA and Prx II were selected from the 25 variables to construct the decision tree. In a training group, the correct prediction percentage for normal control, milder fibrosis, significant fibrosis and early cirrhosis was 100%, 88.9%, 95.2% and 100%, respectively, with an overall correct percent of 95.9%. Conclusion This study showed that 2-D DIGE-based proteomic analysis of the plasma was helpful in screening for new plasma biomarkers for liver disease. The significant up-expression of Prx II could be used in the early

  14. Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity

    Directory of Open Access Journals (Sweden)

    Mulder Nicola

    2010-02-01

    Full Text Available Abstract We consider the problem of biological complexity via a projection of protein-coding genes of complex organisms onto the functional space of the proteome. The latter can be defined as a set of all functions committed by proteins of an organism. Alternative splicing (AS allows an organism to generate diverse mature RNA transcripts from a single mRNA strand and thus it could be one of the key mechanisms of increasing of functional complexity of the organism's proteome and a driving force of biological evolution. Thus, the projection of transcription units (TU and alternative splice-variant (SV forms onto proteome functional space could generate new types of relational networks (e.g. SV-protein function networks, SFN and lead to discoveries of novel evolutionarily conservative functional modules. Such types of networks might provide new reliable characteristics of organism complexity and a better understanding of the evolutionary integration and plasticity of interconnection of genome-transcriptome-proteome functions. Results We use the InterPro and UniProt databases to attribute descriptive features (keywords to protein sequences. UniProt database includes a controlled and curated vocabulary of specific descriptors or keywords. The keywords have been assigned to a protein sequence via conserved domains or via similarity with annotated sequences. Then we consider the unique combinations of keywords as the protein functional labels (FL, which characterize the biological functions of the given protein and construct the contingency tables and graphs providing the projections of transcription units (TU and alternative splice-variants (SV onto all FL of the proteome of a given organism. We constructed SFNs for organisms with different evolutionary history and levels of complexity, and performed detailed statistical parameterization of the networks. Conclusions The application of the algorithm to organisms with different evolutionary history and

  15. Hydrogen Recovery by ECR Plasma Pyrolysis of Methane Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Development of a microgravity and hypogravity compatible Electron Cyclotron Resonance (ECR) Plasma Methane Pyrolysis Reactor is proposed to recover hydrogen which is...

  16. Plasma metabolomics and proteomics profiling after a postprandial challenge reveal subtle diet effects on human metabolic status

    NARCIS (Netherlands)

    Pellis, L.; Erk, M.J. van; Ommen, B. van; Bakker, G.C.M.; Hendriks, H.F.J.; Cnubben, N.H.P.; Kleemann, R.; Someren, E.P. van; Bobeldijk, I.; Rubingh, C.M.; Wopereis, S.

    2012-01-01

    We introduce the metabolomics and proteomics based Postprandial Challenge Test (PCT) to quantify the postprandial response of multiple metabolic processes in humans in a standardized manner. The PCT comprised consumption of a standardized 500 ml dairy shake containing respectively 59, 30 and 12 ener

  17. Non-Thermal Sanitation By Atmospheric Pressure Plasma Project

    Data.gov (United States)

    National Aeronautics and Space Administration — ORBITEC's Non-Thermal Sanitation by Atmospheric Pressure Plasma technology sanitizes fresh fruits and vegetables without the use of consumable chemicals and without...

  18. Hydrogen Recovery by ECR Plasma Pyrolysis of Methane Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Development of a microgravity and hypogravity compatible microwave plasma methane pyrolysis reactor is proposed to recover hydrogen which is lost as methane in the...

  19. Plasma Treatment to Enhance Fuel Cell Water Management Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The objective of this proposal is to further define the potential for plasma treatment technology, developed by the NASA Glenn Research Center (GRC) to modify and...

  20. Reactive Atom Plasma Processing of Slumped Glass Wedges Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Reactive Atom Plasma (RAPTM) process will be evaluated as a rapid and practical method for fabricating precision wedges in glass sheets. The glass sheets are to...

  1. Plasma Extraction of Oxygen from Martian Atmosphere Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Plasma techniques are proposed for the extraction of oxygen from the abundant carbon dioxide contained in the Martian atmosphere (96 % CO2). In this process, CO2 is...

  2. Plasma Catalytic Extraction of Oxygen from the Martian Atmosphere Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Plasma catalytic techniques are proposed for the extraction of oxygen from the abundant carbon dioxide contained in the Martian atmosphere (95% CO2).. The Phase I...

  3. Non-Thermal Sanitation By Atmospheric Pressure Plasma Project

    Data.gov (United States)

    National Aeronautics and Space Administration — ORBITEC proposes to develop a non-thermal technology based on atmospheric-pressure (AP) cold plasma to sanitize foods, food packaging materials, and other hardware...

  4. Use of Differential Scanning Calorimetry and Immunoaffinity Chromatography to Identify Disease Induced Changes in Human Blood Plasma Proteome.

    Science.gov (United States)

    Brudar, Sandi; Černigoj, Urh; Podgornik, Helena; Kržan, Mojca; Prislan, Iztok

    2017-09-01

    Differential scanning calorimetry provides unique signatures of blood plasma samples. Plasma samples from diseased individuals yield specific thermograms, which differ from each other and from plasma samples of healthy individuals. Thermograms from individuals suffering from chronic lymphocytic leukemia, multiple myeloma and acute myeloid leukemia were measured with DSC. To obtain additional information about thermal behaviour of plasma proteins immunoaffinity chromatography was introduced. An immunoextraction of HSA using a chromatographic column with immobilized anti-HSA was carried out in order to enrich less abundant plasma proteins, which could provide a further insight into disease development. Efficiency of HSA depletion and protein composition of fractionated plasma was validated by SDS-PAGE.

  5. Identification of a Novel Function of Adipocyte Plasma Membrane-Associated Protein (APMAP) in Gestational Diabetes Mellitus by Proteomic Analysis of Omental Adipose Tissue.

    Science.gov (United States)

    Ma, Yuhang; Gao, Jing; Yin, Jiajing; Gu, Liping; Liu, Xing; Chen, Su; Huang, Qianfang; Lu, Huifang; Yang, Yuemin; Zhou, Hu; Wang, Yufan; Peng, Yongde

    2016-02-05

    Gestational diabetes mellitus (GDM) is considered as an early stage of type 2 diabetes mellitus. In this study, we compared demographic and clinical data between six GDM subjects and six normal glucose tolerance (NGT; healthy controls) subjects and found that homeostasis model of assessment for insulin resistance index (HOMA-IR) increased in GDM. Many previous studies demonstrated that omental adipose tissue dysfunction could induce insulin resistance. Thus, to investigate the cause of insulin resistance in GDM, we used label-free proteomics to identify differentially expressed proteins in omental adipose tissues from GDM and NGT subjects (data are available via ProteomeXchange with identifier PXD003095). A total of 3528 proteins were identified, including 66 significantly changed proteins. Adipocyte plasma membrane-associated protein (APMAP, a.k.a. C20orf3), one of the differentially expressed proteins, was down-regulated in GDM omental adipose tissues. Furthermore, mature 3T3-L1 adipocytes were used to simulate omental adipocytes. The inhibition of APMAP expression by RNAi impaired insulin signaling and activated NFκB signaling in these adipocytes. Our study revealed that the down-regulation of APMAP in omental adipose tissue may play an important role in insulin resistance in the pathophysiology of GDM.

  6. Identification of phosphorylated MYL12B as a potential plasma biomarker for septic acute kidney injury using a quantitative proteomic approach

    Science.gov (United States)

    Wu, Fan; Dong, Xiu-Juan; Li, Yan-Yan; Zhao, Yan; Xu, Qiu-Lin; Su, Lei

    2015-01-01

    Acute kidney injury (AKI) is a common and increasingly encountered complication in hospitalized patients with critical illness in intensive care units (ICU). According to the etiology, Sepsis-induced AKI (SAKI) is a leading contributor to AKI and significantly has very poor prognosis, which might be related to the late detection when the elevation of BUN and serum creatinine (SCr) is used. Many genes are up-regulated in the damaged kidney with the corresponding protein products appearing in plasma and urine. Some of these are candidate biomarkers for more timely diagnosis of SAKI. Therefore, extensive research efforts over this past decade have been directed at the discovery and validation of novel SAKI biomarkers to detect injury prior to changes in kidney function, a number of serum and urinary proteins, including NGAL, KIM-1, cystatin-C, IL-18, and L-FABP, have been identified for predicting SAKI before a rise in BUN and serum creatinine in several experimental and clinical trainings. Unfortunately, an ideal biomarker of SAKI with highly sensitivity and specificity has not been identified yet. Recent progresses in quantitative proteomics have offered opportunities to discover biomarkers for SAKI. In the present study, kidney tissue samples from SAKI mice were analyzed by two-dimensional differential gel electrophoresis (2D-DIGE), and 4 up-regulated proteins, which were actin (ACTB), myosin regulatory light chain 12B (MYL12B), myosin regulatory light polypeptide 9 (MYL9), and myosin regulatory light chain 12A (MYL12A) were identified by matrix assisted laser desorption ionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF MS). Among all the varied proteins, MYL12B was validated by western blot. Interestingly, there was no change between the SAKI and control kidney tissues, however, phosphorylated MYL12B was detected to be consistent with the proteomics data. Furthermore, phosphorylated MYL12B was found similarly to be increased in SAKI plasma

  7. SciDAC - Center for Plasma Edge Simulation - Project Summary

    Energy Technology Data Exchange (ETDEWEB)

    Parker, Scott [Univ. of Colorado, Boulder, CO (United States)

    2014-11-03

    Final Technical Report: Center for Plasma Edge Simulation (CPES) Principal Investigator: Scott Parker, University of Colorado, Boulder Description/Abstract First-principle simulations of edge pedestal micro-turbulence are performed with the global gyrokinetic turbulence code GEM for both low and high confinement tokamak plasmas. The high confinement plasmas show a larger growth rate, but nonlinearly a lower particle and heat flux. Numerical profiles are obtained from the XGC0 neoclassical code. XGC0/GEM code coupling is implemented under the EFFIS (“End-to-end Framework for Fusion Integrated Simulation”) framework. Investigations are underway to clearly identify the micro-instabilities in the edge pedestal using global and flux-tube gyrokinetic simulation with realistic experimental high confinement profiles. We use both experimental profiles and those obtained using the EFFIS XGC0/GEM coupled code framework. We find there are three types of instabilities at the edge: a low-n, high frequency electron mode, a high-n, low frequency ion mode, and possibly an ion mode like kinetic ballooning mode (KBM). Investigations are under way for the effects of the radial electric field. Finally, we have been investigating how plasmas dominated by ion-temperature gradient (ITG) driven turbulence, how cold Deuterium and Tritium ions near the edge will naturally pinch radially inward towards the core. We call this mechanism “natural fueling.” It is due to the quasi-neutral heat flux dominated nature of the turbulence and still applies when trapped and passing kinetic electron effects are included. To understand this mechanism, examine the situation where the electrons are adiabatic, and there is an ion heat flux. In such a case, lower energy particles move inward and higher energy particles move outward. If a trace amount of cold particles are added, they will move inward.

  8. Plasma physics code contribution to the Mont-Blanc project

    OpenAIRE

    Sáez, Xavier; Soba, Alejandro; Mantsinen, Mervi

    2015-01-01

    This work develops strategies for adapting a particle-in-cell code to heterogeneous computer architectures and, in particular, to an ARM-based prototype of the Mont-Blanc project using OmpSs programming model and the OpenMP and OpenCL languages.

  9. iTRAQ-based proteomic analysis of plasma reveals abnormalities in lipid metabolism proteins in chronic kidney disease-related atherosclerosis

    Science.gov (United States)

    Luczak, Magdalena; Formanowicz, Dorota; Marczak, Łukasz; Suszyńska-Zajczyk, Joanna; Pawliczak, Elżbieta; Wanic-Kossowska, Maria; Stobiecki, Maciej

    2016-09-01

    Patients with chronic kidney disease (CKD) have a considerably higher risk of death due to cardiovascular causes. Using an iTRAQ MS/MS approach, we investigated the alterations in plasma protein accumulation in patients with CKD and classical cardiovascular disease (CVD) without CKD. The proteomic analysis led to the identification of 130 differentially expressed proteins among CVD and CKD patients and healthy volunteers. Bioinformatics analysis revealed that 29 differentially expressed proteins were involved in lipid metabolism and atherosclerosis, 20 of which were apolipoproteins and constituents of high-density lipoprotein (HDL) and low-density lipoprotein (LDL). Although dyslipidemia is common in CKD patients, we found that significant changes in apolipoproteins were not strictly associated with changes in plasma lipid levels. A lack of correlation between apoB and LDL concentration and an inverse relationship of some proteins with the HDL level were revealed. An increased level of apolipoprotein AIV, adiponectin, or apolipoprotein C, despite their anti-atherogenic properties, was not associated with a decrease in cardiovascular event risk in CKD patients. The presence of the distinctive pattern of apolipoproteins demonstrated in this study may suggest that lipid abnormalities in CKD are characterized by more qualitative abnormalities and may be related to HDL function rather than HDL deficiency.

  10. Proteomic Analysis of Plasma-Purified VLDL, LDL, and HDL Fractions from Atherosclerotic Patients Undergoing Carotid Endarterectomy: Identification of Serum Amyloid A as a Potential Marker

    Directory of Open Access Journals (Sweden)

    Antonio J. Lepedda

    2013-01-01

    Full Text Available Apolipoproteins are very heterogeneous protein family, implicated in plasma lipoprotein structural stabilization, lipid metabolism, inflammation, or immunity. Obtaining detailed information on apolipoprotein composition and structure may contribute to elucidating lipoprotein roles in atherogenesis and to developing new therapeutic strategies for the treatment of lipoprotein-associated disorders. This study aimed at developing a comprehensive method for characterizing the apolipoprotein component of plasma VLDL, LDL, and HDL fractions from patients undergoing carotid endarterectomy, by means of two-dimensional electrophoresis (2-DE coupled with Mass Spectrometry analysis, useful for identifying potential markers of plaque presence and vulnerability. The adopted method allowed obtaining reproducible 2-DE maps of exchangeable apolipoproteins from VLDL, LDL, and HDL. Twenty-three protein isoforms were identified by peptide mass fingerprinting analysis. Differential proteomic analysis allowed for identifying increased levels of acute-phase serum amyloid A protein (AP SAA in all lipoprotein fractions, especially in LDL from atherosclerotic patients. Results have been confirmed by western blotting analysis on each lipoprotein fraction using apo AI levels for data normalization. The higher levels of AP SAA found in patients suggest a role of LDL as AP SAA carrier into the subendothelial space of artery wall, where AP SAA accumulates and may exert noxious effects.

  11. Study on the plasma proteomic profiling by using surface enhanced laser desorption ionization time of flight mass spectrometry for setting up a diagnostic model of endometriosis

    Institute of Scientific and Technical Information of China (English)

    Liu Hai-yuan; Liu Chun-yan; Leng Jin-hua; Liu Zhu-feng; Sun Da-wei; Zhu Lan; Lang Jing-he; Zheng Yan-hua; Zhang Jian-zhong

    2007-01-01

    Objective: To determine the plasma proteomic profiling by using surface enhanced laser desorption ionization time of flight mass spectrometry (SELDI-TOF-MS) combined with bioinformatics for screening biomarkers of endometriosis and primarily setting up a diagnostic model of endometriosis.Method.Thirty-six patients with endometriosis diagnosed laparoscopically and thirty-five healthy controls were included in the study.Their serum were analyzed by SELDI and protein chip to generate protein profiling spectra.Student t test was used to compare the peak intensifies of the protein profiling results from the different groups.Biomarker Pattern Software was used to analyze the data between two groups and set up a diagnostic model for endometriosis.Protein profiling spectra from sixteen endometriosis patients and fifteen healthy controls were used double-blindedly to test the efficiency of the diagnostic model and generate the sensitivity and specificity of the model.Result: Fourteen abnormally expressed protein peaks were detected in the plasma of patients with endometriosis (P<0.01).The endometriosis diagnostic model was composed of three protein peaks.It correctly identified 33 of 36 patients with endometriosis and 29 of 35 controls in the training test.In the masked set 14 of 16 patients with endometriosis and 12 of 15 normal controls were correctly identified with sensitivity of 87.5% and specificity of 8o%.Conclusion: Patients with endometriosis have a unique cluster of proteins in plasma detected by SELDI.SELDI provides a new approach for screening novel biomarkers of endometriosis.Its utility in clinical practice need further study.

  12. Protein expression profiles of human lymph and plasma mapped by 2D-DIGE and 1D SDS–PAGE coupled with nanoLC–ESI–MS/MS bottom-up proteomics

    OpenAIRE

    Clement, Cristina C.; Aphkhazava, David; Nieves, Edward; Callaway, Myrasol; Olszewski, Waldemar; Rotzschke, Olaf; Santambrogio, Laura

    2012-01-01

    In this study a proteomic approach was used to define the protein content of matched samples of afferent prenodal lymph and plasma derived from healthy volunteers. The analysis was performed using two analytical methodologies coupled with nanoliquid chromatography-tandem mass spectrometry: one-dimensional gel electrophoresis (1DEF nanoLC Orbitrap–ESI–MS/MS), and two-dimensional fluorescence difference-in-gel electrophoresis (2D-DIGE nanoLC–ESI–MS/MS). The 253 significantly identified proteins...

  13. The PLX- α project: demonstrating the viability of spherically imploding plasma liners as an MIF driver

    Science.gov (United States)

    Hsu, S. C.; Witherspoon, F. D.; Cassibry, J. T.; Gilmore, M.; Samulyak, R.; Stoltz, P.; the PLX-α Team

    2015-11-01

    Under ARPA-E's ALPHA program, the Plasma Liner Experiment-ALPHA (PLX- α) project aims to demonstrate the viability and scalability of spherically imploding plasma liners as a standoff, high-implosion-velocity magneto-inertial-fusion (MIF) driver that is potentially compatible with both low- and high- β targets. The project has three major objectives: (a) advancing existing contoured-gap coaxial-gun technology to achieve higher operational reliability/precision and better control/reproducibility of plasma-jet properties and profiles; (2) conducting ~ π / 2 -solid-angle plasma-liner experiments with 9 guns to demonstrate (along with extrapolations from modeling) that the jet-merging process leads to Mach-number degradation and liner uniformity that are acceptable for MIF; and (3) conducting 4 π experiments with up to 60 guns to demonstrate the formation of an imploding spherical plasma liner for the first time, and to provide empirical ram-pressure and uniformity scaling data for benchmarking our codes and informing us whether the scalings justify further development beyond ALPHA. This talk will provide an overview of the PLX- α project as well as key research results to date. Supported by ARPA-E's ALPHA program; original PLX construction supported by DOE Fusion Energy Sciences.

  14. Nonlocal transient transport and thermal barriers in Rijnhuizen Tokamak project plasmas

    NARCIS (Netherlands)

    Mantica, P.; Galli, P.; Gorini, G.; Hogeweij, G. M. D.; de Kloe, J.; Cardozo, N. J. L.; R. T. P. Team,

    1999-01-01

    In the Rijnhuizen Tokamak Project plasmas, a transient rise of the core electron temperature is observed when hydrogen pellets are injected tangentially to induce fast cooling of the peripheral region. High-resolution Thomson scattering measurements show that the T-e rise is associated with large te

  15. The effects of eating marine- or vegetable-fed farmed trout on the human plasma proteome profiles of healthy men

    DEFF Research Database (Denmark)

    Rentsch, Maria Louise; Lametsch, René; Bügel, Susanne;

    2015-01-01

    of intervention, and after the removal of the twelve most abundant proteins, plasma proteins were separated by two-dimensional gel electrophoresis. Protein spots 4·3 visualised by silver staining were matched by two-dimensional imaging software. Within-subject changes in spots were compared...... between the treatment groups. Differentially affected spots were identified by matrix-assisted laser desorption ionisation-time of flight/time of flight MS and the human Swiss-Prot database. We found 23/681 abundant plasma protein spots, which were up- or down-regulated by the dietary treatment (P...spots differed from those in subjects given the chicken meal, but only three of these were common, and only one spot differed between the two trout groups. In both groups, the affected plasma proteins were involved in biological...

  16. Proteomic analysis of seminal plasma from asthenozoospermia patients reveals proteins that affect oxidative stress responses and semen quality.

    Science.gov (United States)

    Wang, Jun; Wang, Jian; Zhang, Hua-Rong; Shi, Hui-Juan; Ma, Duan; Zhao, Hong-Xin; Lin, Biaoyang; Li, Run-Sheng

    2009-07-01

    Asthenozoospermia (AS) is a common cause of human male infertility. In one study, more than 80% of the samples from infertile men had reduced sperm motility. Seminal plasma is a mixture of secretions from the testis, epididymis and several male accessory glands, including the prostate, seminal vesicles and Cowper's gland. Studies have shown that seminal plasma contains proteins that are important for sperm motility. To further explore the pathophysiological character of AS, we separated the seminal plasma proteins from AS patients and healthy donors using sodium dodecyl sulfate polyacrylamide gel electrophoresis and in-gel digestion, and then subjected the proteins to liquid chromatography-mass spectrometry (LC-MS/MS) analysis. A total of 741 proteins were identified in the seminal plasma, with a false discovery rate of 3.3%. Using spectral counting, we found that 45 proteins were threefold upregulated and 56 proteins were threefold downregulated in the AS group when compared with the control. Most of these proteins originated from the epididymis and prostate. This study identified a rich source of biomarker candidates for male infertility and indicates that functional abnormalities of the epididymis and prostate can contribute to AS. We identified DJ-1-a protein that has been shown elsewhere to be involved in the control of oxidative stress (OS)-as a downregulated protein in AS seminal plasma. The levels of DJ-1 in AS seminal plasma were about half of those in the control samples. In addition, the levels of reactive oxygen species were 3.3-fold higher in the AS samples than in the controls. Taken together, these data suggest that downregulation of DJ-1 is involved in OS in semen, and therefore affects the quality of the semen.

  17. CAPER 3.0: A Scalable Cloud-Based System for Data-Intensive Analysis of Chromosome-Centric Human Proteome Project Data Sets.

    Science.gov (United States)

    Yang, Shuai; Zhang, Xinlei; Diao, Lihong; Guo, Feifei; Wang, Dan; Liu, Zhongyang; Li, Honglei; Zheng, Junjie; Pan, Jingshan; Nice, Edouard C; Li, Dong; He, Fuchu

    2015-09-01

    The Chromosome-centric Human Proteome Project (C-HPP) aims to catalog genome-encoded proteins using a chromosome-by-chromosome strategy. As the C-HPP proceeds, the increasing requirement for data-intensive analysis of the MS/MS data poses a challenge to the proteomic community, especially small laboratories lacking computational infrastructure. To address this challenge, we have updated the previous CAPER browser into a higher version, CAPER 3.0, which is a scalable cloud-based system for data-intensive analysis of C-HPP data sets. CAPER 3.0 uses cloud computing technology to facilitate MS/MS-based peptide identification. In particular, it can use both public and private cloud, facilitating the analysis of C-HPP data sets. CAPER 3.0 provides a graphical user interface (GUI) to help users transfer data, configure jobs, track progress, and visualize the results comprehensively. These features enable users without programming expertise to easily conduct data-intensive analysis using CAPER 3.0. Here, we illustrate the usage of CAPER 3.0 with four specific mass spectral data-intensive problems: detecting novel peptides, identifying single amino acid variants (SAVs) derived from known missense mutations, identifying sample-specific SAVs, and identifying exon-skipping events. CAPER 3.0 is available at http://prodigy.bprc.ac.cn/caper3.

  18. Simulations of Plasma-Liner Formation and Implosion for the PLX- α Project

    Science.gov (United States)

    Samulyak, Roman; Cassibry, Jason; Schillo, Kevin; Shih, Wen; Yates, Kevin; Hsu, Scott; PLX-Alpha Collaboration

    2016-10-01

    Detailed numerical studies of the propagation and merger of high-Mach-number plasma jets and the formation and implosion of plasma liners have been performed using the FronTier and SPH codes enhanced with radiation, physical diffusion, and plasma-EOS models. These simulations support the Plasma Liner Experiment-ALPHA (PLX- α) project (see S. Hsu's talk in this session). Simulations predict properties of plasma liners, in particular 4 π-averaged liner density, ram pressure, and Mach number, the degree of non-uniformity, strength of primary and secondary shock waves, and scalings with the number of plasma jets, initial jet parameters, and other input data. In addition to direct analysis of liner states, simulations also provide synthetic data for direct comparison to experimental data from a multi-chord interferometer and survey and high-resolution spectrometers. Code verification and comparisons as well as predictions for the first series of PLX- α experiments with 6 and 7 jets will be presented. Verified against experimental data, both codes will be used for predictive simulations of plasma liners for PLX- α experiments and potential scaled-up future experiments. Supported by the ARPA-E ALPHA program.

  19. Numerical linear algebra on emerging architectures: The PLASMA and MAGMA projects

    Science.gov (United States)

    Agullo, Emmanuel; Demmel, Jim; Dongarra, Jack; Hadri, Bilel; Kurzak, Jakub; Langou, Julien; Ltaief, Hatem; Luszczek, Piotr; Tomov, Stanimire

    2009-07-01

    The emergence and continuing use of multi-core architectures and graphics processing units require changes in the existing software and sometimes even a redesign of the established algorithms in order to take advantage of now prevailing parallelism. Parallel Linear Algebra for Scalable Multi-core Architectures (PLASMA) and Matrix Algebra on GPU and Multics Architectures (MAGMA) are two projects that aims to achieve high performance and portability across a wide range of multi-core architectures and hybrid systems respectively. We present in this document a comparative study of PLASMA's performance against established linear algebra packages and some preliminary results of MAGMA on hybrid multi-core and GPU systems.

  20. Seminal plasma proteomic and gene expression and ngf location and receptors (TRK1 and NGFR) in rabbit genital system

    OpenAIRE

    JÃsy Maria Arruda de Alencar

    2015-01-01

    The aim this study were (i) to map and identify proteins in seminal plasma of New Zealand white rabbits strain, using the techniques of two-dimensional electrophoresis coupled to mass spectrometry and to estimate associations between these proteins with sperm parameters and (ii) characterize expression of the nerve growth factor polypeptide beta ( -NGF) and its cognate neurotrophic receptor tyrosine kinase type 1 (NTRK1), and nerve growth factor receptor (NGFR) at gonads and sex glands in adu...

  1. Proteomics of MUC1-containing lipid rafts from plasma membranes and exosomes of human breast carcinoma cells MCF-7.

    Science.gov (United States)

    Staubach, Simon; Razawi, Hanieh; Hanisch, Franz-Georg

    2009-05-01

    Apically expressed human MUC1 is known to become endocytosed and either to re-enter the secretory pathway for recycling to the plasma membrane or to be exported by the cells via the formation of multi-vesicular bodies and the release of exosomes. By using recombinant fusion-tagged MUC1 as a bait protein we followed an anti-myc affinity-based approach for isolating subpopulations of lipid rafts from the plasma membranes and exosomes of MCF-7 breast cancer cells. MUC1(+) lipid rafts were not only found to contain genuine raft proteins (flotillin-1, prohibitin, G protein, annexin A2), but also raft-associated proteins linking these to the cytoskeleton (ezrin/villin-2, profilin II, HSP27, gamma-actin, beta-actin) or proteins in complexes with raft proteins, including the bait protein (HSP60, HSP70). Major overlaps were revealed for the subproteomes of plasma membranous and exosomal lipid raft preparations, indicating that MUC1 is sorted into subpopulations of rafts for its trafficking via flotillin-dependent pathways and export via exosomes.

  2. At a glance: Proteomics in China

    Institute of Scientific and Technical Information of China (English)

    HE FuChu

    2011-01-01

    Proteomics is a new science that focuses on the comprehensive analysis of proteins in intact organisms or in molecule machineries,organelles,cells,tissues,or organs.It has become an important area of interests in life sciences and has propelled the rapid development of cutting-edge biotechnology in the 21st century.In response to this,the Human Proteome Organization (HUPO) was launched in 2001.The mission of HUPO is to advocate and promote proteomics worldwide and to initiate the Human Proteome Project (HPP) to decode the human genome and to establish the proteomic basis of human physiology and pathology.Eleven projects including the Human Liver Proteome Project (HLPP) led by China are under way.Governments,multinational companies,particularly pharmaceutical and analytical instrument companies,as well as the genomic company Celera Genomics,have invested heavily,hoping to seize the huge potential of proteomics.=He Fuchu,PhD,is a Member of the Chinese Academy of Sciences,a Member of the Academy of Sciences for the Developing World,and is currently the Director of the State Key Laboratory of Proteomics.He is the President of the Beijing Proteome Research Center and a Professor at the Beijing Institute of Radiation Medicine.He Fuchu is a council member of the Human Proteome Organization (HUPO),co-chair (inaugural chair) of the HUPO Human Liver Proteome Project (HLPP),the vice-president of AOHUPO,and the president of CNHUPO.He received his B.S.degree in genetics from Fudan University,Shanghai,in 1982 and earned his M.S.degree in biochemistry and his PhD in cell biology from the Beijing Institute of Radiation Medicine.His major fields of research are proteomics,genomics,bioinformatics and systems biology,with a special interest in liver physiology and pathology.He is a senior editor of Proteomics and Proteomics-Clinical Application and is an editorial board member of Molecular & Cellular Proteomics and the Journal of Proteome Research and an executive editor of the

  3. Diagnostics and results from coaxial plasma gun development for the PLX- α project

    Science.gov (United States)

    Case, A.; Brockington, S.; Cruz, E.; Witherspoon, F. D.

    2016-10-01

    We present results from the diagnostics used during development of the contoured gap coaxial plasma guns for the PLX- α project at LANL. Plasma-jet diagnostics include fast photodiodes for velocimetry, a ballistic pendulum for total plasmoid momentum, and interferometry for line integrated density. Deflectometry will be used for line integrated perpendicular density gradients. Time-resolved high-resolution spectroscopy using a novel detector and time-integrated survey spectroscopy are used for measurements of velocity and temperature, as well as impurities. We will also use a Faraday cup for density, fast imaging for plume geometry, and time-integrated imaging for overall light emission. Experimental results are compared to the desired target parameters for the plasma jets (up to n 2 ×1016cm-3 , v 50km / s , mass 5gm , radius = 4cm , and length 10cm). This work supported by the ARPA-E ALPHA Program.

  4. First results from the plasma composition spectrometer PROMICS-3 in the Interball project

    OpenAIRE

    Sandahl, I.; S. Barabash; Borg, H.; Budnik, E. Yu.; Dubinin, E. M.; Eklund, U.; Johansson, H.; H. Koskinen; K. Lundin; Lundin, R.; Moström, A.; Pellinen, R.; Pissarenko, N. F.; Pulkkinen, T.; Toivanen, P.

    1997-01-01

    International audience; PROMICS-3 is a plasma experiment flown in the Russian project Interball. It performs three-dimensional (3D) measurements of ions in the energy range 4 eV?70 keV with mass separation and of electrons in the energy range 12 eV?35 keV. The Interball project consists of two main satellites, the Tail Probe and the Auroral Probe, each with one subsatellite. The Interball Tail Probe was launched on 3 August 1995, into a 65° inclination orbit with apogee at about 30 RE. Both m...

  5. Scientific study in solar and plasma physics relative to rocket and balloon projects

    Science.gov (United States)

    Wu, S. T.

    1993-01-01

    The goals of this research are to provide scientific and technical capabilities in the areas of solar and plasma physics contained in research programs and instrumentation development relative to current rocket and balloon projects; to develop flight instrumentation design, flight hardware, and flight program objectives and participate in peer reviews as appropriate; and to participate in solar-terrestrial physics modeling studies and analysis of flight data and provide theoretical investigations as required by these studies.

  6. Molecular biology tools: proteomics techniques in biomarker discovery.

    Science.gov (United States)

    Lottspeich, Friedrich; Kellermann, Josef; Keidel, Eva-Maria

    2010-01-01

    Despite worldwide efforts biomarker discovery by plasma proteomics was not successful so far. Several reasons for this failure are obvious. Mainly, proteome diversity is remarkable between different individuals and is caused by genetic, environmental and life style parameters. To recognize disease related proteins that could serve as potential biomarkers is only feasible by investigating a non realizable large number of patients. Furthermore, plasma proteomics comprises enormous technical hurdles for quantitative analysis. High reproducibility of blood sampling in clinical routine is hard to achieve. Quantitative proteome analysis has to struggle with the complexity of millions of protein species comprising typical plasma proteins, cellular leakage proteins and antibodies and concentration differences of more than 1011 between high and low abundant proteins. Therefore, no successful quantitative and comprehensive plasma proteome analysis is reported so far. A novel proteomics strategy is proposed for biomarker discovery in plasma. Instead of comparing the plasma proteome of different individuals it is recommended to analyze the proteomes of different time points of a single individual during the development of a disease. This strategy is realized by the use of plasma of the Bavarian Red Cross Blood Bank, were three million samples are stored under standardized conditions. To achieve reliable data the isotope coded protein labelling proteomics technology was used.

  7. Multivariate protein signatures of pre-clinical Alzheimer's disease in the Alzheimer's disease neuroimaging initiative (ADNI plasma proteome dataset.

    Directory of Open Access Journals (Sweden)

    Daniel Johnstone

    Full Text Available BACKGROUND: Recent Alzheimer's disease (AD research has focused on finding biomarkers to identify disease at the pre-clinical stage of mild cognitive impairment (MCI, allowing treatment to be initiated before irreversible damage occurs. Many studies have examined brain imaging or cerebrospinal fluid but there is also growing interest in blood biomarkers. The Alzheimer's Disease Neuroimaging Initiative (ADNI has generated data on 190 plasma analytes in 566 individuals with MCI, AD or normal cognition. We conducted independent analyses of this dataset to identify plasma protein signatures predicting pre-clinical AD. METHODS AND FINDINGS: We focused on identifying signatures that discriminate cognitively normal controls (n = 54 from individuals with MCI who subsequently progress to AD (n = 163. Based on p value, apolipoprotein E (APOE showed the strongest difference between these groups (p = 2.3 × 10(-13. We applied a multivariate approach based on combinatorial optimization ((α,β-k Feature Set Selection, which retains information about individual participants and maintains the context of interrelationships between different analytes, to identify the optimal set of analytes (signature to discriminate these two groups. We identified 11-analyte signatures achieving values of sensitivity and specificity between 65% and 86% for both MCI and AD groups, depending on whether APOE was included and other factors. Classification accuracy was improved by considering "meta-features," representing the difference in relative abundance of two analytes, with an 8-meta-feature signature consistently achieving sensitivity and specificity both over 85%. Generating signatures based on longitudinal rather than cross-sectional data further improved classification accuracy, returning sensitivities and specificities of approximately 90%. CONCLUSIONS: Applying these novel analysis approaches to the powerful and well-characterized ADNI dataset has identified sets of

  8. Modeling of the merging, liner formation, implosion of hypervelocity plasma jets for the PLX- α project

    Science.gov (United States)

    Cassibry, Jason; Hsu, Scott; Schillo, Kevin; Samulyak, Roman; Stoltz, Peter; Beckwith, Kris

    2015-11-01

    A suite of numerical tools will support the conical and 4 π plasma-liner-formation experiments for the PLX- α project. A new Lagrangian particles (LP) method will provide detailed studies of the merging of plasma jets and plasma-liner formation/convergence. A 3d smooth particle hydrodynamic (SPH) code will simulate conical (up to 9 jets) and 4 π spherical (up to 60 jets) liner formation and implosion. Both LP and SPH will use the same tabular EOS generated by Propaceos, thermal conductivity, optically thin radiation and physical viscosity models. With LP and SPH,the major objectives are to study Mach-number degradation during jet merging, provide RMS amplitude and wave number of the liner nonuniformity at the leading edge, and develop scaling laws for ram pressure and liner uniformity as a function of jet parameters. USIM, a 3D multi-fluid plasma code, will be used to perform 1D and 2D simulations of plasma-jet-driven magneto-inertial fusion (PJMIF) to identify initial conditions in which the ``liner gain'' exceeds unity. A brief overview of the modeling program will be provided. Results from SPH modeling to support the PLX- α experimental design will also be presented, including preliminary ram-pressure scaling and non-uniformity characterization.

  9. Genomes to Proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  10. First results from the plasma composition spectrometer PROMICS-3 in the Interball project

    Directory of Open Access Journals (Sweden)

    I. Sandahl

    Full Text Available PROMICS-3 is a plasma experiment flown in the Russian project Interball. It performs three-dimensional (3D measurements of ions in the energy range 4 eV–70 keV with mass separation and of electrons in the energy range 12 eV–35 keV. The Interball project consists of two main satellites, the Tail Probe and the Auroral Probe, each with one subsatellite. The Interball Tail Probe was launched on 3 August 1995, into a 65° inclination orbit with apogee at about 30 RE. Both main satellites carry identical PROMICS-3 instruments and thus direct comparisons of the particle distributions will be possible once the Auroral Probe is launched. Furthermore, PROMICS-3-Tail is the first instrument measuring the 3D ion distribution function in the magnetospheric boundary layers at high latitudes. In this paper we describe the PROMICS-3 instrument and show initial results from the Tail probe, measurements of the magnetosheath, plasma sheet, and ring current plasmas.

  11. The Mochi project: a field theory approach to plasma dynamics and self-organization

    Science.gov (United States)

    You, Setthivoine; von der Linden, Jens; Lavine, Eric Sander; Card, Alexander; Carroll, Evan

    2016-10-01

    The Mochi project is designed to study the interaction between plasma flows and magnetic fields from the point-of-view of canonical flux tubes. The Mochi Labjet experiment is being commissioned after achieving first plasma. Analytical and numerical tools are being developed to visualize canonical flux tubes. One analytical tool described here is a field theory approach to plasma dynamics and self-organization. A redefinition of the Lagrangian of a multi-particle system in fields reformulates the single-particle, kinetic, and fluid equations governing fluid and plasma dynamics as a single set of generalized Maxwell's equations and Ohm's law for canonical force-fields. The Lagrangian includes new terms representing the coupling between the motion of particle distributions, between distributions and electromagnetic fields, with relativistic contributions. The formulation shows that the concepts of self-organization and canonical helicity transport are applicable across single-particle, kinetic, and fluid regimes, at classical and relativistic scales. The theory gives the basis for comparing canonical helicity change to energy change in general systems. This work is supported by by US DOE Grant DE-SC0010340.

  12. A project based on multi-configuration Dirac-Fock calculations for plasma spectroscopy

    Science.gov (United States)

    Comet, M.; Pain, J.-C.; Gilleron, F.; Piron, R.

    2017-09-01

    We present a project dedicated to hot plasma spectroscopy based on a Multi-Configuration Dirac-Fock (MCDF) code, initially developed by J. Bruneau. The code is briefly described and the use of the transition state method for plasma spectroscopy is detailed. Then an opacity code for local-thermodynamic-equilibrium plasmas using MCDF data, named OPAMCDF, is presented. Transition arrays for which the number of lines is too large to be handled in a Detailed Line Accounting (DLA) calculation can be modeled within the Partially Resolved Transition Array method or using the Unresolved Transition Arrays formalism in jj-coupling. An improvement of the original Partially Resolved Transition Array method is presented which gives a better agreement with DLA computations. Comparisons with some absorption and emission experimental spectra are shown. Finally, the capability of the MCDF code to compute atomic data required for collisional-radiative modeling of plasma at non local thermodynamic equilibrium is illustrated. In addition to photoexcitation, this code can be used to calculate photoionization, electron impact excitation and ionization cross-sections as well as autoionization rates in the Distorted-Wave or Close Coupling approximations. Comparisons with cross-sections and rates available in the literature are discussed.

  13. Numerical linear algebra on emerging architectures: The PLASMA and MAGMA projects

    Energy Technology Data Exchange (ETDEWEB)

    Agullo, Emmanuel; Demmel, Jim; Dongarra, Jack; Hadri, Bilel; Kurzak, Jakub; Langou, Julien; Ltaief, Hatem; Luszczek, Piotr [Department of Electrical Engineering and Computer Science, University of Tennessee (United States); Tomov, Stanimire, E-mail: eagullo@eecs.utk.ed, E-mail: dongarra@eecs.utk.ed, E-mail: hadri@eecs.utk.ed, E-mail: kurzak@eecs.utk.ed, E-mail: ltaief@eecs.utk.ed, E-mail: luszczek@eecs.utk.ed, E-mail: tomov@eecs.utk.ed, E-mail: demmel@cs.berkeley.ed, E-mail: julien.langou@ucdenver.ed

    2009-07-01

    The emergence and continuing use of multi-core architectures and graphics processing units require changes in the existing software and sometimes even a redesign of the established algorithms in order to take advantage of now prevailing parallelism. Parallel Linear Algebra for Scalable Multi-core Architectures (PLASMA) and Matrix Algebra on GPU and Multics Architectures (MAGMA) are two projects that aims to achieve high performance and portability across a wide range of multi-core architectures and hybrid systems respectively. We present in this document a comparative study of PLASMA's performance against established linear algebra packages and some preliminary results of MAGMA on hybrid multi-core and GPU systems.

  14. Beryllium plasma-facing components for the ITER-like wall project at JET

    Energy Technology Data Exchange (ETDEWEB)

    Rubel, M J; Sundelin, P [Alfven Laboratory, Royal Institute of Technology, Association Euratom-VR (Sweden); Bailescu, V [Nuclear Fuel Plant, Pitesti (Romania); Coad, J P; Matthews, G F; Pedrick, L; Riccardo, V; Villedieu, E [Culham Science Centre, Euratom-UKAEA Fusion Association, Abingdon (United Kingdom); Hirai, T; Linke, J [IEF-2, Forschungszentrum Juelich, Association Euratom-FZJ, Juelich (Germany); Likonen, J [VTT, Association Euratom-Tekes, 02044 VTT (Finland); Lungu, C P [NILPRP, Association Euratom-MEdC, Bucharest (Romania)], E-mail: rubel@kth.se

    2008-03-15

    ITER-Like Wall Project has been launched at the JET tokamak in order to study a tokamak operation with beryllium components on the main chamber wall and tungsten in the divertor. To perform this first comprehensive test of both materials in a thermonuclear fusion environment, a broad program has been undertaken to develop plasma-facing components and assess their performance under high power loads. The paper provides a concise report on scientific and technical issues in the development of a beryllium first wall at JET.

  15. Platelet proteomics.

    Science.gov (United States)

    Zufferey, Anne; Fontana, Pierre; Reny, Jean-Luc; Nolli, Severine; Sanchez, Jean-Charles

    2012-01-01

    Platelets are small cell fragments, produced by megakaryocytes, in the bone marrow. They play an important role in hemostasis and diverse thrombotic disorders. They are therefore primary targets of antithrombotic therapies. They are implicated in several pathophysiological pathways, such as inflammation or wound repair. In blood circulation, platelets are activated by several pathways including subendothelial matrix and thrombin, triggering the formation of the platelet plug. Studying their proteome is a powerful approach to understand their biology and function. However, particular attention must be paid to different experimental parameters, such as platelet quality and purity. Several technologies are involved during the platelet proteome processing, yielding information on protein identification, characterization, localization, and quantification. Recent technical improvements in proteomics combined with inter-disciplinary strategies, such as metabolomic, transcriptomics, and bioinformatics, will help to understand platelets biological mechanisms. Therefore, a comprehensive analysis of the platelet proteome under different environmental conditions may contribute to elucidate complex processes relevant to platelet function regarding bleeding disorders or platelet hyperreactivity and identify new targets for antiplatelet therapy.

  16. The Project PLASMONX for Plasma Acceleration Experiments and a Thomson X-Ray Source at SPARC

    CERN Document Server

    Serafini, Luca; Alessandria, Franco; Bacci, Alberto; Baldeschi, Walter; Barbini, Alessandro; Bellaveglia, Marco; Bertolucci, Sergio; Biagini, Maria; Boni, Roberto; Bonifacio, Rodolfo; Boscolo, Ilario; Boscolo, Manuela; Bottigli, Ubaldo; Broggi, Francesco; Castellano, Michele; Cecchetti, Carlo A; Cialdi, Simone; Clozza, Alberto; De Martinis, Carlo; Di Pirro, Giampiero; Drago, Alessandro; Esposito, Adolfo; Ferrario, Massimo; Ficcadenti, L; Filippetto, Daniele; Fusco, Valeria; Galimberti, Marco; Gallo, Alessandro; Gatti, Giancarlo; Ghigo, Andrea; Giove, Dario; Giulietti, Antonio; Giulietti, Danilo; Gizzi, Leonida A; Golosio, Bruno; Guiducci, Susanna; Incurvati, Maurizio; Köster, Petra; Labate, Luca; Ligi, Carlo; Marcellini, Fabio; Maroli, Cesare; Mauri, Marco; Migliorati, Mauro; Mostacci, Andrea; Oliva, Pier N; Palumbo, Luigi; Pellegrino, Luigi; Petrillo, Vittoria; Piovella, Nicola; Poggiu, Angela; Pozzoli, Roberto; Preger, Miro; Ricci, Ruggero; Rome, Massimiliano; Rossi, Antonella; Sanelli, Claudio; Serio, Mario; Sgamma, Francesco; Spataro, Bruno; Stecchi, Alessandro; Stella, Angelo; Stumbo, Simone; Tazzioli, Franco; Tommasini, Paolo; Vaccarezza, Cristina; Vescovi, Mario; Vicario, Carlo

    2005-01-01

    We present the status of the activity on the project PLASMONX, which foresees the installation of a multi-TW Ti:Sa laser system at the CNR-ILIL laboratory to conduct plasma acceleration experiments and the construction of an additional beam line at SPARC to develop a Thomson X-ray source at INFN-LNF. After pursuing self-injection experiments at ILIL, when the electron beam at SPARC will be available the SPARC laser system will be upgraded to TW power level in order to conduct either external injection plasma acceleration experiments and ultra-bright X-ray pulse generation with the Thomson source. Results of numerical simulations modeling the interaction of the SPARC electron beam and the counter-propagating laser beam are presented with detailed discussion of the monochromatic X-ray beam spectra generated by Compton backscattering: X-ray energies are tunable in the range 20 to 1000 keV, with pulse duration from 30 fs to 20 ps. Preliminary simulations of plasma acceleration with self-injection are illustrated,...

  17. The proteome browser web portal.

    Science.gov (United States)

    Goode, Robert J A; Yu, Simon; Kannan, Anitha; Christiansen, Jeffrey H; Beitz, Anthony; Hancock, William S; Nice, Edouard; Smith, A Ian

    2013-01-01

    In 2010, the Human Proteome Organization launched the Human Proteome Project (HPP), aimed at identifying and characterizing the proteome of the human body. To support complete coverage, one arm of the project will take a gene- or chromosomal-centric strategy (C-HPP) aimed at identifying at least one protein product from each protein-coding gene. Despite multiple large international biological databases housing genomic and protein data, there is currently no single system that integrates updated pertinent information from each of these data repositories and assembles the information into a searchable format suitable for the type of global proteomics effort proposed by the C-HPP. We have undertaken the goal of producing a data integration and analysis software system and browser for the C-HPP effort and of making data collections from this resource discoverable through metadata repositories, such as Australian National Data Service's Research Data Australia. Here we present our vision and progress toward the goal of developing a comprehensive data integration and analysis software tool that provides a snapshot of currently available proteomic related knowledge around each gene product, which will ultimately assist in analyzing biological function and the study of human physiology in health and disease.

  18. Proteomic analysis.

    Science.gov (United States)

    Cosette, Pascal; Jouenne, Thierry

    2014-01-01

    Proteome provides highly valuable information on the amount, modifications, and subcellular localization of polypeptides. Accordingly, geneticists, molecular biologists, and biochemists have logically applied these new tools to respond to different lines of biological questions (inventory of proteins, impact of a mutation, dynamics of protein regulation under a given exposure, …). However, even if the results obtained are very informative, this approach needs an excellent experimental design which ensures robustness and thus yields reproducibility. The present chapter gives appropriate methods for assessing the proteome of Pseudomonas aeruginosa by using a two-dimensional gel electrophoresis approach. Protocols for crude protein extraction, protein separation by using immobilized pH gradients, and protein identification by Liquid Chromatography coupled with tandem Mass Spectrometry (LC-MS/MS) are given.

  19. Building ProteomeTools based on a complete synthetic human proteome.

    Science.gov (United States)

    Zolg, Daniel P; Wilhelm, Mathias; Schnatbaum, Karsten; Zerweck, Johannes; Knaute, Tobias; Delanghe, Bernard; Bailey, Derek J; Gessulat, Siegfried; Ehrlich, Hans-Christian; Weininger, Maximilian; Yu, Peng; Schlegl, Judith; Kramer, Karl; Schmidt, Tobias; Kusebauch, Ulrike; Deutsch, Eric W; Aebersold, Ruedi; Moritz, Robert L; Wenschuh, Holger; Moehring, Thomas; Aiche, Stephan; Huhmer, Andreas; Reimer, Ulf; Kuster, Bernhard

    2017-03-01

    We describe ProteomeTools, a project building molecular and digital tools from the human proteome to facilitate biomedical research. Here we report the generation and multimodal liquid chromatography-tandem mass spectrometry analysis of >330,000 synthetic tryptic peptides representing essentially all canonical human gene products, and we exemplify the utility of these data in several applications. The resource (available at http://www.proteometools.org) will be extended to >1 million peptides, and all data will be shared with the community via ProteomicsDB and ProteomeXchange.

  20. The Numerical Tokamak Project (NTP) simulation of turbulent transport in the core plasma: A grand challenge in plasma physics

    Energy Technology Data Exchange (ETDEWEB)

    1993-12-01

    The long-range goal of the Numerical Tokamak Project (NTP) is the reliable prediction of tokamak performance using physics-based numerical tools describing tokamak physics. The NTP is accomplishing the development of the most advanced particle and extended fluid model`s on massively parallel processing (MPP) environments as part of a multi-institutional, multi-disciplinary numerical study of tokamak core fluctuations. The NTP is a continuing focus of the Office of Fusion Energy`s theory and computation program. Near-term HPCC work concentrates on developing a predictive numerical description of the core plasma transport in tokamaks driven by low-frequency collective fluctuations. This work addresses one of the greatest intellectual challenges to our understanding of the physics of tokamak performance and needs the most advanced computational resources to progress. We are conducting detailed comparisons of kinetic and fluid numerical models of tokamak turbulence. These comparisons are stimulating the improvement of each and the development of hybrid models which embody aspects of both. The combination of emerging massively parallel processing hardware and algorithmic improvements will result in an estimated 10**2--10**6 performance increase. Development of information processing and visualization tools is accelerating our comparison of computational models to one another, to experimental data, and to analytical theory, providing a bootstrap effect in our understanding of the target physics. The measure of success is the degree to which the experimentally observed scaling of fluctuation-driven transport may be predicted numerically. The NTP is advancing the HPCC Initiative through its state-of-the-art computational work. We are pushing the capability of high performance computing through our efforts which are strongly leveraged by OFE support.

  1. Personalized medicine beyond genomics: alternative futures in big data-proteomics, environtome and the social proteome.

    Science.gov (United States)

    Özdemir, Vural; Dove, Edward S; Gürsoy, Ulvi K; Şardaş, Semra; Yıldırım, Arif; Yılmaz, Şenay Görücü; Ömer Barlas, I; Güngör, Kıvanç; Mete, Alper; Srivastava, Sanjeeva

    2017-01-01

    No field in science and medicine today remains untouched by Big Data, and psychiatry is no exception. Proteomics is a Big Data technology and a next generation biomarker, supporting novel system diagnostics and therapeutics in psychiatry. Proteomics technology is, in fact, much older than genomics and dates to the 1970s, well before the launch of the international Human Genome Project. While the genome has long been framed as the master or "elite" executive molecule in cell biology, the proteome by contrast is humble. Yet the proteome is critical for life-it ensures the daily functioning of cells and whole organisms. In short, proteins are the blue-collar workers of biology, the down-to-earth molecules that we cannot live without. Since 2010, proteomics has found renewed meaning and international attention with the launch of the Human Proteome Project and the growing interest in Big Data technologies such as proteomics. This article presents an interdisciplinary technology foresight analysis and conceptualizes the terms "environtome" and "social proteome". We define "environtome" as the entire complement of elements external to the human host, from microbiome, ambient temperature and weather conditions to government innovation policies, stock market dynamics, human values, political power and social norms that collectively shape the human host spatially and temporally. The "social proteome" is the subset of the environtome that influences the transition of proteomics technology to innovative applications in society. The social proteome encompasses, for example, new reimbursement schemes and business innovation models for proteomics diagnostics that depart from the "once-a-life-time" genotypic tests and the anticipated hype attendant to context and time sensitive proteomics tests. Building on the "nesting principle" for governance of complex systems as discussed by Elinor Ostrom, we propose here a 3-tiered organizational architecture for Big Data science such as

  2. Internet and web projects for fusion plasma science and education. Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    Eastman, Timothy E. [Senior Research Associate, Silver Spring, MD (United States)

    1999-08-30

    The plasma web site at http://www.plasmas.org provides comprehensive coverage of all plasma science and technology with site links worldwide. Prepared to serve the general public, students, educators, researchers, and decision-makers, the site covers basic plasma physics, fusion energy, magnetic confinement fusion, high energy density physics include ICF, space physics and astrophysics, pulsed-power, lighting, waste treatment, plasma technology, plasma theory, simulations and modeling.

  3. Proteomic Investigations into Hemodialysis Therapy

    Directory of Open Access Journals (Sweden)

    Mario Bonomini

    2015-12-01

    Full Text Available The retention of a number of solutes that may cause adverse biochemical/biological effects, called uremic toxins, characterizes uremic syndrome. Uremia therapy is based on renal replacement therapy, hemodialysis being the most commonly used modality. The membrane contained in the hemodialyzer represents the ultimate determinant of the success and quality of hemodialysis therapy. Membrane’s performance can be evaluated in terms of removal efficiency for unwanted solutes and excess fluid, and minimization of negative interactions between the membrane material and blood components that define the membrane’s bio(incompatibility. Given the high concentration of plasma proteins and the complexity of structural functional relationships of this class of molecules, the performance of a membrane is highly influenced by its interaction with the plasma protein repertoire. Proteomic investigations have been increasingly applied to describe the protein uremic milieu, to compare the blood purification efficiency of different dialyzer membranes or different extracorporeal techniques, and to evaluate the adsorption of plasma proteins onto hemodialysis membranes. In this article, we aim to highlight investigations in the hemodialysis setting making use of recent developments in proteomic technologies. Examples are presented of why proteomics may be helpful to nephrology and may possibly affect future directions in renal research.

  4. MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes

    DEFF Research Database (Denmark)

    Zhang, Yanling; Zhang, Yong; Adachi, Jun;

    2007-01-01

    Mass spectrometry (MS)-based proteomics has become a powerful technology to map the protein composition of organelles, cell types and tissues. In our department, a large-scale effort to map these proteomes is complemented by the Max-Planck Unified (MAPU) proteome database. MAPU contains several...... body fluid proteomes; including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. The liver proteome is represented with 3200 proteins. By employing high resolution MS......://www.mapuproteome.com using a clickable interface of cell or body parts. Proteome data can be queried across proteomes by protein name, accession number, sequence similarity, peptide sequence and annotation information. More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome. Basic...

  5. Effect of Ambipolar Potential on the Propulsive Performance of the GDM Plasma Thruster Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The gasdynamic mirror (GDM) plasma thruster has the ability to confine high-density plasma for the length of time required to heat it to the temperatures...

  6. Numerical Modeling of Plasma-Liner Formation and Implosion for the PLX- α Project

    Science.gov (United States)

    Cassibry, Jason; Samulyak, Roman; Schillo, Kevin; Shih, Wen; Hsu, Scott

    2016-10-01

    Numerical simulations of the propagation, merging, and implosion of supersonic plasma jets have been performed using the FronTier and smooth particle hydrodynamics (SPH) codes in support of the PLX- α project. The physics includes radiation, heat conduction using Braginskii thermal conductivities, ion viscosity, and tabular equations of state using LTE and non-LTE models. A parametric analysis provides scaling of peak ram pressure and Mach number vs. number of jets, initial density, initial jet velocity, and species including nitrogen, neon, argon, krypton, and xenon. Conical simulations of 6 and 7 jets support near-term experiments, which facilitate diagnostic access for assessing the quality of the liner during merge. Solid angle averaged and standard deviation of ram pressure and Mach number reveal the variation in these properties during formation and implosion. Spherical harmonic mode-number analysis of spherical slices of ram pressure at various radii and times provide a quantitative means to assess the evolution of liner non-uniformity. Supported by the ARPA-E ALPHA program.

  7. LXCat: A web-based, community-wide project on data for modeling low temperature plasmas

    Science.gov (United States)

    Pitchford, L. C.

    2014-10-01

    LXCat is an open-access website (www.lxcat.net) for exchanging data related to ion and electron transport and scattering cross sections in cold, neutral gases. At present 30 people from 12 countries have contributed to the LXCat project. This presentation will focus on the status of the data available for electrons on LXCat. These data are primarily in the form of ``complete'' sets of cross sections, compiled or calculated by different contributors, covering a range of energies from thermal up to about 1 keV. The cross section data can be used directly in Monte Carlo simulations and can also be used as input to Boltzmann equation solvers. Solution of the homogeneous, steady-state Boltzmann equation yields electron energy distribution functions (edf) as a function of reduced electric field strength, E/N, integrals over which yield electron transport and rate coefficients. The transport and rate coefficient data are required input for fluid models of low temperature plasmas. Evaluation of the cross section data sets available on LXCat is a key issue. To this end, the LXCat team has been making systematic intercomparisons of cross section data and comparisons of calculated and measured transport and rate coefficients. Our evaluations have been reported previously for noble gases and for common atmospheric gases. The LXCat team is now evaluating data for more complex molecules.

  8. Mining the granule proteome

    DEFF Research Database (Denmark)

    Albrethsen, Jakob; Goetze, Jens P; Johnsen, Anders H

    2015-01-01

    Proteomics of secretory granules is an emerging strategy for identifying secreted proteins, including potentially novel candidate biomarkers and peptide hormones. In addition, proteomics can provide information about the abundance, localization and structure (post-translational modification) of g...

  9. The UCSC Proteome Browser

    OpenAIRE

    Hsu, Fan; Tom H Pringle; Kuhn, Robert M.; Karolchik, Donna; Diekhans, Mark; Haussler, David; Kent, W. James

    2004-01-01

    The University of California Santa Cruz (UCSC) Proteome Browser provides a wealth of protein information presented in graphical images and with links to other protein-related Internet sites. The Proteome Browser is tightly integrated with the UCSC Genome Browser. For the first time, Genome Browser users have both the genome and proteome worlds at their fingertips simultaneously. The Proteome Browser displays tracks of protein and genomic sequences, exon structure, polarity, hydrophobicity, lo...

  10. Proteomics of the Peroxisome

    OpenAIRE

    2006-01-01

    Genomes provide us with a blue print for the potential of a cell. However, the activity of a cell is expressed in its proteome. Full understanding of the complexity of cells demands a comprehensive view of the proteome; its interactions, activity states and organization. Comprehensive proteomic approaches applied to peroxisomes have yielded new insights into the organelle and its dynamic interplay with other cellular structures. As technologies and methodologies improve proteomics hold the pr...

  11. Efficient Isolation and Quantitative Proteomic Analysis of Cancer Cell Plasma Membrane Proteins for Identification of Metastasis-Associated Cell Surface Markers

    DEFF Research Database (Denmark)

    Lund, Rikke; Leth-Larsen, Rikke; Jensen, Ole N

    2009-01-01

    Cell surface membrane proteins are involved in central processes such as cell signaling, cell-cell interactions, ion and solute transport, and they seem to play a pivotal role in several steps of the metastatic process of cancer cells. The low abundance and hydrophobic nature of cell surface...... membrane proteins complicate their purification and identification by MS. We used two isogenic cell lines with opposite metastatic capabilities in nude mice to optimize cell surface membrane protein purification and to identify potential novel markers of metastatic cancer. The cell surface membrane...... proteins were isolated by centrifugation/ultracentrifugation steps, followed by membrane separation using a Percoll/sucrose density gradient. The gradient fractions containing the cell surface membrane proteins were identified by enzymatic assays. Stable isotope labeling of the proteome of the metastatic...

  12. Dense Medium Plasma Water Purification Reactor (DMP WaPR) Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Dense Medium Plasma Water Purification Reactor offers significant improvements over existing water purification technologies used in Advanced Life Support...

  13. A Plasma Aerocapture and Entry System for Manned Missions and Planetary Deep Space Orbiters Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Plasma Magnetoshell is based on demonstrated experimental results and the successful implementation would dramatically decrease mission risk, launch cost, mass,...

  14. Final Report for completed IPP Project:"Development of Plasma Ablation for Soft Tissue and Bone Surgery"

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Ian

    2009-09-01

    ArthroCare is a medical device company that develops, manufactures, and markets an advanced surgical tool, a plasma electro-surgical system for cutting and removing tissue. The hand-held electrical discharge device produces plasma in a biocompatible conductive fluid and tissue to which it is applied during surgery. Its products allow surgeons to operate with increased precision and accuracy, limiting damage to surrounding tissue thereby reducing pain and speeding recovery for the patient. In the past, the design of ArthfoCare's plasma wands has been an empirical undertaking. One goal of this R&D program was to put the phenomena involved on a sound scientific footing, allowing optimization of existing plasma based electro-surgery system technology, and the design and manufacture of new and improved kinds of scalpels, in particular for the surgical cutting of bone. Another important related goal of the program was to develop, through an experimental approach, new plasma wand approaches to the cutting ('shaving') of hard bone tissue. The goals of the CRADA were accomplished - computer models were used to predict important parameters of the plasma discharge and the bone environment, and several different approaches to bone-shaving were developed and demonstrated. The primary goal of the project was to develop and demonstrate an atmospheric-pressure plasma tool that is suitable for surgical use for shaving bone in humans. This goal was accomplished, in fact with several different alternative plasma approaches. High bone ablation speeds were measured. The use of probes ('plasma wand' - the surgical tool) with moving active electrodes was also explored, and there are advantages to this method. Another important feature is that the newly-exposed bone surface have only a very thin necrosis layer; this feature was demonstrated. This CRADA has greatly advanced our understanding of bone removal by atmospheric pressure plasmas in liquid, and puts Arthro

  15. Oolemmal proteomics – identification of highly abundant heat shock proteins and molecular chaperones in the mature mouse egg and their localization on the plasma membrane

    Science.gov (United States)

    Calvert, Meredith E; Digilio, Laura C; Herr, John C; Coonrod, Scott A

    2003-01-01

    Background The mature mouse egg contains the full complement of maternal proteins required for fertilization, the transition to zygotic transcription, and the beginning stages of embryogenesis. Many of these proteins remain to be characterized, therefore in this study we have identified highly abundant egg proteins using a proteomic approach and found that several of these proteins also appear to localize to the egg surface. Characterization of such molecules will provide important insight into the cellular events of fertilization and early development. Methods In order to identify some of the more abundant egg proteins, whole egg extracts were resolved on coomassie-stained two-dimensional (2D) PAGE gels. Several highly abundant protein spots were cored and microsequenced by tandem mass spectrometry (TMS), and determined to be molecular chaperone proteins. Concurrent experiments were performed to identify oolemmal proteins using 2D avidin blotting. Proteins spots that appeared to be surface labeled by biotinylation were correlated with the initial coomassie-stained reference gel. Surprisingly, some of the surface labelled proteins corresponded to those abundant chaperone proteins previously identified. To confirm whether these molecules are accumulating at the oolemmal surface in eggs, we performed immunofluoresence on live, zona-free eggs using antibodies to HSP70, HSP90, GRP94, GRP78, calreticulin and calnexin. Results The putative surface-labeled proteins identified by biotinylation included the molecular chaperones HSP70 (MW 70 KDa, pI 5.5), HSP90a (MW 85 KDa, pI 4.9), GRP94 (MW 92 KDa, pI 4.7), GRP78 (MW 72 KDa, pI 5.0), Oxygen regulated protein 150 (ORP150; MW 111 KDa, pI 5.1), Calreticulin (MW 48 KDa, pI 4.3), Calnexin (MW 65 KDa, pI 4.5), and Protein disulfide isomerase (PDI; MW 57 KDa, pI 4.8). Immunofluoresence results showed that antibodies to HSP90, GRP94, GRP78 and calreticulin were reactive with oolemmal proteins. We were unable to confirm surface

  16. Oolemmal proteomics – identification of highly abundant heat shock proteins and molecular chaperones in the mature mouse egg and their localization on the plasma membrane

    Directory of Open Access Journals (Sweden)

    Herr John C

    2003-02-01

    Full Text Available Abstract Background The mature mouse egg contains the full complement of maternal proteins required for fertilization, the transition to zygotic transcription, and the beginning stages of embryogenesis. Many of these proteins remain to be characterized, therefore in this study we have identified highly abundant egg proteins using a proteomic approach and found that several of these proteins also appear to localize to the egg surface. Characterization of such molecules will provide important insight into the cellular events of fertilization and early development. Methods In order to identify some of the more abundant egg proteins, whole egg extracts were resolved on coomassie-stained two-dimensional (2D PAGE gels. Several highly abundant protein spots were cored and microsequenced by tandem mass spectrometry (TMS, and determined to be molecular chaperone proteins. Concurrent experiments were performed to identify oolemmal proteins using 2D avidin blotting. Proteins spots that appeared to be surface labeled by biotinylation were correlated with the initial coomassie-stained reference gel. Surprisingly, some of the surface labelled proteins corresponded to those abundant chaperone proteins previously identified. To confirm whether these molecules are accumulating at the oolemmal surface in eggs, we performed immunofluoresence on live, zona-free eggs using antibodies to HSP70, HSP90, GRP94, GRP78, calreticulin and calnexin. Results The putative surface-labeled proteins identified by biotinylation included the molecular chaperones HSP70 (MW 70 KDa, pI 5.5, HSP90a (MW 85 KDa, pI 4.9, GRP94 (MW 92 KDa, pI 4.7, GRP78 (MW 72 KDa, pI 5.0, Oxygen regulated protein 150 (ORP150; MW 111 KDa, pI 5.1, Calreticulin (MW 48 KDa, pI 4.3, Calnexin (MW 65 KDa, pI 4.5, and Protein disulfide isomerase (PDI; MW 57 KDa, pI 4.8. Immunofluoresence results showed that antibodies to HSP90, GRP94, GRP78 and calreticulin were reactive with oolemmal proteins. We were unable to

  17. Oolemmal proteomics--identification of highly abundant heat shock proteins and molecular chaperones in the mature mouse egg and their localization on the plasma membrane.

    Science.gov (United States)

    Calvert, Meredith E; Digilio, Laura C; Herr, John C; Coonrod, Scott A

    2003-02-14

    The mature mouse egg contains the full complement of maternal proteins required for fertilization, the transition to zygotic transcription, and the beginning stages of embryogenesis. Many of these proteins remain to be characterized, therefore in this study we have identified highly abundant egg proteins using a proteomic approach and found that several of these proteins also appear to localize to the egg surface. Characterization of such molecules will provide important insight into the cellular events of fertilization and early development. In order to identify some of the more abundant egg proteins, whole egg extracts were resolved on coomassie-stained two-dimensional (2D) PAGE gels. Several highly abundant protein spots were cored and microsequenced by tandem mass spectrometry (TMS), and determined to be molecular chaperone proteins. Concurrent experiments were performed to identify oolemmal proteins using 2D avidin blotting. Proteins spots that appeared to be surface labeled by biotinylation were correlated with the initial coomassie-stained reference gel. Surprisingly, some of the surface labelled proteins corresponded to those abundant chaperone proteins previously identified. To confirm whether these molecules are accumulating at the oolemmal surface in eggs, we performed immunofluoresence on live, zona-free eggs using antibodies to HSP70, HSP90, GRP94, GRP78, calreticulin and calnexin. The putative surface-labeled proteins identified by biotinylation included the molecular chaperones HSP70 (MW 70 KDa, pI 5.5), HSP90a (MW 85 KDa, pI 4.9), GRP94 (MW 92 KDa, pI 4.7), GRP78 (MW 72 KDa, pI 5.0), Oxygen regulated protein 150 (ORP150; MW 111 KDa, pI 5.1), Calreticulin (MW 48 KDa, pI 4.3), Calnexin (MW 65 KDa, pI 4.5), and Protein disulfide isomerase (PDI; MW 57 KDa, pI 4.8). Immunofluoresence results showed that antibodies to HSP90, GRP94, GRP78 and calreticulin were reactive with oolemmal proteins. We were unable to confirm surface localization of HSP70 or

  18. Quantitative transporter proteomics by liquid chromatography with tandem mass spectrometry: addressing methodologic issues of plasma membrane isolation and expression-activity relationship.

    Science.gov (United States)

    Kumar, Vineet; Prasad, Bhagwat; Patilea, Gabriela; Gupta, Anshul; Salphati, Laurent; Evers, Raymond; Hop, Cornelis E C A; Unadkat, Jashvant D

    2015-02-01

    To predict transporter-mediated drug disposition using physiologically based pharmacokinetic models, one approach is to measure transport activity and relate it to protein expression levels in cell lines (overexpressing the transporter) and then scale these to via in vitro to in vivo extrapolation (IVIVE). This approach makes two major assumptions. First, that the expression of the transporter is predominantly in the plasma membrane. Second, that there is a linear correlation between expression level and activity of the transporter protein. The present study was conducted to test these two assumptions. We evaluated two commercially available kits that claimed to separate plasma membrane from other cell membranes. The Qiagen Qproteome kit yielded very little protein in the fraction purported to be the plasma membrane. The Abcam Phase Separation kit enriched the plasma membrane but did not separate it from other intracellular membranes. For the Abcam method, the expression level of organic anion-transporting polypeptides (OATP) 1B1/2B1 and breast cancer resistance protein (BCRP) proteins in all subcellular fractions isolated from cells or human liver tissue tracked that of Na⁺-K⁺ ATPase. Assuming that Na⁺-K⁺ ATPase is predominantly located in the plasma membrane, these data suggest that the transporters measured are also primarily located in the plasma membrane. Using short hairpin RNA, we created clones of cell lines with varying degrees of OATP1B1 or BCRP expression level. In these clones, transport activity of OATP1B1 or BCRP was highly correlated with protein expression level (r² > 0.9). These data support the use of transporter expression level data and activity data from transporter overexpressing cell lines for IVIVE of transporter-mediated disposition of drugs.

  19. Proteomic analysis of heparin-binding proteins from human seminal plasma: a step towards identification of molecular markers of male fertility

    Indian Academy of Sciences (India)

    Vijay Kumar; Md Imtaiyaz Hassan; Anil Kumar Tomar; Tara Kashav; Jaya Nautiyal; Sarman Singh; Tej P Singh; Savita Yadav

    2009-12-01

    Glycosaminoglycans, especially heparin, are involved in various cell processes such as apoptosis, cell cycle control, platelet activation, capacitation, acrosome reaction and sperm decondensation. Heparin-binding proteins (HBPs) are essential constituents of human seminal fluid, which bind to sperm lipids containing the phosphorylcholine group and mediate the fertilization process. We utilized a proteomic set-up consisting of affinity chromatography, isoelectric focusing (IEF) coupled with matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI TOF/MS) for protein analysis of human HBPs. We resolved 70 different spots on two-dimensional (2-D) gel and subsequently identified these proteins. Forty different types of proteins were identified. Functional analysis revealed that 38% of the proteins belonged to the enzyme category, 20% were involved in RNA processing and transcription, 18% in structure and transport function, and 16% in cell recognition and signal transduction. We also identified 8% of proteins with unknown functions, although their expression in seminal fluid has been documented. Proteins of seminal fluid that bind heparin may be directly involved in sperm capacitation and acrosome reaction (AR), which are the two critical steps for fertilization. This information on HBPs would be useful for identifying potential biomarkers of fertility in the near future.

  20. Proteome of human plasma very low-density lipoprotein and low-density lipoprotein exhibits a link with coagulation and lipid metabolism

    NARCIS (Netherlands)

    Dashty Rahmatabady, Monireh; Motazacker, Mohammad M.; Levels, Johannes; de Vries, Marcel; Mahmoudi, Morteza; Peppelenbosch, Maikel; Rezaee, Farhad

    2014-01-01

    Apart from transporting lipids through the body, the human plasma lipoproteins very low-density lipoprotein (VLDL) and low-density lipoprotein (LDL) are also thought to serve as a modality for intra-organismal protein transfer, shipping proteins with important roles in inflammation and thrombosis fr

  1. HIGH ENERGY REPLACEMENT FOR TEFLON PROPELLANT IN PULSED PLASMA THRUSTERS Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This program will utilize a well-characterized Pulsed Plasma Thruster (PPT) to test experimental high-energy extinguishable solid propellants (HE), instead of...

  2. Development of a Novel Non-Equilibrium Pulsed Plasma Ignition Module for High Altitude Turbojets Project

    Data.gov (United States)

    National Aeronautics and Space Administration — An experimental research program focusing on design, development, and testing of a novel nonequilibrium plasma ignition module is proposed. The ignition module will...

  3. High Performance Plasma Channel Insulators for High Power Hall Thrusters Project

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA missions for planetary exploration require high power, long-life Hall thrusters. However, thruster power and lifetime are limited by the erosion of plasma...

  4. Shock Wave Boundary Layer Interaction Control Using Pulsed DBD Plasma Actuators Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Active flow control using dielectric barrier discharge (DBD) plasma actuators is an attractive option for both reduction of complexity of aircraft systems required...

  5. Simulation Tool for Dielectric Barrier Discharge Plasma Actuators at Atmospheric and Sub-Atmospheric Pressures Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Traditional approaches for active flow separation control using dielectric barrier discharge (DBD) plasma actuators are limited to relatively low-speed flows and...

  6. Effect of Ambipolar Potential on the Propulsive Performance of the GDM Plasma Thruster Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Gasdynamic Mirror (GDM) thruster is an electric propulsion device, without electrodes, that will magnetically confine a plasma with such density and temperature...

  7. Simulation Tool for Dielectric Barrier Discharge Plasma Actuators at Atmospheric and Sub-Atmospheric Pressures Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Traditional approaches for active flow separation control using dielectric barrier discharge (DBD) plasma actuators are limited to relatively low-speed flows and...

  8. High Performance Plasma Channel Insulators for High Power Hall Thrusters Project

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA missions for planetary exploration require high power, long-life Hall thrusters. However, thruster power and lifetime are limited by the erosion of plasma...

  9. Methods, algorithms and tools in computational proteomics: a practical point of view.

    Science.gov (United States)

    Matthiesen, Rune

    2007-08-01

    Computational MS-based proteomics is an emerging field arising from the demand of high throughput analysis in numerous large-scale experimental proteomics projects. The review provides a broad overview of a number of computational tools available for data analysis of MS-based proteomics data and gives appropriate literature references to detailed description of algorithms. The review provides, to some extent, discussion of algorithms and methods for peptide and protein identification using MS data, quantitative proteomics, and data storage. The hope is that it will stimulate discussion and further development in computational proteomics. Computational proteomics deserves more scientific attention. There are far fewer computational tools and methods available for proteomics compared to the number of microarray tools, despite the fact that data analysis in proteomics is much more complex than microarray analysis.

  10. Proteomics and Its Application in Biomarker Discovery and Drug Development

    Institute of Scientific and Technical Information of China (English)

    He Qing-Yu; Chiu Jen-Fu

    2004-01-01

    Proteomics is a research field aiming to characterize molecular and cellular dynamics in protein expression and function on a global level. The introduction of proteomics has been greatly broadening our view and accelerating our path in various medical researches. The most significant advantage of proteomics is its ability to examine a whole proteome or sub-proteome in a single experiment so that the protein alterations corresponding to a pathological or biochemical condition at a given time can be considered in an integrated way. Proteomic technology has been extensively used to tackle a wide variety of medical subjects including biomarker discovery and drug development. By complement with other new technique advance in genomics and bioinformatics,proteomics has a great potential to make considerable contribution to biomarker identification and revolutionize drug development process. A brief overview of the proteomic technologies will be provided and the application of proteomics in biomarker discovery and drug development will be discussed using our current research projects as examples.

  11. STEM CELLS AND PROTEOMICS

    Institute of Scientific and Technical Information of China (English)

    ZHOU Yong-ming; GUO Tian-nan; HUANG Shi-ang

    2006-01-01

    The distinctive features of proteomics are large-scale and high throughput. The key techniques of proteomics are two-dimensional gel electrophoresis, mass spectrometry and bioinformatics. Stem cell can differentiate into all kinds of cells, tissues and organs. There are many proteins and cytokines involved in the process of differentiation. Applying proteomics techniques to the research of the complex process of stem cell differentiation is of great importance to study the mechanism and applications of stem cell differentiation.

  12. Combination of Multiple Spectral Libraries Improves the Current Search Methods Used to Identify Missing Proteins in the Chromosome-Centric Human Proteome Project.

    Science.gov (United States)

    Cho, Jin-Young; Lee, Hyoung-Joo; Jeong, Seul-Ki; Kim, Kwang-Youl; Kwon, Kyung-Hoon; Yoo, Jong Shin; Omenn, Gilbert S; Baker, Mark S; Hancock, William S; Paik, Young-Ki

    2015-12-01

    Approximately 2.9 billion long base-pair human reference genome sequences are known to encode some 20 000 representative proteins. However, 3000 proteins, that is, ~15% of all proteins, have no or very weak proteomic evidence and are still missing. Missing proteins may be present in rare samples in very low abundance or be only temporarily expressed, causing problems in their detection and protein profiling. In particular, some technical limitations cause missing proteins to remain unassigned. For example, current mass spectrometry techniques have high limits and error rates for the detection of complex biological samples. An insufficient proteome coverage in a reference sequence database and spectral library also raises major issues. Thus, the development of a better strategy that results in greater sensitivity and accuracy in the search for missing proteins is necessary. To this end, we used a new strategy, which combines a reference spectral library search and a simulated spectral library search, to identify missing proteins. We built the human iRefSPL, which contains the original human reference spectral library and additional peptide sequence-spectrum match entries from other species. We also constructed the human simSPL, which contains the simulated spectra of 173 907 human tryptic peptides determined by MassAnalyzer (version 2.3.1). To prove the enhanced analytical performance of the combination of the human iRefSPL and simSPL methods for the identification of missing proteins, we attempted to reanalyze the placental tissue data set (PXD000754). The data from each experiment were analyzed using PeptideProphet, and the results were combined using iProphet. For the quality control, we applied the class-specific false-discovery rate filtering method. All of the results were filtered at a false-discovery rate of libraries, iRefSPL and simSPL, were designed to ensure no overlap of the proteome coverage. They were shown to be complementary to spectral library

  13. CMPD: cancer mutant proteome database.

    Science.gov (United States)

    Huang, Po-Jung; Lee, Chi-Ching; Tan, Bertrand Chin-Ming; Yeh, Yuan-Ming; Julie Chu, Lichieh; Chen, Ting-Wen; Chang, Kai-Ping; Lee, Cheng-Yang; Gan, Ruei-Chi; Liu, Hsuan; Tang, Petrus

    2015-01-01

    Whole-exome sequencing, which centres on the protein coding regions of disease/cancer associated genes, represents the most cost-effective method to-date for deciphering the association between genetic alterations and diseases. Large-scale whole exome/genome sequencing projects have been launched by various institutions, such as NCI, Broad Institute and TCGA, to provide a comprehensive catalogue of coding variants in diverse tissue samples and cell lines. Further functional and clinical interrogation of these sequence variations must rely on extensive cross-platforms integration of sequencing information and a proteome database that explicitly and comprehensively archives the corresponding mutated peptide sequences. While such data resource is a critical for the mass spectrometry-based proteomic analysis of exomic variants, no database is currently available for the collection of mutant protein sequences that correspond to recent large-scale genomic data. To address this issue and serve as bridge to integrate genomic and proteomics datasets, CMPD (http://cgbc.cgu.edu.tw/cmpd) collected over 2 millions genetic alterations, which not only facilitates the confirmation and examination of potential cancer biomarkers but also provides an invaluable resource for translational medicine research and opportunities to identify mutated proteins encoded by mutated genes.

  14. Cell wall proteins: a new insight through proteomics.

    Science.gov (United States)

    Jamet, Elisabeth; Canut, Hervé; Boudart, Georges; Pont-Lezica, Rafael F

    2006-01-01

    Cell wall proteins are essential constituents of plant cell walls; they are involved in modifications of cell wall components, wall structure, signaling and interactions with plasma membrane proteins at the cell surface. The application of proteomic approaches to the cell wall compartment raises important questions: are there technical problems specific to cell wall proteomics? What kinds of proteins can be found in Arabidopsis walls? Are some of them unexpected? What sort of post-translational modifications have been characterized in cell wall proteins to date? The purpose of this review is to discuss the experimental results obtained to date using proteomics, as well as some of the new questions challenging future research.

  15. Proteome of human plasma very low-density lipoprotein and low-density lipoprotein exhibits a link with coagulation and lipid metabolism.

    Science.gov (United States)

    Dashty, M; Motazacker, M M; Levels, J; de Vries, M; Mahmoudi, M; Peppelenbosch, M P; Rezaee, F

    2014-03-03

    Apart from transporting lipids through the body, the human plasma lipoproteins very low-density lipoprotein (VLDL) and low-density lipoprotein (LDL) are also thought to serve as a modality for intra-organismal protein transfer, shipping proteins with important roles in inflammation and thrombosis from the site of synthesis to effector locations. To better understand the role of VLDL and LDL in the transport of proteins, we applied a combination of LTQ ORBITRAP-XL (nLC-MS/MS) with both in-SDS-PAGE gel and in-solution tryptic digestion of pure and defined VLDL and LDL fractions. We identified the presence of 95 VLDL- and 51 LDL-associated proteins including all known apolipoproteins and lipid transport proteins, and intriguingly a set of coagulation proteins, complement system and anti- microbial proteins. Prothrombin, protein S, fibrinogen γ, PLTP, CETP, CD14 and LBP were present on VLDL but not on LDL. Prenylcysteine oxidase 1, dermcidin, cathelicidin antimicrobial peptide, TFPI-1 and fibrinogen α chain were associated with both VLDL and LDL. Apo A-V is only present on VLDL and not on LDL. Collectively, this study provides a wealth of knowledge on the protein constituents of the human plasma lipoprotein system and strongly supports the notion that protein shuttling through this system is involved in the regulation of biological processes. Human diseases related to proteins carried by VLDL and LDL can be divided in three major categories: 1 - dyslipidaemia, 2 - atherosclerosis and vascular disease, and 3 - coagulation disorders.

  16. Coaxial Plasma Gun Development for the ARPA-E PLX- α Project

    Science.gov (United States)

    Witherspoon, F. Douglas; Case, Andrew; Brockington, Samuel

    2015-11-01

    We describe the renewed effort to design and build coaxial plasma guns appropriate for a scaling study of spherically imploding plasma liners as a standoff magneto-inertial-fusion driver under the ARPA-E Accelerating Low-Cost Plasma Heating And Assembly (ALPHA) program. HyperV joins LANL, UAH, UNM, BNL, and Tech-X to develop, build, operate and analyze a 60 plasma gun experiment using the existing PLX facility at LANL. The guns will be designed to operate over a scaling range of operating parameters: 0.5-5.0 mg of Ar, Ne, N2, Kr, and Xe; 20-60 km/s; 1016 -1017 cm-3 muzzle density; and up to 7.5 kJ stored energy per gun. Each gun is planned to incorporate contoured gaps, fast dense gas injection and triggering, and innovative integral sparkgap switching and pfn configurations to reduce inductance, cost, and complexity, and to increase efficiency and system reliability. We will describe the overall design approach for the guns and pulsed power systems. This work supported by the ARPA-E ALPHA Program.

  17. Laser-Plasma Sources for Soft-X-Ray Projection Lithography

    NARCIS (Netherlands)

    F. Bijkerk,; Shmaenok, L.; Vanhonk, A.; Bastiaensen, R.; Platonov, Y. Y.; Shevelko, A. P.; Mitrofanov, A. V.; Voss, F.; Desor, R.; Frowein, H.; Nikolaus, B.

    1994-01-01

    Results are reported concerning high-repetition-rate excimer lasers with average powers up to 415 W and their usage for generating laser-plasma soft X-ray sources. A conversion efficiency of laser light into monochromatized soft X-ray radiation of 0.7% at 13.5 nm (2% bandwidth) was achieved using an

  18. Laser-Plasma Sources for Soft-X-Ray Projection Lithography

    NARCIS (Netherlands)

    F. Bijkerk,; Shmaenok, L.; Vanhonk, A.; Bastiaensen, R.; Platonov, Y. Y.; Shevelko, A. P.; Mitrofanov, A. V.; Voss, F.; Desor, R.; Frowein, H.; Nikolaus, B.

    1994-01-01

    Results are reported concerning high-repetition-rate excimer lasers with average powers up to 415 W and their usage for generating laser-plasma soft X-ray sources. A conversion efficiency of laser light into monochromatized soft X-ray radiation of 0.7% at 13.5 nm (2% bandwidth) was achieved using an

  19. Simulation of Plasma Jet Merger and Liner Formation within the PLX- α Project

    Science.gov (United States)

    Samulyak, Roman; Chen, Hsin-Chiang; Shih, Wen; Hsu, Scott

    2015-11-01

    Detailed numerical studies of the propagation and merger of high Mach number argon plasma jets and the formation of plasma liners have been performed using the newly developed method of Lagrangian particles (LP). The LP method significantly improves accuracy and mathematical rigor of common particle-based numerical methods such as smooth particle hydrodynamics while preserving their main advantages compared to grid-based methods. A brief overview of the LP method will be presented. The Lagrangian particle code implements main relevant physics models such as an equation of state for argon undergoing atomic physics transformation, radiation losses in thin optical limit, and heat conduction. Simulations of the merger of two plasma jets are compared with experimental data from past PLX experiments. Simulations quantify the effect of oblique shock waves, ionization, and radiation processes on the jet merger process. Results of preliminary simulations of future PLX- alpha experiments involving the ~ π / 2 -solid-angle plasma-liner configuration with 9 guns will also be presented. Partially supported by ARPA-E's ALPHA program.

  20. Micro-scale Plasma Arc Gasification for Waste Treatment and Energy Production Project

    Science.gov (United States)

    Caraccio, Anne

    2015-01-01

    As NASA continues to develop technology for spaceflight beyond low earth orbit, we must develop the right systems for sustaining human life on a long duration or planetary mission. Plasma arc gasification (PAG) is an energy efficient mechanism of waste management for power generation and synthetic gas(syngas) production.

  1. Diagnostic Suite for HyperV Coaxial Plasma Gun Development for the PLX- α Project

    Science.gov (United States)

    Case, Andrew; Brockington, Sam; Witherspoon, F. Douglas

    2015-11-01

    We present the diagnostic suite to be used during development of the coaxial guns HyperV will deliver to LANL in support of the ARPA-E Accelerating Low-Cost Plasma Heating And Assembly (ALPHA) program. For plasma jet diagnostics this includes fast photodiodes for velocimetry, a ballistic pendulum for measuring total plasmoid momentum, interferometry for line integrated plasma density, deflectometry for line integrated perpendicular density gradient measurements, and spectroscopy, both time resolved high resolution spectroscopy using a novel detector developed by HyperV and time integrated survey spectroscopy, for measurements of velocity and temperature as well as impurities. In addition, we plan to use fast pressure probes for stagnation pressure, a Faraday cup for density, fast imaging for plume geometry and time integrated imaging for overall light emission. A novel low resolution long record length camera developed by HyperV will also be used for plume diagnostics. For diagnostics of gun operation, we will use Rogowski coils to measure current, voltage dividers for voltages, B-dot probes for magnetic field, and time resolved fast photodiodes to measure plasmoid velocity inside the accelerator. This work supported by the ARPA-E ALPHA program.

  2. Achievement report for fiscal 1999 on project for supporting the formation of energy/environmental technology verification project. International joint verification research project (Verification project relative to ignition and NOx reduction using plasma sub-burner in pulverized coal-fired furnace); 1999 nendo plasma sabubana ni yoru bifuntan nenshoro ni okeru chakka oyobi NO{sub x} teigen gijutsu ni kansuru jissho project seika hokokusho

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-03-01

    This project is executed through the cooperation of a Russian research institute, Akita Prefectural University, and the Ishikawajima-Harima Heavy Industries Co., Ltd. In the development of a plasma sub-burner and the basic research for its verification, a pulverized coal burning plasma sub-burner is designed and fabricated, a basic burning experiment is conducted for the plasma sub-burner, and plasma stabilization in a pulverized coal flow is simulated. In the verification study of the ignition by the plasma sub-burner in a pulverized coal-fired furnace, it is found that the newly-developed plasma sub-burner satisfies the prescribed operating conditions in the system and that the ignition of pulverized coal takes place across the air ratio range of 0.5-1.5 when pulverized coal is fed to the sub-burner. It is also found that NOx is reduced a great deal when a plasma operating on an orifice gas of air or nitrogen is generated in a gas which contains NOx. (NEDO)

  3. A proteomic analysis of human hemodialysis fluid

    DEFF Research Database (Denmark)

    Molina, Henrik; Bunkenborg, Jakob; Reddy, G Hanumanthu;

    2005-01-01

    The vascular compartment is an easily accessible compartment that provides an opportunity to measure analytes for diagnostic, prognostic, or therapeutic indications. Both serum and plasma have been analyzed extensively by proteomic approaches in an effort to catalog all proteins and polypeptides......., including cytokines, were only present as predicted transcripts in data bases and thus represent novel proteins. The proteins identified in this study could serve as biomarkers in serum using more sensitive methods such as ELISA-specific antibodies....

  4. Subcellular Proteomics of Soybean under Flooding Stress

    Institute of Scientific and Technical Information of China (English)

    Setsuko Komatsu

    2012-01-01

    Flooding is an environmental stress found worldwide and may increase in frequency due to changes in global climate,and causes significant reductions in the growth and yield of several crops.The application of proteomics techniques to clarify the molecular mechanisms underlying crop responses to flooding stress may facilitate the development of flood tolerant crops.To understand the response mechanism of soybean under flooding stress,proteomics analysis was carried out.Especially,subcellular proteomics studies have led to a better understanding of the mechanism of flooding stress tolerance in soybean.The effects of flooding stress on root plasma membrane were analyzed using an aqueous two-phase partitioning method in combination with gel-based and gel-free proteomics techniques.The results led to the following conclusions:proteins located in the cell wall were increased in the plasma membrane of flooded plants,indicating the contribution of plasma membrane to modification of the cell wall; superoxide dismutase was increased,indicating that the antioxidative system may play a crucial role in protecting cells from oxidative damage following exposure to flooding stress; heat shock cognate 70 kDa protein likely plays a significant role in protecting other proteins from denaturation and degradation during flooding stress; and signaling proteins might work cooperatively to regulate plasma membrane H +-ATPase and maintain ion homeostasis.Cell wall proteins were isolated from root of flooding stressed plants via sucrose gradient centrifugation and analyzed using gel-based proteomics technique.Cell wall proteins identified were related to lignification,and these results indicated that a decrease of lignification-related proteins is related to flooding decreased ROS and jasmonate biosynthesis.And also,lignin staining confirmed that lignification was suppressed in the roots of flooding stressed soybeans.Mitochondrial fractions were purified from root of flooding stressed

  5. Human Spermatozoa Quantitative Proteomic Signature Classifies Normo- and Asthenozoospermia.

    Science.gov (United States)

    Saraswat, Mayank; Joenväärä, Sakari; Jain, Tushar; Tomar, Anil Kumar; Sinha, Ashima; Singh, Sarman; Yadav, Savita; Renkonen, Risto

    2017-01-01

    Scarcely understood defects lead to asthenozoospermia, which results in poor fertility outcomes. Incomplete knowledge of these defects hinders the development of new therapies and reliance on interventional therapies, such as in vitro fertilization, increases. Sperm cells, being transcriptionally and translationally silent, necessitate the proteomic approach to study the sperm function. We have performed a differential proteomics analysis of human sperm and seminal plasma and identified and quantified 667 proteins in sperm and 429 proteins in seminal plasma data set, which were used for further analysis. Statistical and mathematical analysis combined with pathway analysis and self-organizing maps clustering and correlation was performed on the data set.It was found that sperm proteomic signature combined with statistical analysis as opposed to the seminal plasma proteomic signature can differentiate the normozoospermic versus the asthenozoospermic sperm samples. This is despite the results that some of the seminal plasma proteins have big fold changes among classes but they fall short of statistical significance. S-Plot of the sperm proteomic data set generated some high confidence targets, which might be implicated in sperm motility pathways. These proteins also had the area under the curve value of 0.9 or 1 in ROC curve analysis.Various pathways were either enriched in these proteomic data sets by pathway analysis or they were searched by their constituent proteins. Some of these pathways were axoneme activation and focal adhesion assembly, glycolysis, gluconeogenesis, cellular response to stress and nucleosome assembly among others. The mass spectrometric data is available via ProteomeXchange with identifier PXD004098.

  6. Proteomics in medical microbiology.

    Science.gov (United States)

    Cash, P

    2000-04-01

    The techniques of proteomics (high resolution two-dimensional electrophoresis and protein characterisation) are widely used for microbiological research to analyse global protein synthesis as an indicator of gene expression. The rapid progress in microbial proteomics has been achieved through the wide availability of whole genome sequences for a number of bacterial groups. Beyond providing a basic understanding of microbial gene expression, proteomics has also played a role in medical areas of microbiology. Progress has been made in the use of the techniques for investigating the epidemiology and taxonomy of human microbial pathogens, the identification of novel pathogenic mechanisms and the analysis of drug resistance. In each of these areas, proteomics has provided new insights that complement genomic-based investigations. This review describes the current progress in these research fields and highlights some of the technical challenges existing for the application of proteomics in medical microbiology. The latter concern the analysis of genetically heterogeneous bacterial populations and the integration of the proteomic and genomic data for these bacteria. The characterisation of the proteomes of bacterial pathogens growing in their natural hosts remains a future challenge.

  7. Proteomics in pulmonary medicine.

    Science.gov (United States)

    Bowler, Russell P; Ellison, Misoo C; Reisdorph, Nichole

    2006-08-01

    Proteomics is the study of the entire protein complement of the genome (the proteome) in a biological system. Proteomic studies require a multidisciplinary approach and have only been practical with the convergence of technical and methodologic improvements including the following: advances in mass spectrometry and genomic sequencing that now permit the identification and relative quantization of small amounts (femtomole) of nearly any single protein; new methods in gel electrophoresis that allow the detection of subtle changes in protein expression, including posttranslational modifications; automation and miniaturization that permit high-throughput analysis of clinical samples; and new bioinformatics and computational methods that facilitate analysis and interpretation of the abundant data that are generated by proteomics experiments. This convergence makes proteomics studies practical for pulmonary researchers using BAL fluid, lung tissue, blood, and exhaled breath condensates, and will facilitate the research of complex, multifactorial lung diseases such as acute lung injury and COPD. This review describes how proteomics experiments are conducted and interpreted, their limitations, and how proteomics has been used in clinical pulmonary medicine.

  8. Proteomic Analysis of Plasma from California Sea Lions (Zalophus californianus Reveals Apolipoprotein E as a Candidate Biomarker of Chronic Domoic Acid Toxicosis.

    Directory of Open Access Journals (Sweden)

    Benjamin A Neely

    Full Text Available Domoic acid toxicosis (DAT in California sea lions (Zalophus californianus is caused by exposure to the marine biotoxin domoic acid and has been linked to massive stranding events and mortality. Diagnosis is based on clinical signs in addition to the presence of domoic acid in body fluids. Chronic DAT further is characterized by reoccurring seizures progressing to status epilepticus. Diagnosis of chronic DAT is often slow and problematic, and minimally invasive tests for DAT have been the focus of numerous recent biomarker studies. The goal of this study was to retrospectively profile plasma proteins in a population of sea lions with chronic DAT and those without DAT using two dimensional gel electrophoresis to discover whether individual, multiple, or combinations of protein and clinical data could be utilized to identify sea lions with DAT. Using a training set of 32 sea lion sera, 20 proteins and their isoforms were identified that were significantly different between the two groups (p<0.05. Interestingly, 11 apolipoprotein E (ApoE charge forms were decreased in DAT samples, indicating that ApoE charge form distributions may be important in the progression of DAT. In order to develop a classifier of chronic DAT, an independent blinded test set of 20 sea lions, seven with chronic DAT, was used to validate models utilizing ApoE charge forms and eosinophil counts. The resulting support vector machine had high sensitivity (85.7% with 92.3% negative predictive value and high specificity (92.3% with 85.7% positive predictive value. These results suggest that ApoE and eosinophil counts along with machine learning can perform as a robust and accurate tool to diagnose chronic DAT. Although this analysis is specifically focused on blood biomarkers and routine clinical data, the results demonstrate promise for future studies combining additional variables in multidimensional space to create robust classifiers.

  9. Projection on Proper elements for code control: Verification, numerical convergence, and reduced models. Application to plasma turbulence simulations

    Science.gov (United States)

    Cartier-Michaud, T.; Ghendrih, P.; Sarazin, Y.; Abiteboul, J.; Bufferand, H.; Dif-Pradalier, G.; Garbet, X.; Grandgirard, V.; Latu, G.; Norscini, C.; Passeron, C.; Tamain, P.

    2016-02-01

    The Projection on Proper elements (PoPe) is a novel method of code control dedicated to (1) checking the correct implementation of models, (2) determining the convergence of numerical methods, and (3) characterizing the residual errors of any given solution at very low cost. The basic idea is to establish a bijection between a simulation and a set of equations that generate it. Recovering equations is direct and relies on a statistical measure of the weight of the various operators. This method can be used in any number of dimensions and any regime, including chaotic ones. This method also provides a procedure to design reduced models and quantify its ratio of cost to benefit. PoPe is applied to a kinetic and a fluid code of plasma turbulence.

  10. Implementation of a 3D halo neutral model in the TRANSP code and application to projected NSTX-U plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Medley, S. S. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Liu, D. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Univ. of California, Irvine, CA (United States). Dept. of Physics and Astronomy; Gorelenkova, M. V. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Heidbrink, W. W. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Univ. of California, Irvine, CA (United States). Dept. of Physics and Astronomy; Stagner, L. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Univ. of California, Irvine, CA (United States). Dept. of Physics and Astronomy

    2016-01-12

    A 3D halo neutral code developed at the Princeton Plasma Physics Laboratory and implemented for analysis using the TRANSP code is applied to projected National Spherical Torus eXperiment-Upgrade (NSTX-U plasmas). The legacy TRANSP code did not handle halo neutrals properly since they were distributed over the plasma volume rather than remaining in the vicinity of the neutral beam footprint as is actually the case. The 3D halo neutral code uses a 'beam-in-a-box' model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components produce first generation halo neutrals that are tracked through successive generations until an ionization event occurs or the descendant halos exit the box. The 3D halo neutral model and neutral particle analyzer (NPA) simulator in the TRANSP code have been benchmarked with the Fast-Ion D-Alpha simulation (FIDAsim) code, which provides Monte Carlo simulations of beam neutral injection, attenuation, halo generation, halo spatial diffusion, and photoemission processes. When using the same atomic physics database, TRANSP and FIDAsim simulations achieve excellent agreement on the spatial profile and magnitude of beam and halo neutral densities and the NPA energy spectrum. The simulations show that the halo neutral density can be comparable to the beam neutral density. These halo neutrals can double the NPA flux, but they have minor effects on the NPA energy spectrum shape. The TRANSP and FIDAsim simulations also suggest that the magnitudes of beam and halo neutral densities are relatively sensitive to the choice of the atomic physics databases.

  11. Implementation of a 3D halo neutral model in the TRANSP code and application to projected NSTX-U plasmas

    Science.gov (United States)

    Medley, S. S.; Liu, D.; Gorelenkova, M. V.; Heidbrink, W. W.; Stagner, L.

    2016-02-01

    A 3D halo neutral code developed at the Princeton Plasma Physics Laboratory and implemented for analysis using the TRANSP code is applied to projected National Spherical Torus eXperiment-Upgrade (NSTX-U plasmas). The legacy TRANSP code did not handle halo neutrals properly since they were distributed over the plasma volume rather than remaining in the vicinity of the neutral beam footprint as is actually the case. The 3D halo neutral code uses a ‘beam-in-a-box’ model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components produce first generation halo neutrals that are tracked through successive generations until an ionization event occurs or the descendant halos exit the box. The 3D halo neutral model and neutral particle analyzer (NPA) simulator in the TRANSP code have been benchmarked with the Fast-Ion D-Alpha simulation (FIDAsim) code, which provides Monte Carlo simulations of beam neutral injection, attenuation, halo generation, halo spatial diffusion, and photoemission processes. When using the same atomic physics database, TRANSP and FIDAsim simulations achieve excellent agreement on the spatial profile and magnitude of beam and halo neutral densities and the NPA energy spectrum. The simulations show that the halo neutral density can be comparable to the beam neutral density. These halo neutrals can double the NPA flux, but they have minor effects on the NPA energy spectrum shape. The TRANSP and FIDAsim simulations also suggest that the magnitudes of beam and halo neutral densities are relatively sensitive to the choice of the atomic physics databases.

  12. Proteomics applied to exercise physiology: a cutting-edge technology.

    Science.gov (United States)

    Petriz, Bernardo A; Gomes, Clarissa P; Rocha, Luiz A O; Rezende, Taia M B; Franco, Octávio L

    2012-03-01

    Exercise research has always drawn the attention of the scientific community because it can be widely applied to sport training, health improvement, and disease prevention. For many years numerous tools have been used to investigate the several physiological adaptations induced by exercise stimuli. Nowadays a closer look at the molecular mechanisms underlying metabolic pathways and muscular and cardiovascular adaptation to exercise are among the new trends in exercise physiology research. Considering this, to further understand these adaptations as well as pathology attenuation by exercise, several studies have been conducted using molecular investigations, and this trend looks set to continue. Through enormous biotechnological advances, proteomic tools have facilitated protein analysis within complex biological samples such as plasma and tissue, commonly used in exercise research. Until now, classic proteomic tools such as one- and two-dimensional polyacrylamide gel electrophoresis have been used as standard approaches to investigate proteome modulation by exercise. Furthermore, other recently developed in gel tools such as differential gel electrophoresis (DIGE) and gel-free techniques such as the protein labeling methods (ICAT, SILAC, and iTRAQ) have empowered proteomic quantitative analysis, which may successfully benefit exercise proteomic research. However, despite the three decades of 2-DE development, neither classic nor novel proteomic tools have been convincingly explored by exercise researchers. To this end, this review gives an overview of the directions in which exercise-proteome research is moving and examines the main tools that can be used as a novel strategy in exercise physiology investigation.

  13. Proteomics Research in Schizophrenia

    OpenAIRE

    2016-01-01

    Despite intense scientific efforts, the neuropathology and pathophysiology of schizophrenia are poorly understood. Proteomic studies, by testing large numbers of proteins for associations with disease, may contribute to the understanding of the molecular mechanisms of schizophrenia. They may also indicate the types and locations of cells most likely to harbor pathological alterations. Investigations using proteomic approaches have already provided much information on quantitative and qualitat...

  14. PROTEOMICS in aquaculture

    DEFF Research Database (Denmark)

    Rodrigues, Pedro M.; Silva, Tomé S.; Dias, Jorge

    2012-01-01

    growth in production is still expected for decades to come. Aquaculture is, though, a very competitive market, and a global awareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organism through a sustainable production has enhanced the importance...... nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue. This article is part of a Special Issue entitled: Farm animal proteomics....

  15. Cell Wall Proteome

    OpenAIRE

    Boudart, Georges; Minic, Zoran; Albenne, Cécile; Canut, Hervé; Jamet, Elisabeth; Pont-Lezica, Rafael F

    2007-01-01

    In this chapter, we will focus on the contribution of proteomics to the identification and determination of the structure and function of CWPs as well as discussing new perspectives in this area. The great variety of proteins found in the plant cell wall is described. Some families, such as glycoside hydrolases, proteases, lectins, and inhibitors of cell wall modifying enzymes, are discussed in detail. Examples of the use of proteomic techniques to elucidate the structure of various cell wall...

  16. The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results

    OpenAIRE

    Jones, A.R.; Eisenacher, M.; Mayer, G.; Kohlbacher, O.; Siepen, J.; Hubbard, S. J.; Selley, J. N.; Searle, B.C.; Shofstahl, J.; Seymour, S. L.; R. Julian; Binz, P.-A.; Deutsch, E. W.; Hermjakob, H.; Reisinger, F

    2012-01-01

    We report the release of mzIdentML, an exchange standard for peptide and protein identification data, designed by the Proteomics Standards Initiative. The format was developed by the Proteomics Standards Initiative in collaboration with instrument and software vendors, and the developers of the major open-source projects in proteomics. Software implementations have been developed to enable conversion from most popular proprietary and open-source formats, and mzIdentML will soon be supported b...

  17. Proteome-wide analysis and diel proteomic profiling of the cyanobacterium Arthrospira platensis PCC 8005.

    Directory of Open Access Journals (Sweden)

    Sabine Matallana-Surget

    Full Text Available The filamentous cyanobacterium Arthrospira platensis has a long history of use as a food supply and it has been used by the European Space Agency in the MELiSSA project, an artificial microecosystem which supports life during long-term manned space missions. This study assesses progress in the field of cyanobacterial shotgun proteomics and light/dark diurnal cycles by focusing on Arthrospira platensis. Several fractionation workflows including gel-free and gel-based protein/peptide fractionation procedures were used and combined with LC-MS/MS analysis, enabling the overall identification of 1306 proteins, which represents 21% coverage of the theoretical proteome. A total of 30 proteins were found to be significantly differentially regulated under light/dark growth transition. Interestingly, most of the proteins showing differential abundance were related to photosynthesis, the Calvin cycle and translation processes. A novel aspect and major achievement of this work is the successful improvement of the cyanobacterial proteome coverage using a 3D LC-MS/MS approach, based on an immobilized metal affinity chromatography, a suitable tool that enabled us to eliminate the most abundant protein, the allophycocyanin. We also demonstrated that cell growth follows a light/dark cycle in A. platensis. This preliminary proteomic study has highlighted new characteristics of the Arthrospira platensis proteome in terms of diurnal regulation.

  18. Proteome-wide analysis and diel proteomic profiling of the cyanobacterium Arthrospira platensis PCC 8005.

    Science.gov (United States)

    Matallana-Surget, Sabine; Derock, Jérémy; Leroy, Baptiste; Badri, Hanène; Deschoenmaeker, Frédéric; Wattiez, Ruddy

    2014-01-01

    The filamentous cyanobacterium Arthrospira platensis has a long history of use as a food supply and it has been used by the European Space Agency in the MELiSSA project, an artificial microecosystem which supports life during long-term manned space missions. This study assesses progress in the field of cyanobacterial shotgun proteomics and light/dark diurnal cycles by focusing on Arthrospira platensis. Several fractionation workflows including gel-free and gel-based protein/peptide fractionation procedures were used and combined with LC-MS/MS analysis, enabling the overall identification of 1306 proteins, which represents 21% coverage of the theoretical proteome. A total of 30 proteins were found to be significantly differentially regulated under light/dark growth transition. Interestingly, most of the proteins showing differential abundance were related to photosynthesis, the Calvin cycle and translation processes. A novel aspect and major achievement of this work is the successful improvement of the cyanobacterial proteome coverage using a 3D LC-MS/MS approach, based on an immobilized metal affinity chromatography, a suitable tool that enabled us to eliminate the most abundant protein, the allophycocyanin. We also demonstrated that cell growth follows a light/dark cycle in A. platensis. This preliminary proteomic study has highlighted new characteristics of the Arthrospira platensis proteome in terms of diurnal regulation.

  19. Characterization of protein complexes using targeted proteomics.

    Science.gov (United States)

    Gomez, Yassel Ramos; Gallien, Sebastien; Huerta, Vivian; van Oostrum, Jan; Domon, Bruno; Gonzalez, Luis Javier

    2014-01-01

    Biological systems are not only controlled by the abundance of individual proteins, but also by the formation of complexes and the dynamics of protein-protein interactions. The identification of the components of protein complexes can be obtained by shotgun proteomics using affinity purification coupled to mass spectrometry. Such studies include the analyses of several samples and experimental controls in order to discriminate true specific interactions from unspecific interactions and contaminants. However, shotgun proteomics have limited quantification capabilities for low abundant proteins on large sample sets due to the undersampling and the stochastic precursor ion selection. In this context, targeted proteomics constitutes a powerful analytical tool to systematically detect and quantify peptides in multiple samples, for instance those obtained from affinity purification experiments. Hypothesis-driven strategies have mainly relied on the selected reaction monitoring (SRM) technique performed on triple quadrupole instruments, which enables highly selective and sensitive measurements of peptides, acting as surrogates of the pre-selected proteins, over a wide range of concentrations. More recently, novel quantitative methods based on high resolution instruments, such as the parallel reaction monitoring (PRM) technique implemented on the quadrupole-orbitrap instrument, have arisen and provided alternatives to perform quantitative analyses with enhanced selectivity.The application of targeted proteomics to protein-protein interaction experiments from plasma and other physiological fluid samples and the inclusion of parallel reaction monitoring (PRM), combined with other recent technology developments opens a vast area for clinical application of proteomics. It is anticipated that it will reveal valuable information about specific, individual, responses against drugs, exogenous proteins or pathogens.

  20. Environmental proteomics and metallomics.

    Science.gov (United States)

    López-Barea, Juan; Gómez-Ariza, José Luis

    2006-04-01

    Monitoring environmental pollution using biomarkers requires detailed knowledge about the markers, and many only allow a partial assessment of pollution. New proteomic methods (environmental proteomics) can identify proteins that, after validation, might be useful as alternative biomarkers, although this approach also has its limitations, derived mainly from their application to non-model organisms. Initial studies using environmental proteomics were carried out in animals exposed to model pollutants, and led to the concept of protein expression signatures. Experiments have been carried out in model organisms (yeast, Arabidopsis, rat cells, or mice) exposed to model contaminants. Over the last few years, proteomics has been applied to organisms from ecosystems with different pollution levels, forming the basis of an environmental branch in proteomics. Another focus is connected with the presence of metals bound to biomolecules, which adds an additional dimension to metal-biomolecule and metalloprotein characterization - the field of metallomics. The metallomic approach considers the metallome: a whole individual metal or metalloid species within a cell or tissue. A metallomic analytical approach (MAA) is proposed as a new tool to study and identify metalloproteins.

  1. Beer and wort proteomics.

    Science.gov (United States)

    Iimure, Takashi; Kihara, Makoto; Sato, Kazuhiro

    2014-01-01

    Proteome analysis provides a way to identify proteins related to the quality traits of beer. A number of protein species in beer and wort have been identified by two-dimensional gel electrophoresis combined with enzyme digestion such as trypsin, followed by mass spectrometry analyses and/or liquid chromatography mass/mass spectrometry. In addition, low molecular weight polypeptides in beer have been identified by the combination of non-enzyme digestion and mass analyses. These data sets of various molecular weight polypeptides (i.e., proteomes) provide a platform for analyzing protein functions in beer. Several novel proteins related to beer quality traits such as foam stability and haze formation have been identified by analyzing these proteomes. Some of the proteins have been applied to the development of efficient protein or DNA markers for trait selection in malting barley breeding. In this chapter, recent proteome studies of beer and wort are reviewed, and the methods and protocols of beer and wort proteome analysis are described.

  2. Towards a functional definition of the mitochondrial human proteome

    Directory of Open Access Journals (Sweden)

    Mauro Fasano

    2016-03-01

    Full Text Available The mitochondrial human proteome project (mt-HPP was initiated by the Italian HPP group as a part of both the chromosome-centric initiative (C-HPP and the “biology and disease driven” initiative (B/D-HPP. In recent years several reports highlighted how mitochondrial biology and disease are regulated by specific interactions with non-mitochondrial proteins. Thus, it is of great relevance to extend our present view of the mitochondrial proteome not only to those proteins that are encoded by or transported to mitochondria, but also to their interactors that take part in mitochondria functionality. Here, we propose a graphical representation of the functional mitochondrial proteome by retrieving mitochondrial proteins from the NeXtProt database and adding to the network their interactors as annotated in the IntAct database. Notably, the network may represent a reference to map all the proteins that are currently being identified in mitochondrial proteomics studies.

  3. Proteomics of Foodborne Bacterial Pathogens

    Science.gov (United States)

    Fagerquist, Clifton K.

    This chapter is intended to be a relatively brief overview of proteomic techniques currently in use for the identification and analysis of microorganisms with a special emphasis on foodborne pathogens. The chapter is organized as follows. First, proteomic techniques are introduced and discussed. Second, proteomic applications are presented specifically as they relate to the identification and qualitative/quantitative analysis of foodborne pathogens.

  4. Tools for the Validation of Genomes and Transcriptomes with Proteomics data

    DEFF Research Database (Denmark)

    Pang, Chi Nam Ignatius; Aya, Carlos; Tay, Aidan;

    Aims With the large amount of genomics and proteomics data currently available, there remains a lack of tools to integrate data from these two fields. This project aims to provide a ‘nexus’ for integrating genomics and transcriptomics data generated from next-generation sequencing with proteomics...

  5. EXPLORATORY PLASMA BIOCHEMISTRY REFERENCE INTERVALS FOR URAL OWLS (STRIX URALENSIS, PALLAS 1771) FROM THE AUSTRIAN REINTRODUCTION PROJECT.

    Science.gov (United States)

    Scope, Alexandra; Schwendenwein, Ilse; Stanclova, Gabriela; Vobornik, Angela; Zink, Richard

    2016-06-01

    The Ural owl (Strix uralensis) is the biggest forest-living owl in Austria; however, it became extinct in Austria through poaching and habitat loss more than half a century ago. The birds examined in the present study were breeding pairs from the reintroduction project with the aim of determining exploratory plasma biochemistry reference intervals in Ural owls and evaluating the amount of biological variation between seasons, sexes, and ages. A total of 45 birds were sampled, including 13 adult males, 14 adult females, and 18 juvenile birds. Remarkably, almost all of the analytes showed significant differences between the subgroups, primarily between seasons, followed by age and sex. Only creatinkinase, glucose, lactatdehydrogenase, and triglycerides did not show any significant variations. Despite partitioning of reference values into subgroups according to biological variation diminishing the number of reference individuals in the respective groups, the resulting smaller reference intervals will improve medical assessment. The results of the present study once again demonstrate that significant seasonal fluctuations must be expected and considered in the interpretation. It can be assumed that these differences are probably even greater in free-range birds with considerable changes in food quantity and quality during and between years.

  6. Proteomics in uveal melanoma.

    LENUS (Irish Health Repository)

    Ramasamy, Pathma

    2014-01-01

    Uveal melanoma is the most common primary intraocular malignancy in adults, with an incidence of 5-7 per million per year. It is associated with the development of metastasis in about 50% of cases, and 40% of patients with uveal melanoma die of metastatic disease despite successful treatment of the primary tumour. The survival rates at 5, 10 and 15 years are 65%, 50% and 45% respectively. Unlike progress made in many other areas of cancer, uveal melanoma is still poorly understood and survival rates have remained similar over the past 25 years. Recently, advances made in molecular genetics have improved our understanding of this disease and stratification of patients into low risk and high risk for developing metastasis. However, only a limited number of studies have been performed using proteomic methods. This review will give an overview of various proteomic technologies currently employed in life sciences research, and discuss proteomic studies of uveal melanoma.

  7. Establishing Substantial Equivalence: Proteomics

    Science.gov (United States)

    Lovegrove, Alison; Salt, Louise; Shewry, Peter R.

    Wheat is a major crop in world agriculture and is consumed after processing into a range of food products. It is therefore of great importance to determine the consequences (intended and unintended) of transgenesis in wheat and whether genetically modified lines are substantially equivalent to those produced by conventional plant breeding. Proteomic analysis is one of several approaches which can be used to address these questions. Two-dimensional PAGE (2D PAGE) remains the most widely available method for proteomic analysis, but is notoriously difficult to reproduce between laboratories. We therefore describe methods which have been developed as standard operating procedures in our laboratory to ensure the reproducibility of proteomic analyses of wheat using 2D PAGE analysis of grain proteins.

  8. Proteomics and insect immunity

    Directory of Open Access Journals (Sweden)

    L Shi

    2006-01-01

    Full Text Available Insect innate immunity is both a model for vertebrate immunity as well as a key system that impactsmedically important pathogens that are transmitted by insects. Recent developments in proteomics andprotein identification techniques combined with the completion of genome sequences for Anophelesgambiae and Drosophila melanogaster provided the tools for examining insect immunity at a new level ofmolecular detail. Application of proteomics to insect immunity resulted in predictions of new roles inimmunity for proteins already known in other contexts (e.g. ferritin, transferrin, Chi-lectins and helped totarget specific members of multi-gene families that respond to different pathogens (e.g. serine proteases,thioester proteins. In addition, proteomics studies verify that post-translational modifications play a keyrole in insect immunity since many of the identified proteins are modified in some way. These studiescomplement recent work on insect transcriptomes and provide new directions for further investigation ofinnate immunity.

  9. Quest for novel cardiovascular biomarkers by proteomic analysis.

    Science.gov (United States)

    Vivanco, Fernando; Martín-Ventura, Jose L; Duran, Mari Carmen; Barderas, Maria G; Blanco-Colio, Luis; Dardé, Verónica M; Mas, Sebastián; Meilhac, Olivier; Michel, Jean B; Tuñón, Jose; Egido, Jesús

    2005-01-01

    Atherosclerosis, and the resulting coronary heart disease and stroke, is the most common cause of death in developed countries. Atherosclerosis is an inflammatory process that results in the development of complex lesions or plaques that protrude into the arterial lumen. Plaque rupture and thrombosis result in the acute clinical complications of myocardial infarction (MI) and stroke. Although certain risk factors (dyslipidemias, diabetes, hypertension) and humoral markers of plaque vulnerability (C-reactive protein, interleukin-6, 10 and 18, CD40L) have been identified, a highly sensitive and specific biomarker or protein profile, which could provide information on the stability/vulnerability of atherosclerotic lesions, remains to be identified. In this review, we report several proteomic approaches which have been applied to circulating or resident cells, atherosclerotic plaques or plasma, in the search for new proteins that could be used as cardiovascular biomarkers. First, an example using a differential proteomic approach (2-DE and MS) comparing the secretome from control mammary arteries and atherosclerotic plaques is displayed. Among the different proteins identified, we showed that low levels of HSP-27 could be a potential marker of atherosclerosis. Second, we have revised several studies performed in cells involved in the pathogenesis of atherosclerosis (foam cells and smooth muscle cells). Another approach consists of performing proteomic analysis on circulating cells or plasma, which will provide a global view of the whole body response to atherosclerotic aggression. Circulating cells can bear information reflecting directly an inflammatory or pro-coagulant state related to the pathology. As an illustration, we report that circulating monocytes and plasma in patients with acute coronary syndromes has disclosed that mature Cathepsin D is increased both in the plasma and monocytes of these patients. Finally, the problems of applying proteomic approach

  10. Development of Energy Efficient, Multi-Channel, Pulsed Plasma Generator for High-Speed Flow Control by Localized Arc Filament Plasma Actuators Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The research team at The Ohio State University has been developing technologies to suppress jet noise using localized arc filament plasma actuators and are in the...

  11. [Proteomics in infectious diseases].

    Science.gov (United States)

    Quero, Sara; Párraga-Niño, Noemí; García-Núñez, Marian; Sabrià, Miquel

    2016-04-01

    Infectious diseases have a high incidence in the population, causing a major impact on global health. In vitro culture of microorganisms is the first technique applied for infection diagnosis which is laborious and time consuming. In recent decades, efforts have been focused on the applicability of "Omics" sciences, highlighting the progress provided by proteomic techniques in the field of infectious diseases. This review describes the management, processing and analysis of biological samples for proteomic research. Copyright © 2014 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  12. Multimarker proteomic profiling for the prediction of cardiovascular mortality in patients with chronic heart failure.

    Directory of Open Access Journals (Sweden)

    Gilles Lemesle

    Full Text Available Risk stratification of patients with systolic chronic heart failure (HF is critical to better identify those who may benefit from invasive therapeutic strategies such as cardiac transplantation. Proteomics has been used to provide prognostic information in various diseases. Our aim was to investigate the potential value of plasma proteomic profiling for risk stratification in HF. A proteomic profiling using surface enhanced laser desorption ionization - time of flight - mass spectrometry was performed in a case/control discovery population of 198 patients with systolic HF (left ventricular ejection fraction <45%: 99 patients who died from cardiovascular cause within 3 years and 99 patients alive at 3 years. Proteomic scores predicting cardiovascular death were developed using 3 regression methods: support vector machine, sparse partial least square discriminant analysis, and lasso logistic regression. Forty two ion m/z peaks were differentially intense between cases and controls in the discovery population and were used to develop proteomic scores. In the validation population, score levels were higher in patients who subsequently died within 3 years. Similar areas under the curves (0.66 - 0.68 were observed for the 3 methods. After adjustment on confounders, proteomic scores remained significantly associated with cardiovascular mortality. Use of the proteomic scores allowed a significant improvement in discrimination of HF patients as determined by integrated discrimination improvement and net reclassification improvement indexes. In conclusion, proteomic analysis of plasma proteins may help to improve risk prediction in HF patients.

  13. Red blood cell (RBC) membrane proteomics--Part I: Proteomics and RBC physiology.

    Science.gov (United States)

    Pasini, Erica M; Lutz, Hans U; Mann, Matthias; Thomas, Alan W

    2010-01-03

    Membrane proteomics is concerned with accurately and sensitively identifying molecules involved in cell compartmentalisation, including those controlling the interface between the cell and the outside world. The high lipid content of the environment in which these proteins are found often causes a particular set of problems that must be overcome when isolating the required material before effective HPLC-MS approaches can be performed. The membrane is an unusually dynamic cellular structure since it interacts with an ever changing environment. A full understanding of this critical cell component will ultimately require, in addition to proteomics, lipidomics, glycomics, interactomics and study of post-translational modifications. Devoid of nucleus and organelles in mammalian species other than camelids, and constantly in motion in the blood stream, red blood cells (RBCs) are the sole mammalian oxygen transporter. The fact that mature mammalian RBCs have no internal membrane-bound organelles, somewhat simplifies proteomics analysis of the plasma membrane and the fact that it has no nucleus disqualifies microarray based methods. Proteomics has the potential to provide a better understanding of this critical interface, and thereby assist in identifying new approaches to diseases.

  14. Improved Recovery and Identification of Membrane Proteins from Rat Hepatic Cells using a Centrifugal Proteomic Reactor*

    Science.gov (United States)

    Zhou, Hu; Wang, Fangjun; Wang, Yuwei; Ning, Zhibin; Hou, Weimin; Wright, Theodore G.; Sundaram, Meenakshi; Zhong, Shumei; Yao, Zemin; Figeys, Daniel

    2011-01-01

    Despite their importance in many biological processes, membrane proteins are underrepresented in proteomic analysis because of their poor solubility (hydrophobicity) and often low abundance. We describe a novel approach for the identification of plasma membrane proteins and intracellular microsomal proteins that combines membrane fractionation, a centrifugal proteomic reactor for streamlined protein extraction, protein digestion and fractionation by centrifugation, and high performance liquid chromatography-electrospray ionization-tandem MS. The performance of this approach was illustrated for the study of the proteome of ER and Golgi microsomal membranes in rat hepatic cells. The centrifugal proteomic reactor identified 945 plasma membrane proteins and 955 microsomal membrane proteins, of which 63 and 47% were predicted as bona fide membrane proteins, respectively. Among these proteins, >800 proteins were undetectable by the conventional in-gel digestion approach. The majority of the membrane proteins only identified by the centrifugal proteomic reactor were proteins with ≥2 transmembrane segments or proteins with high molecular mass (e.g. >150 kDa) and hydrophobicity. The improved proteomic reactor allowed the detection of a group of endocytic and/or signaling receptor proteins on the plasma membrane, as well as apolipoproteins and glycerolipid synthesis enzymes that play a role in the assembly and secretion of apolipoprotein B100-containing very low density lipoproteins. Thus, the centrifugal proteomic reactor offers a new analytical tool for structure and function studies of membrane proteins involved in lipid and lipoprotein metabolism. PMID:21749988

  15. Improved recovery and identification of membrane proteins from rat hepatic cells using a centrifugal proteomic reactor.

    Science.gov (United States)

    Zhou, Hu; Wang, Fangjun; Wang, Yuwei; Ning, Zhibin; Hou, Weimin; Wright, Theodore G; Sundaram, Meenakshi; Zhong, Shumei; Yao, Zemin; Figeys, Daniel

    2011-10-01

    Despite their importance in many biological processes, membrane proteins are underrepresented in proteomic analysis because of their poor solubility (hydrophobicity) and often low abundance. We describe a novel approach for the identification of plasma membrane proteins and intracellular microsomal proteins that combines membrane fractionation, a centrifugal proteomic reactor for streamlined protein extraction, protein digestion and fractionation by centrifugation, and high performance liquid chromatography-electrospray ionization-tandem MS. The performance of this approach was illustrated for the study of the proteome of ER and Golgi microsomal membranes in rat hepatic cells. The centrifugal proteomic reactor identified 945 plasma membrane proteins and 955 microsomal membrane proteins, of which 63 and 47% were predicted as bona fide membrane proteins, respectively. Among these proteins, >800 proteins were undetectable by the conventional in-gel digestion approach. The majority of the membrane proteins only identified by the centrifugal proteomic reactor were proteins with ≥ 2 transmembrane segments or proteins with high molecular mass (e.g. >150 kDa) and hydrophobicity. The improved proteomic reactor allowed the detection of a group of endocytic and/or signaling receptor proteins on the plasma membrane, as well as apolipoproteins and glycerolipid synthesis enzymes that play a role in the assembly and secretion of apolipoprotein B100-containing very low density lipoproteins. Thus, the centrifugal proteomic reactor offers a new analytical tool for structure and function studies of membrane proteins involved in lipid and lipoprotein metabolism.

  16. The minotaur proteome

    DEFF Research Database (Denmark)

    Bunkenborg, Jakob; García, Guadalupe Espadas; Paz, Marcia Ivonne Peña;

    2010-01-01

    Cell culture is a fundamental tool in proteomics where mammalian cells are cultured in vitro using a growth medium often supplemented with 5-15% FBS. Contamination by bovine proteins is difficult to avoid because of adherence to the plastic vessel and the cultured cells. We have generated peptide...

  17. Shaping the mitochondrial proteome.

    NARCIS (Netherlands)

    Gabaldon, T.; Huynen, M.A.

    2004-01-01

    Mitochondria are eukaryotic organelles that originated from a single bacterial endosymbiosis some 2 billion years ago. The transition from the ancestral endosymbiont to the modern mitochondrion has been accompanied by major changes in its protein content, the so-called proteome. These changes

  18. The proteome of lysosomes.

    Science.gov (United States)

    Schröder, Bernd A; Wrocklage, Christian; Hasilik, Andrej; Saftig, Paul

    2010-11-01

    Lysosomes are organelles of eukaryotic cells that are critically involved in the degradation of macromolecules mainly delivered by endocytosis and autophagocytosis. Degradation is achieved by more than 60 hydrolases sequestered by a single phospholipid bilayer. The lysosomal membrane facilitates interaction and fusion with other compartments and harbours transport proteins catalysing the export of catabolites, thereby allowing their recycling. Lysosomal proteins have been addressed in various proteomic studies that are compared in this review regarding the source of material, the organelle/protein purification scheme, the proteomic methodology applied and the proteins identified. Distinguishing true constituents of an organelle from co-purifying contaminants is a central issue in subcellular proteomics, with additional implications for lysosomes as being the site of degradation of many cellular and extracellular proteins. Although many of the lysosomal hydrolases were identified by classical biochemical approaches, the knowledge about the protein composition of the lysosomal membrane has remained fragmentary for a long time. Using proteomics many novel lysosomal candidate proteins have been discovered and it can be expected that their functional characterisation will help to understand functions of lysosomes at a molecular level that have been characterised only phenomenologically so far and to generally deepen our understanding of this indispensable organelle.

  19. Xylem sap proteomics.

    Science.gov (United States)

    de Bernonville, Thomas Dugé; Albenne, Cécile; Arlat, Matthieu; Hoffmann, Laurent; Lauber, Emmanuelle; Jamet, Elisabeth

    2014-01-01

    Proteomic analysis of xylem sap has recently become a major field of interest to understand several biological questions related to plant development and responses to environmental clues. The xylem sap appears as a dynamic fluid undergoing changes in its proteome upon abiotic and biotic stresses. Unlike cell compartments which are amenable to purification in sufficient amount prior to proteomic analysis, the xylem sap has to be collected in particular conditions to avoid contamination by intracellular proteins and to obtain enough material. A model plant like Arabidopsis thaliana is not suitable for such an analysis because efficient harvesting of xylem sap is difficult. The analysis of the xylem sap proteome also requires specific procedures to concentrate proteins and to focus on proteins predicted to be secreted. Indeed, xylem sap proteins appear to be synthesized and secreted in the root stele or to originate from dying differentiated xylem cells. This chapter describes protocols to collect xylem sap from Brassica species and to prepare total and N-glycoprotein extracts for identification of proteins by mass spectrometry analyses and bioinformatics.

  20. Analyzing the platelet proteome.

    Science.gov (United States)

    García, Angel; Zitzmann, Nicole; Watson, Steve P

    2004-08-01

    During the last 10 years, mass spectrometry (MS) has become a key tool for protein analysis and has underpinned the emerging field of proteomics. Using high-throughput tandem MS/MS following protein separation, it is potentially possible to analyze hundreds to thousands of proteins in a sample at a time. This technology can be used to analyze the protein content (i.e., the proteome) of any cell or tissue and complements the powerful field of genomics. The technology is particularly suitable for platelets because of the absence of a nucleus. Cellular proteins can be separated by either gel-based methods such as two-dimensional gel electrophoresis or one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis followed by liquid chromatography (LC) -MS/MS or by multidimensional LC-MS/MS. Prefractionation techniques, such as subcellular fractionations or immunoprecipitations, can be used to improve the analysis. Each method has particular advantages and disadvantages. Proteomics can be used to compare the proteome of basal and diseased platelets, helping to reveal information on the molecular basis of the disease.

  1. Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

    Science.gov (United States)

    Deutsch, Eric W; Orchard, Sandra; Binz, Pierre-Alain; Bittremieux, Wout; Eisenacher, Martin; Hermjakob, Henning; Kawano, Shin; Lam, Henry; Mayer, Gerhard; Menschaert, Gerben; Perez-Riverol, Yasset; Salek, Reza M; Tabb, David L; Tenzer, Stefan; Vizcaíno, Juan Antonio; Walzer, Mathias; Jones, Andrew R

    2017-09-15

    The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthermore, new standards are currently either in the final stages of completion (proBed and proBAM for proteogenomics results as well as PEFF) or in early stages of design (a spectral library standard format, a universal spectrum identifier, the qcML quality control format, and the Protein Expression Interface (PROXI) web services Application Programming Interface). In this work we review the current status of all of these aspects of the PSI, describe synergies with other efforts such as the ProteomeXchange Consortium, the Human Proteome Project, and the metabolomics community, and provide a look at future directions of the PSI.

  2. jPOSTrepo: an international standard data repository for proteomes

    Science.gov (United States)

    Okuda, Shujiro; Watanabe, Yu; Moriya, Yuki; Kawano, Shin; Yamamoto, Tadashi; Matsumoto, Masaki; Takami, Tomoyo; Kobayashi, Daiki; Araki, Norie; Yoshizawa, Akiyasu C.; Tabata, Tsuyoshi; Sugiyama, Naoyuki; Goto, Susumu; Ishihama, Yasushi

    2017-01-01

    Major advancements have recently been made in mass spectrometry-based proteomics, yielding an increasing number of datasets from various proteomics projects worldwide. In order to facilitate the sharing and reuse of promising datasets, it is important to construct appropriate, high-quality public data repositories. jPOSTrepo (https://repository.jpostdb.org/) has successfully implemented several unique features, including high-speed file uploading, flexible file management and easy-to-use interfaces. This repository has been launched as a public repository containing various proteomic datasets and is available for researchers worldwide. In addition, our repository has joined the ProteomeXchange consortium, which includes the most popular public repositories such as PRIDE in Europe for MS/MS datasets and PASSEL for SRM datasets in the USA. Later MassIVE was introduced in the USA and accepted into the ProteomeXchange, as was our repository in July 2016, providing important datasets from Asia/Oceania. Accordingly, this repository thus contributes to a global alliance to share and store all datasets from a wide variety of proteomics experiments. Thus, the repository is expected to become a major repository, particularly for data collected in the Asia/Oceania region. PMID:27899654

  3. Market opportunity in computational proteomics.

    Science.gov (United States)

    Razvi, Enal

    2002-03-01

    The current exuberance on the potential of proteomics as a means to deploy the wealth of the human genome is expected to last into the coming years. Unlike the genome, a finite entity with a fixed number of base pairs of the genetic material, the proteome is "plastic", changing throughout growth and development and environmental stresses, as well as in pathological situations. Our proteomes change over time, and therefore there is no one proteome; the proteome is for practical purposes an infinite entity. It is therefore crucial to build systems that are capable of manipulating the information content that is the proteome, thence the need for computational proteomics as a discipline. In this Market View article, we present the industry landscape that is emerging in the computational proteomics space. This space is still in its infancy and for the most part undefined; therefore we seek to present the market opportunity in informatics in the drug discovery space and then extend that to an examination of industry trends in proteomics. Thus, the gestalt is a set of predictions as to the evolution of the landscape in computational proteomics over the coming years.

  4. Proteome-Wide Analysis and Diel Proteomic Profiling of the Cyanobacterium Arthrospira platensis PCC 8005

    OpenAIRE

    2014-01-01

    The filamentous cyanobacterium Arthrospira platensis has a long history of use as a food supply and it has been used by the European Space Agency in the MELiSSA project, an artificial microecosystem which supports life during long-term manned space missions. This study assesses progress in the field of cyanobacterial shotgun proteomics and light/dark diurnal cycles by focusing on Arthrospira platensis. Several fractionation workflows including gel-free and gel-based protein/peptide fractionat...

  5. Micro Plasma Spectrometer Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The need for electrostatic analyzers to measure ion and electron fluxes in near-Earth space is nearly ubiquitous in Heliophysics missions. In the latest example,...

  6. Advancing cell biology through proteomics in space and time (PROSPECTS).

    Science.gov (United States)

    Lamond, Angus I; Uhlen, Mathias; Horning, Stevan; Makarov, Alexander; Robinson, Carol V; Serrano, Luis; Hartl, F Ulrich; Baumeister, Wolfgang; Werenskiold, Anne Katrin; Andersen, Jens S; Vorm, Ole; Linial, Michal; Aebersold, Ruedi; Mann, Matthias

    2012-03-01

    The term "proteomics" encompasses the large-scale detection and analysis of proteins and their post-translational modifications. Driven by major improvements in mass spectrometric instrumentation, methodology, and data analysis, the proteomics field has burgeoned in recent years. It now provides a range of sensitive and quantitative approaches for measuring protein structures and dynamics that promise to revolutionize our understanding of cell biology and molecular mechanisms in both human cells and model organisms. The Proteomics Specification in Time and Space (PROSPECTS) Network is a unique EU-funded project that brings together leading European research groups, spanning from instrumentation to biomedicine, in a collaborative five year initiative to develop new methods and applications for the functional analysis of cellular proteins. This special issue of Molecular and Cellular Proteomics presents 16 research papers reporting major recent progress by the PROSPECTS groups, including improvements to the resolution and sensitivity of the Orbitrap family of mass spectrometers, systematic detection of proteins using highly characterized antibody collections, and new methods for absolute as well as relative quantification of protein levels. Manuscripts in this issue exemplify approaches for performing quantitative measurements of cell proteomes and for studying their dynamic responses to perturbation, both during normal cellular responses and in disease mechanisms. Here we present a perspective on how the proteomics field is moving beyond simply identifying proteins with high sensitivity toward providing a powerful and versatile set of assay systems for characterizing proteome dynamics and thereby creating a new "third generation" proteomics strategy that offers an indispensible tool for cell biology and molecular medicine.

  7. Proteome research in food science.

    Science.gov (United States)

    Pischetsrieder, Monika; Baeuerlein, Rainer

    2009-09-01

    The proteome is the totality of proteins present in a biological sample. In contrast to the static genome, the proteome is highly dynamic, influenced by the genome and many external factors, such as the state of development, tissue type, metabolic state, and various interactions. Thus, the proteome reflects very closely the biological (and chemical) processes occurring in a system. For proteome analysis, gel based and shotgun methods are most widely applied. Because of the potential to generate a systematic view of protein composition and biological as well as chemical interactions, the application of proteome analysis in food science is steadily growing. This tutorial review introduces several fields in food science, where proteomics has been successfully applied: analysis of food composition, safety assessment of genetically modified food, the search for marker proteins for food authentication, identification of food allergens, systematic analysis of the physiological activity of food, analysis of the effects of processing on food proteins and the improvement of food quality.

  8. An introduction to proteome bioinformatics.

    Science.gov (United States)

    Jones, Andrew R; Hubbard, Simon J

    2010-01-01

    This book is part of the Methods in Molecular Biology series, and provides a general overview of computational approaches used in proteome research. In this chapter, we give an overview of the scope of the book in terms of current proteomics experimental techniques and the reasons why computational approaches are needed. We then give a summary of each chapter, which together provide a picture of the state of the art in proteome bioinformatics research.

  9. Organization of Proteomics Data With YassDB

    DEFF Research Database (Denmark)

    Lind-Thomsen, Allan; Laukens, Kris; Matthiesen, Rune

    2007-01-01

    In recent years the organization of mass spectrometry (MS) data obtained in large-scale proteomics projects became an important issue. This has catalyzed the development of a few different database schemes for storing MS data, as well as some dedicated user interfaces. However, many...

  10. Plant redox proteomics

    DEFF Research Database (Denmark)

    Navrot, Nicolas; Finnie, Christine; Svensson, Birte

    2011-01-01

    In common with other aerobic organisms, plants are exposed to reactive oxygen species resulting in formation of post-translational modifications related to protein oxidoreduction (redox PTMs) that may inflict oxidative protein damage. Accumulating evidence also underscores the importance of redox...... PTMs in regulating enzymatic activities and controlling biological processes in plants. Notably, proteins controlling the cellular redox state, e.g. thioredoxin and glutaredoxin, appear to play dual roles to maintain oxidative stress resistance and regulate signal transduction pathways via redox PTMs....... To get a comprehensive overview of these types of redox-regulated pathways there is therefore an emerging interest to monitor changes in redox PTMs on a proteome scale. Compared to some other PTMs, e.g. protein phosphorylation, redox PTMs have received less attention in plant proteome analysis, possibly...

  11. Pre-fractionation strategies to resolve pea (Pisum sativum) sub-proteomes

    Science.gov (United States)

    Meisrimler, Claudia-Nicole; Menckhoff, Ljiljana; Kukavica, Biljana M.; Lüthje, Sabine

    2015-01-01

    Legumes are important crop plants and pea (Pisum sativum L.) has been investigated as a model with respect to several physiological aspects. The sequencing of the pea genome has not been completed. Therefore, proteomic approaches are currently limited. Nevertheless, the increasing numbers of available EST-databases as well as the high homology of the pea and medicago genome (Medicago truncatula Gaertner) allow the successful identification of proteins. Due to the un-sequenced pea genome, pre-fractionation approaches have been used in pea proteomic surveys in the past. Aside from a number of selective proteome studies on crude extracts and the chloroplast, few studies have targeted other components such as the pea secretome, an important sub-proteome of interest due to its role in abiotic and biotic stress processes. The secretome itself can be further divided into different sub-proteomes (plasma membrane, apoplast, cell wall proteins). Cell fractionation in combination with different gel-electrophoresis, chromatography methods and protein identification by mass spectrometry are important partners to gain insight into pea sub-proteomes, post-translational modifications and protein functions. Overall, pea proteomics needs to link numerous existing physiological and biochemical data to gain further insight into adaptation processes, which play important roles in field applications. Future developments and directions in pea proteomics are discussed. PMID:26539198

  12. Pre-fractionation strategies to resolve pea (Pisum sativum sub-proteomes

    Directory of Open Access Journals (Sweden)

    Claudia Nicole Meisrimler

    2015-10-01

    Full Text Available Legumes are important crop plants and pea (Pisum sativum L. has been investigated as a model with respect to several physiological aspects. The sequencing of the pea genome has not been completed. Therefore, proteomic approaches are currently limited. Nevertheless, the increasing numbers of available EST-databases as well as the high homology of the pea and medicago genome (Medicago truncatula G. allow the successful identification of proteins. Due to the un-sequenced pea genome, pre-fractionation approaches have been used in pea proteomic surveys in the past. Aside from a number of selective proteome studies on crude extracts and the chloroplast, few studies have targeted other components such as the pea secretome, an important sub-proteome of interest due to its role in abiotic and biotic stress processes. The secretome itself can be further divided into different sub-proteomes (plasma membrane, apoplast, cell wall proteins. Cell fractionation in combination with different gel-electrophoresis, chromatography methods and protein identification by mass spectrometry are important partners to gain insight into pea sub-proteomes, post-translational modifications and protein functions. Overall, pea proteomics needs to link numerous existing physiological and biochemical data to gain further insight into adaptation processes, which play important roles in field applications. Future developments and directions in pea proteomics are discussed.

  13. Calorimetric monitoring of the serum proteome in schizophrenia patients

    Energy Technology Data Exchange (ETDEWEB)

    Krumova, Sashka [Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, Sofia 1113 (Bulgaria); Rukova, Blaga [Department of Medical Genetics, Medical University of Sofia, 2 Zdrave Str., Sofia 1431 (Bulgaria); Todinova, Svetla [Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, Sofia 1113 (Bulgaria); Gartcheva, Lidia [National Specialized Hospital for Active Treating of Haematological Diseases, 6 Plovdivsko pole Str., Sofia 1756 (Bulgaria); Milanova, Vihra [Department of Psychiatry, Medical University of Sofia, 1 Sv. Georgi Sofiiski Str., Sofia 1431 (Bulgaria); Toncheva, Draga [Department of Medical Genetics, Medical University of Sofia, 2 Zdrave Str., Sofia 1431 (Bulgaria); Taneva, Stefka G., E-mail: stefka.germanova@ehu.es [Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, Sofia 1113 (Bulgaria)

    2013-11-20

    Highlights: • DSC reveals modified thermal behavior of blood serum from schizophrenic patients. • The high-abundance portion of the serum proteome is thermally stabilized in Sz. • The Sz plasma thermograms are classified in four distinct calorimetric groups. • The effectiveness of drug treatment correlates with the plasma thermodynamic behavior. - Abstract: Schizophrenia (Sz) is a multifactorial mental disorder with high frequency. Due to its chronic and relapsing nature there is a strong need for biomarkers for early psychosis detection and objective evaluation of drug (usually antipsychotics) treatment effect. Here differential scanning calorimetry (DSC) is applied to thermodynamically characterize the blood serum proteome of paranoid schizophrenia patients on routine antipsychotic treatment in comparison to healthy controls. DSC revealed significant modifications in the thermodynamic behavior of blood sera from Sz patients, the overall thermal profile being changed in all Sz cases under study. The calorimetric profiles were classified in four distinct groups, reflecting different thermal stabilization of the high-abundance portion of the serum proteome. The observed positive (thermograms becoming closer to the healthy profile) or negative (thermograms deviating stronger from the healthy profile) proteome thermal stability switches and the Sz thermograms persistence in patients’ follow-up corresponded well with the effect of drug treatment.

  14. Microfluidic Analytical Separator for Proteomics Project

    Data.gov (United States)

    National Aeronautics and Space Administration — SHOT proposes an innovative microfluidic device designed to effect a 2-dimensional resolution of a mixture of proteins based on isoelectric point (pI) and molecular...

  15. Microfluidic Analytical Separator for Proteomics Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed innovation is a microfluidic device designed to effect a 2-dimensional resolution of a mixture of proteins based on isoelectric point (pI) and molecular...

  16. Plasma Sensor for High Bandwidth Mass-Flow Measurements at High Mach Numbers with RF Link Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposal is aimed at the development of a miniature high bandwidth (1 MHz class) plasma sensor for flow measurements at high enthalpies. This device uses a...

  17. Changes in plasma protein levels as an early indication of a bloodstream infection

    Science.gov (United States)

    Joenväärä, Sakari; Kaartinen, Johanna; Järvinen, Asko; Renkonen, Risto

    2017-01-01

    Blood culture is the primary diagnostic test performed in a suspicion of bloodstream infection to detect the presence of microorganisms and direct the treatment. However, blood culture is slow and time consuming method to detect blood stream infections or separate septic and/or bacteremic patients from others with less serious febrile disease. Plasma proteomics, despite its challenges, remains an important source for early biomarkers for systemic diseases and might show changes before direct evidence from bacteria can be obtained. We have performed a plasma proteomic analysis, simultaneously at the time of blood culture sampling from ten blood culture positive and ten blood culture negative patients, and quantified 172 proteins with two or more unique peptides. Principal components analysis, Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) and ROC curve analysis were performed to select protein(s) features which can classify the two groups of samples. We propose a number of candidates which qualify as potential biomarkers to select the blood culture positive cases from negative ones. Pathway analysis by two methods revealed complement activation, phagocytosis pathway and alterations in lipid metabolism as enriched pathways which are relevant for the condition. Data are available via ProteomeXchange with identifier PXD005022. PMID:28235076

  18. A novel method for sample preparation of fresh lung cancer tissue for proteomics analysis by tumor cell enrichment and removal of blood contaminants

    OpenAIRE

    Orre Lotta; Bergman Per; Elmberger Göran; Pernemalm Maria; De Petris Luigi; Lewensohn Rolf; Lehtiö Janne

    2010-01-01

    Abstract Background In-depth proteomics analyses of tumors are frequently biased by the presence of blood components and stromal contamination, which leads to large experimental variation and decreases the proteome coverage. We have established a reproducible method to prepare freshly collected lung tumors for proteomics analysis, aiming at tumor cell enrichment and reduction of plasma protein contamination. We obtained enriched tumor-cell suspensions (ETS) from six lung cancer cases (two ade...

  19. The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data

    Directory of Open Access Journals (Sweden)

    Rolf Apweiler

    2006-04-01

    Full Text Available The Proteomics Standards Initiative (PSI aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Initially the fields of protein–protein interactions (PPI and mass spectroscopy have been targeted and the inaugural meeting of the PSI addressed the questions of data storage and exchange in both of these areas. The PPI group rapidly reached consensus as to the minimum requirements for a data exchange model; an XML draft is now being produced. The mass spectroscopy group have achieved major advances in the definition of a required data model and working groups are currently taking these discussions further. A further meeting is planned in January 2003 to advance both these projects.

  20. Organization of Proteomics Data With YassDB

    DEFF Research Database (Denmark)

    Lind-Thomsen, Allan; Laukens, Kris; Matthiesen, Rune

    2007-01-01

    In recent years the organization of mass spectrometry (MS) data obtained in large-scale proteomics projects became an important issue. This has catalyzed the development of a few different database schemes for storing MS data, as well as some dedicated user interfaces. However, many of these proj......In recent years the organization of mass spectrometry (MS) data obtained in large-scale proteomics projects became an important issue. This has catalyzed the development of a few different database schemes for storing MS data, as well as some dedicated user interfaces. However, many...... of these projects are still rather immature and often do not cover all needs. Because our needs were quite specific, it was necessary to build a database that accommodates all the major types of experiments generated in house and that could be easily extended by new modules made by collaborators or students...

  1. Aptamer-based multiplexed proteomic technology for biomarker discovery.

    Directory of Open Access Journals (Sweden)

    Larry Gold

    Full Text Available BACKGROUND: The interrogation of proteomes ("proteomics" in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology and medicine. METHODOLOGY/PRINCIPAL FINDINGS: We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 µL of serum or plasma. Our current assay measures 813 proteins with low limits of detection (1 pM median, 7 logs of overall dynamic range (~100 fM-1 µM, and 5% median coefficient of variation. This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected. Proteins in complex matrices such as plasma are measured with a process that transforms a signature of protein concentrations into a corresponding signature of DNA aptamer concentrations, which is quantified on a DNA microarray. Our assay takes advantage of the dual nature of aptamers as both folded protein-binding entities with defined shapes and unique nucleotide sequences recognizable by specific hybridization probes. To demonstrate the utility of our proteomics biomarker discovery technology, we applied it to a clinical study of chronic kidney disease (CKD. We identified two well known CKD biomarkers as well as an additional 58 potential CKD biomarkers. These results demonstrate the potential utility of our technology to rapidly discover unique protein signatures characteristic of various disease states. CONCLUSIONS/SIGNIFICANCE: We describe a versatile and powerful tool that allows large-scale comparison of proteome profiles among discrete populations. This unbiased and highly multiplexed search engine will enable the discovery of novel biomarkers in a manner that is unencumbered by our incomplete knowledge of biology, thereby helping to advance the next

  2. A comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage.

    Science.gov (United States)

    Vialas, Vital; Sun, Zhi; Reales-Calderón, Jose A; Hernáez, María L; Casas, Vanessa; Carrascal, Montserrat; Abián, Joaquín; Monteoliva, Lucía; Deutsch, Eric W; Moritz, Robert L; Gil, Concha

    2016-01-10

    To provide new and expanded proteome documentation of the opportunistically pathogen Candida albicans, we have developed new protein extraction and analysis routines to provide a new, extended and enhanced version of the C. albicans PeptideAtlas. Two new datasets, resulting from experiments consisting of exhaustive subcellular fractionations and different growing conditions, plus two additional datasets from previous experiments on the surface and the secreted proteomes, have been incorporated to increase the coverage of the proteome. High resolution precursor mass spectrometry (MS) and ion trap tandem MS spectra were analyzed with three different search engines using a database containing allele-specific sequences. This approach, novel for a large-scale C. albicans proteomics project, was combined with the post-processing and filtering implemented in the Trans Proteomic Pipeline consistently used in the PeptideAtlas project and resulted in 49,372 additional peptides (3-fold increase) and 1630 more proteins (1.6-fold increase) identified in the new C. albicans PeptideAtlas with respect to the previous build. A total of 71,310 peptides and 4174 canonical (minimal non-redundant set) proteins (4115 if one protein per pair of alleles is considered) were identified representing 66% of the 6218 proteins in the predicted proteome. This makes the new PeptideAtlas build the most comprehensive C. albicans proteomics resource available and the only large-scale one with detections of individual alleles.

  3. Towards the standardization of mitochondrial proteomics: the Italian mt-HPP initiative.

    Science.gov (United States)

    Alberio, Tiziana; Pieroni, Luisa; Ronci, Maurizio; Banfi, Cristina; Bongarzone, Italia; Bottoni, Patrizia; Brioschi, Maura; Caterino, Marianna; Chinello, Clizia; Cormio, Antonella; Cozzolino, Flora; Cunsolo, Vincenzo; Fontana, Simona; Garavaglia, Barbara; Giusti, Laura; Greco, Viviana; Lucacchini, Antonio; Maffioli, Elisa; Magni, Fulvio; Monteleone, Francesca; Monti, Maria; Monti, Valentina; Musicco, Clara; Petrosillo, Giuseppe; Porcelli, Vito; Saletti, Rosaria; Scatena, Roberto; Soggiu, Alessio; Tedeschi, Gabriella; Zilocchi, Mara; Roncada, Paola; Urbani, Andrea; Fasano, Mauro

    2017-08-22

    The mitochondrial Human Proteome Project aims at understanding the function of the mitochondrial proteome and its crosstalk with the proteome of other organelles. Being able to choose a suitable and validated enrichment protocol of functional mitochondria, based on the specific needs of the downstream proteomics analysis, would greatly help the researchers in the field. Mitochondrial fractions from ten model cell lines were prepared using three enrichment protocols and analyzed on seven different LC-MS/MS platforms. All data were processed using neXtProt as reference database. The data are available for the Human Proteome Project purposes through the ProteomeXchange Consortium with the identifier PXD007053. The processed datasets were analysed using a suite of R routines to perform a statistical analysis and to retrieve subcellular and sub-mitochondrial localizations. Although the overall number of identified total and mitochondrial proteins was not significantly dependent on the enrichment protocol, specific line to line differences were observed. Moreover, the protein lists were mapped to a network representing the functional mitochondrial proteome, encompassing mitochondrial proteins and their first interactors. More than 80% of the identified proteins resulted nodes of this network but with a different ability in co-isolating mitochondria-associated structures for each enrichment protocol/cell line pair.

  4. The proteome: structure, function and evolution.

    Science.gov (United States)

    Fleming, Keiran; Kelley, Lawrence A; Islam, Suhail A; MacCallum, Robert M; Muller, Arne; Pazos, Florencio; Sternberg, Michael J E

    2006-03-29

    This paper reports two studies to model the inter-relationships between protein sequence, structure and function. First, an automated pipeline to provide a structural annotation of proteomes in the major genomes is described. The results are stored in a database at Imperial College, London (3D-GENOMICS) that can be accessed at www.sbg.bio.ic.ac.uk. Analysis of the assignments to structural superfamilies provides evolutionary insights. 3D-GENOMICS is being integrated with related proteome annotation data at University College London and the European Bioinformatics Institute in a project known as e-protein (http://www.e-protein.org/). The second topic is motivated by the developments in structural genomics projects in which the structure of a protein is determined prior to knowledge of its function. We have developed a new approach PHUNCTIONER that uses the gene ontology (GO) classification to supervise the extraction of the sequence signal responsible for protein function from a structure-based sequence alignment. Using GO we can obtain profiles for a range of specificities described in the ontology. In the region of low sequence similarity (around 15%), our method is more accurate than assignment from the closest structural homologue. The method is also able to identify the specific residues associated with the function of the protein family.

  5. The seed nuclear proteome.

    Science.gov (United States)

    Repetto, Ombretta; Rogniaux, Hélène; Larré, Colette; Thompson, Richard; Gallardo, Karine

    2012-01-01

    Understanding the regulatory networks coordinating seed development will help to manipulate seed traits, such as protein content and seed weight, in order to increase yield and seed nutritional value of important food crops, such as legumes. Because of the cardinal role of the nucleus in gene expression, sub-proteome analyses of nuclei from developing seeds were conducted, taking advantage of the sequences available for model species. In this review, we discuss the strategies used to separate and identify the nuclear proteins at a stage when the seed is preparing for reserve accumulation. We present how these data provide an insight into the complexity and distinctive features of the seed nuclear proteome. We discuss the presence of chromatin-modifying enzymes and proteins that have roles in RNA-directed DNA methylation and which may be involved in modifying genome architecture in preparation for seed filling. Specific features of the seed nuclei at the transition between the stage of cell divisions and that of cell expansion and reserve deposition are described here which may help to manipulate seed quality traits, such as seed weight.

  6. Proteomic analysis of GPI-anchored membrane proteins

    DEFF Research Database (Denmark)

    Jung, Hye Ryung; Jensen, Ole Nørregaard

    2006-01-01

    Glycosyl-phosphatidyl-inositol-anchored proteins (GPI-APs) represent a subset of post-translationally modified proteins that are tethered to the outer leaflet of the plasma membrane via a C-terminal GPI anchor. GPI-APs are found in a variety of eukaryote species, from pathogenic microorganisms...... to humans. GPI-APs confer important cellular functions as receptors, enzymes and scaffolding molecules. Specific enzymes and detergent extraction methods combined with separation technologies and mass spectrometry permit proteomic analysis of GPI-APs from plasma membrane preparations to reveal cell...

  7. Proteomic analysis of GPI-anchored membrane proteins

    DEFF Research Database (Denmark)

    Jung, Hye Ryung; Jensen, Ole Nørregaard

    2006-01-01

    to humans. GPI-APs confer important cellular functions as receptors, enzymes and scaffolding molecules. Specific enzymes and detergent extraction methods combined with separation technologies and mass spectrometry permit proteomic analysis of GPI-APs from plasma membrane preparations to reveal cell......Glycosyl-phosphatidyl-inositol-anchored proteins (GPI-APs) represent a subset of post-translationally modified proteins that are tethered to the outer leaflet of the plasma membrane via a C-terminal GPI anchor. GPI-APs are found in a variety of eukaryote species, from pathogenic microorganisms...

  8. Proteomics in Pancreatic Cancer Research

    Directory of Open Access Journals (Sweden)

    Ruihui Geng

    2011-01-01

    Full Text Available Pancreatic cancer is a highly aggressive malignancy with a poor prognosis and deeply affects the life of people. Therefore, the earlier diagnosis and better treatments are urgently needed. In recent years, the proteomic technologies are well established and growing rapidly and have been widely applied in clinical applications, especially in pancreatic cancer research. In this paper, we attempt to discuss the development of current proteomic technologies and the application of proteomics to the field of pancreatic cancer research. This will explore the potential perspective in revealing pathogenesis, making the diagnosis earlier and treatment.

  9. Proteomics in obstetrics and gynecology

    Directory of Open Access Journals (Sweden)

    Seema Lekhwani

    2011-01-01

    Full Text Available Proteomics helps to understand the basic biological processes critical to normal cellular functions as well as the development of diseases. It identifies the essential components of these processes and exploits these components as targets in the development of new methods to prevent or treat diseases. Proteomics, although in an infancy stage in India, has the potential to complement and further enlarge the wealth of information in medicine, especially in the field of cancer. This article reviews the recent progress in proteomic techniques and their applications in the field of obstetrics and gynecology.

  10. Immunocapture strategies in translational proteomics.

    Science.gov (United States)

    Fredolini, Claudia; Byström, Sanna; Pin, Elisa; Edfors, Fredrik; Tamburro, Davide; Iglesias, Maria Jesus; Häggmark, Anna; Hong, Mun-Gwan; Uhlen, Mathias; Nilsson, Peter; Schwenk, Jochen M

    2016-01-01

    Aiming at clinical studies of human diseases, antibody-assisted assays have been applied to biomarker discovery and toward a streamlined translation from patient profiling to assays supporting personalized treatments. In recent years, integrated strategies to couple and combine antibodies with mass spectrometry-based proteomic efforts have emerged, allowing for novel possibilities in basic and clinical research. Described in this review are some of the field's current and emerging immunocapture approaches from an affinity proteomics perspective. Discussed are some of their advantages, pitfalls and opportunities for the next phase in clinical and translational proteomics.

  11. Ovarian Cancer Proteomic, Phosphoproteomic, and Glycoproteomic Data Released - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) scientists have just released a comprehensive dataset of the proteomic analysis of high grade serous ovarian tumor samples,

  12. Development and standardization of multiplexed antibody microarrays for use in quantitative proteomics.

    Science.gov (United States)

    Perlee, Lt; Christiansen, J; Dondero, R; Grimwade, B; Lejnine, S; Mullenix, M; Shao, W; Sorette, M; Tchernev, Vt; Patel, Dd; Kingsmore, Sf

    2004-12-15

    BACKGROUND: Quantitative proteomics is an emerging field that encompasses multiplexed measurement of many known proteins in groups of experimental samples in order to identify differences between groups. Antibody arrays are a novel technology that is increasingly being used for quantitative proteomics studies due to highly multiplexed content, scalability, matrix flexibility and economy of sample consumption. Key applications of antibody arrays in quantitative proteomics studies are identification of novel diagnostic assays, biomarker discovery in trials of new drugs, and validation of qualitative proteomics discoveries. These applications require performance benchmarking, standardization and specification. RESULTS: Six dual-antibody, sandwich immunoassay arrays that measure 170 serum or plasma proteins were developed and experimental procedures refined in more than thirty quantitative proteomics studies. This report provides detailed information and specification for manufacture, qualification, assay automation, performance, assay validation and data processing for antibody arrays in large scale quantitative proteomics studies. CONCLUSION: The present report describes development of first generation standards for antibody arrays in quantitative proteomics. Specifically, it describes the requirements of a comprehensive validation program to identify and minimize antibody cross reaction under highly multiplexed conditions; provides the rationale for the application of standardized statistical approaches to manage the data output of highly replicated assays; defines design requirements for controls to normalize sample replicate measurements; emphasizes the importance of stringent quality control testing of reagents and antibody microarrays; recommends the use of real-time monitors to evaluate sensitivity, dynamic range and platform precision; and presents survey procedures to reveal the significance of biomarker findings.

  13. Development and standardization of multiplexed antibody microarrays for use in quantitative proteomics

    Directory of Open Access Journals (Sweden)

    Sorette M

    2004-12-01

    Full Text Available Abstract Background Quantitative proteomics is an emerging field that encompasses multiplexed measurement of many known proteins in groups of experimental samples in order to identify differences between groups. Antibody arrays are a novel technology that is increasingly being used for quantitative proteomics studies due to highly multiplexed content, scalability, matrix flexibility and economy of sample consumption. Key applications of antibody arrays in quantitative proteomics studies are identification of novel diagnostic assays, biomarker discovery in trials of new drugs, and validation of qualitative proteomics discoveries. These applications require performance benchmarking, standardization and specification. Results Six dual-antibody, sandwich immunoassay arrays that measure 170 serum or plasma proteins were developed and experimental procedures refined in more than thirty quantitative proteomics studies. This report provides detailed information and specification for manufacture, qualification, assay automation, performance, assay validation and data processing for antibody arrays in large scale quantitative proteomics studies. Conclusion The present report describes development of first generation standards for antibody arrays in quantitative proteomics. Specifically, it describes the requirements of a comprehensive validation program to identify and minimize antibody cross reaction under highly multiplexed conditions; provides the rationale for the application of standardized statistical approaches to manage the data output of highly replicated assays; defines design requirements for controls to normalize sample replicate measurements; emphasizes the importance of stringent quality control testing of reagents and antibody microarrays; recommends the use of real-time monitors to evaluate sensitivity, dynamic range and platform precision; and presents survey procedures to reveal the significance of biomarker findings.

  14. The Proteomics Big Challenge for Biomarkers and New Drug-Targets Discovery

    Directory of Open Access Journals (Sweden)

    Rosa Terracciano

    2012-10-01

    Full Text Available In the modern process of drug discovery, clinical, functional and chemical proteomics can converge and integrate synergies. Functional proteomics explores and elucidates the components of pathways and their interactions which, when deregulated, lead to a disease condition. This knowledge allows the design of strategies to target multiple pathways with combinations of pathway-specific drugs, which might increase chances of success and reduce the occurrence of drug resistance. Chemical proteomics, by analyzing the drug interactome, strongly contributes to accelerate the process of new druggable targets discovery. In the research area of clinical proteomics, proteome and peptidome mass spectrometry-profiling of human bodily fluid (plasma, serum, urine and so on, as well as of tissue and of cells, represents a promising tool for novel biomarker and eventually new druggable targets discovery. In the present review we provide a survey of current strategies of functional, chemical and clinical proteomics. Major issues will be presented for proteomic technologies used for the discovery of biomarkers for early disease diagnosis and identification of new drug targets.

  15. Integrated GlycoProteome Analyzer (I-GPA) for Automated Identification and Quantitation of Site-Specific N-Glycosylation.

    Science.gov (United States)

    Park, Gun Wook; Kim, Jin Young; Hwang, Heeyoun; Lee, Ju Yeon; Ahn, Young Hee; Lee, Hyun Kyoung; Ji, Eun Sun; Kim, Kwang Hoe; Jeong, Hoi Keun; Yun, Ki Na; Kim, Yong-Sam; Ko, Jeong-Heon; An, Hyun Joo; Kim, Jae Han; Paik, Young-Ki; Yoo, Jong Shin

    2016-02-17

    Human glycoproteins exhibit enormous heterogeneity at each N-glycosite, but few studies have attempted to globally characterize the site-specific structural features. We have developed Integrated GlycoProteome Analyzer (I-GPA) including mapping system for complex N-glycoproteomes, which combines methods for tandem mass spectrometry with a database search and algorithmic suite. Using an N-glycopeptide database that we constructed, we created novel scoring algorithms with decoy glycopeptides, where 95 N-glycopeptides from standard α1-acid glycoprotein were identified with 0% false positives, giving the same results as manual validation. Additionally automated label-free quantitation method was first developed that utilizes the combined intensity of top three isotope peaks at three highest MS spectral points. The efficiency of I-GPA was demonstrated by automatically identifying 619 site-specific N-glycopeptides with FDR ≤ 1%, and simultaneously quantifying 598 N-glycopeptides, from human plasma samples that are known to contain highly glycosylated proteins. Thus, I-GPA platform could make a major breakthrough in high-throughput mapping of complex N-glycoproteomes, which can be applied to biomarker discovery and ongoing global human proteome project.

  16. Proteomics in farm animals models of human diseases.

    Science.gov (United States)

    Ceciliani, Fabrizio; Restelli, Laura; Lecchi, Cristina

    2014-10-01

    The need to provide in vivo complex environments to understand human diseases strongly relies on the use of animal models, which traditionally include small rodents and rabbits. It is becoming increasingly evident that the few species utilised to date cannot be regarded as universal. There is a great need for new animal species that are naturally endowed with specific features relevant to human diseases. Farm animals, including pigs, cows, sheep and horses, represent a valid alternative to commonly utilised rodent models. There is an ample scope for the application of proteomic techniques in farm animals, and the establishment of several proteomic maps of plasma and tissue has clearly demonstrated that farm animals provide a disease environment that closely resembles that of human diseases. The present review offers a snapshot of how proteomic techniques have been applied to farm animals to improve their use as biomedical models. Focus will be on specific topics of biomedical research in which farm animal models have been characterised through the application of proteomic techniques.

  17. Dissecting plasmodesmata molecular composition by mass spectrometry-based proteomics.

    Directory of Open Access Journals (Sweden)

    Emmanuelle Maria Françoise Bayer

    2013-01-01

    Full Text Available In plants, the intercellular communication through the membranous channels called plasmodesmata (PD; singular plasmodesma plays pivotal roles in the orchestration of development, defence responses and viral propagation. PD are dynamic structures embedded in the plant cell wall that are defined by specialised domains of the endoplasmic reticulum and the plasma membrane. PD structure and unique functions are guaranteed by their particular molecular composition. Yet, up to recent years and despite numerous approaches such as mutant screens, immunolocalisation or screening of random cDNAs, only few PD proteins had been conclusively identified and characterised. A clear breakthrough in the search of PD constituents came from mass-spectrometry-based proteomic approaches coupled with subcellular fractionation strategies. Due to their position, firmly anchored in the extracellular matrix, PD are notoriously difficult to isolate for biochemical analysis. Proteomic-based approaches have therefore first relied on the use of cell wall fractions containing embedded PD then on free PD fractions whereby PD membranes were released from the walls by enzymatic degradation. To discriminate between likely contaminants and PD protein candidates, bioinformatics tools have often been used in combination with proteomic approaches. GFP fusion proteins of selected candidates have confirmed the PD association of several protein families. Here we review the accomplishments and limitations of the proteomic based strategies to unravel the functional and structural complexity of PD. We also discuss the role of the identified PD associated proteins.

  18. Unique proteomic signatures distinguish macrophages and dendritic cells.

    Directory of Open Access Journals (Sweden)

    Lev Becker

    Full Text Available Monocytes differentiate into heterogeneous populations of tissue macrophages and dendritic cells (DCs that regulate inflammation and immunity. Identifying specific populations of myeloid cells in vivo is problematic, however, because only a limited number of proteins have been used to assign cellular phenotype. Using mass spectrometry and bone marrow-derived cells, we provided a global view of the proteomes of M-CSF-derived macrophages, classically and alternatively activated macrophages, and GM-CSF-derived DCs. Remarkably, the expression levels of half the plasma membrane proteins differed significantly in the various populations of cells derived in vitro. Moreover, the membrane proteomes of macrophages and DCs were more distinct than those of classically and alternatively activated macrophages. Hierarchical cluster and dual statistical analyses demonstrated that each cell type exhibited a robust proteomic signature that was unique. To interrogate the phenotype of myeloid cells in vivo, we subjected elicited peritoneal macrophages harvested from wild-type and GM-CSF-deficient mice to mass spectrometric and functional analysis. Unexpectedly, we found that peritoneal macrophages exhibited many features of the DCs generated in vitro. These findings demonstrate that global analysis of the membrane proteome can help define immune cell phenotypes in vivo.

  19. Proteomics of early zebrafish embryos

    Directory of Open Access Journals (Sweden)

    Heisenberg Carl-Philipp

    2006-01-01

    Full Text Available Abstract Background Zebrafish (D. rerio has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D gel electrophoresis and proteomics have yet to be developed. Results As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for proteomics in zebrafish from sample preparation to mass spectrometry (MS, including a comparison of databases for MS identification of zebrafish proteins. Conclusion The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis.

  20. Quantitative Proteome Mapping of Nitrotyrosines

    Energy Technology Data Exchange (ETDEWEB)

    Bigelow, Diana J.; Qian, Weijun

    2008-02-10

    An essential first step in the understanding disease and environmental perturbations is the early and quantitative detection of the increased levels of the inflammatory marker nitrotyrosine, as compared with its endogenous levels within the tissue or cellular proteome. Thus, methods that successfully address a proteome-wide quantitation of nitrotyrosine and related oxidative modifications can provide early biomarkers of risk and progression of disease as well as effective strategies for therapy. Multidimensional separations LC coupled with tandem mass spectrometry (LC-MS/MS) has, in recent years, significantly expanded our knowledge of human (and mammalian model system) proteomes including some nascent work in identification of post-translational modifications. In the following review, we discuss the application of LC-MS/MS for quantitation and identification of nitrotyrosine-modified proteins within the context of complex protein mixtures presented in mammalian proteomes.

  1. Proteomics: technology development and applications.

    Science.gov (United States)

    Walton, S Patrick; Jayaraman, Arul

    2009-02-01

    Technology development in, and the application of, proteomics are emerging areas among chemical engineers and others who presented at the 2008 American Institute of Chemical Engineers (AIChE) Annual Meeting. Overall, the centennial meeting offered a broad current perspective on the discipline of chemical engineering as it enters its second century. Biomedical and biochemical engineering continue to grow as important facets of the discipline. Within these, the value and applicability of proteomics were demonstrated in a number of interesting presentations. This year, as in the recent past, the AIChE Annual Meeting was held in conjunction with the American Electrophoresis Society Annual Meeting. American Electrophoresis Society presenters offered further academic and industrial viewpoints on the still-developing role of proteomics and proteomic technologies in biological and clinical analyses.

  2. Proteomics of Skeletal Muscle

    DEFF Research Database (Denmark)

    Deshmukh, Atul

    2016-01-01

    Skeletal muscle is the largest tissue in the human body and plays an important role in locomotion and whole body metabolism. It accounts for ~80% of insulin stimulated glucose disposal. Skeletal muscle insulin resistance, a primary feature of Type 2 diabetes, is caused by a decreased ability...... of muscle to respond to circulating insulin. Physical exercise improves insulin sensitivity and whole body metabolism and remains one of the most promising interventions for the prevention of Type 2 diabetes. Insulin resistance and exercise adaptations in skeletal muscle might be a cause, or consequence......, of altered protein expressions profiles and/or their posttranslational modifications (PTMs). Mass spectrometry (MS)-based proteomics offer enormous promise for investigating the molecular mechanisms underlying skeletal muscle insulin resistance and exercise-induced adaptation; however, skeletal muscle...

  3. The plant mitochondrial proteome

    DEFF Research Database (Denmark)

    Millar, A.H.; Heazlewood, J.L.; Kristensen, B.K.

    2005-01-01

    The plant mitochondrial proteome might contain as many as 2000-3000 different gene products, each of which might undergo post-translational modification. Recent studies using analytical methods, such as one-, two- and three-dimensional gel electrophoresis and one- and two-dimensional liquid...... chromatography linked on-line with tandem mass spectrometry, have identified >400 mitochondrial proteins, including subunits of mitochondrial respiratory complexes, supercomplexes, phosphorylated proteins and oxidized proteins. The results also highlight a range of new mitochondrial proteins, new mitochondrial...... functions and possible new mechanisms for regulating mitochondrial metabolism. More than 70 identified proteins in Arabidopsis mitochondrial samples lack similarity to any protein of known function. In some cases, unknown proteins were found to form part of protein complexes, which allows a functional...

  4. Spectral library searching in proteomics.

    Science.gov (United States)

    Griss, Johannes

    2016-03-01

    Spectral library searching has become a mature method to identify tandem mass spectra in proteomics data analysis. This review provides a comprehensive overview of available spectral library search engines and highlights their distinct features. Additionally, resources providing spectral libraries are summarized and tools presented that extend experimental spectral libraries by simulating spectra. Finally, spectrum clustering algorithms are discussed that utilize the same spectrum-to-spectrum matching algorithms as spectral library search engines and allow novel methods to analyse proteomics data.

  5. Proteomics Characterization of Exosome Cargo

    OpenAIRE

    Schey, Kevin L.; Luther, J. Matthew; Rose, Kristie L

    2015-01-01

    Characterization of exosomal cargo is of significant interest because this cargo can provide clues to exosome biogenesis, targeting, and cellular effects and may be a source of biomarkers for disease diagnosis, prognosis and response to treatment. With recent improvements in proteomics technologies, both qualitative and quantitative characterization of exosomal proteins is possible. Here we provide a brief review of exosome proteomics studies and provide detailed protocols for global qualitat...

  6. The Succinated Proteome

    Energy Technology Data Exchange (ETDEWEB)

    Merkley, Eric D.; Metz, Thomas O.; Smith, Richard D.; Baynes, John; Frizell, Norma

    2014-03-30

    Succination is a chemical modification of cysteine in protein by the Krebs cycle intermediate, fumarate, yielding S-(2-succino)cysteine (2SC). Intracellular fumarate concentration and succination of proteins are increased by hyperpolarization of the inner mitochondrial membrane, in concert with mitochondrial, endoplasmic reticulum (ER) and oxidative stress in adipocytes grown in high glucose medium and in adipose tissue in obesity and diabetes. Increased succination of proteins is also detected in the kidney of a fumarase conditional knock-out mouse which develops renal tumors. Keap1, the gatekeeper of the antioxidant response, was identified as a major succinated protein in renal cancer cells, suggesting that succination may play a role in activation of the antioxidant response. A wide range of proteins is subject to succination, including enzymes, adipokines, cytoskeletal proteins and ER chaperones with functional cysteine residues. There is also significant overlap between succinated and glutathionylated proteins, and with proteins containing cysteine residues that are readily oxidized to the sulfenic (cysteic) acid. Succination of adipocyte proteins is inhibited by uncouplers, which discharge the mitochondrial membrane potential (Δψm) and by ER stress inhibitors. 2SC serves as a biomarker of mitochondrial stress or dysfunction in chronic diseases, such as obesity, diabetes and cancer, and recent studies suggest that succination is a mechanistic link between mitochondrial dysfunction, oxidative and ER stress, and cellular progression toward apoptosis. In this article, we review the history of the succinated proteome and the challenges associated with measuring this non-enzymatic post-translational modification of proteins by proteomics approaches.

  7. Quantitative proteomic profiling of membrane proteins from the mouse brain cortex, hippocampus, and cerebellum using the HysTag reagent: mapping of neurotransmitter receptors and ion channels

    DEFF Research Database (Denmark)

    Olsen, Jesper V; Nielsen, Peter Aa; Andersen, Jens R

    2007-01-01

    of recently developed methods for isolation of membrane proteins from 10-20 mg brain tissue [Nielsen, P.Aa., Olsen, J.V., Podtelejnokov, A.V., Andersen, J.R., Mann, M., Wisniewski, J.R., 2005. Proteomic mapping of brain plasma membrane proteins. Mol. Cell. Proteomics 4, 402--408] and the Hys......Analysis of the brain proteome and studying brain diseases through clinical biopsies and animal disease models require methods of quantitative proteomics that are sensitive and allow identification and quantification of low abundant membrane proteins from minute amount of tissue. Taking advantage......Tag-quantification method [Olsen, J.V., Andersen, J.R., Nielsen, P.Aa., Nielsen, M.L., Figeys, D., Mann, M., Wisniewski, J.R., 2004. HysTag---A novel proteomic qualification tool applied to differential analysis of membrane proteins from distinct areas of mouse brain. Mol. Cell. Proteomics 3, 82--92] we performed...

  8. PoPe (Projection on Proper elements) for code control: verification, numerical convergence and reduced models. Application to plasma turbulence simulations

    CERN Document Server

    Cartier-Michaud, T; Sarazin, Y; Abiteboul, J; Bufferand, H; Dif-Pradalier, G; Garbet, X; Grandgirard, V; Latu, G; Norscini, C; Passeron, C; Tamain, P

    2015-01-01

    The Projection on Proper elements (PoPe) is a novel method of code control dedicated to 1) checking the correct implementation of models, 2) determining the convergence of numerical methods and 3) characterizing the residual errors of any given solution at very low cost. The basic idea is to establish a bijection between a simulation and a set of equations that generate it. Recovering equations is direct and relies on a statistical measure of the weight of the various operators. This method can be used in any dimensions and any regime, including chaotic ones. This method also provides a procedure to design reduced models and quantify the ratio costs to benefits. PoPe is applied to a kinetic and a fluid code of plasma turbulence.

  9. Mass Spectrometry-based Proteomics in Acute Respiratory Distress Syndrome: A Powerful Modality for Pulmonary Precision Medicine

    Science.gov (United States)

    Xu, Xue-Feng; Dai, Hua-Ping; Li, Yan-Ming; Xiao, Fei; Wang, Chen

    2016-01-01

    Objective: Acute respiratory distress syndrome (ARDS) is an acute and lethal clinical syndrome that is characterized by hypoxemic respiratory failure and diffuse alveolar inflammatory damage. This review aimed to search and discuss the mass spectrometry (MS)-based proteomic studies on different subsets of ARDS patients. Data Sources: Original research articles were collected from the PubMed database published in English up to December 2015. Study Selection: The literature search was done using the term “(acute lung injury OR acute respiratory distress syndrome) AND (proteomics OR proteome OR mass spectrum OR differential in-gel electrophoresis OR two-dimensional polyacrylamide gel electrophoresis)”. Related original research articles were included and were carefully analyzed. Results: Eight original proteomic researches on ARDS patients were found. The common proteomic modalities were two-dimensional (2D) high-performance liquid chromatography-based electronic spray ion-MS/MS and 2D-polyacrylamide gel electrophoresis/differential in-gel electrophoresis-based matrix-assisted laser desorption ionization-time of flight/MS. They compared the proteome between ARDS patients and normal controls and analyzed the dynamic changes of proteome at different ARDS stages or severity. The disturbed proteome in ARDS patients includes plasma acute-phase proteins, inflammatory/immune-associated proteins, and coagulation proteins. Conclusions: Although several previous studies have provided some useful information about the lung proteome in ARDS patients and gained several interesting disease-associated biomarkers, clinical proteomic studies in ARDS patients are still in the initial stage. An increased cooperation is still needed to establish a global and faithful database containing disease-specific proteome from the largest ARDS subsets. PMID:27647196

  10. Advances in plant proteomics-key techniques of proteome

    Institute of Scientific and Technical Information of China (English)

    Songlin RUAN; Huasheng MA; Shiheng WANG; Ya XIN; Lihua QIAN; Jianxing TONG; Jie WANG

    2008-01-01

    Following the completion of genome sequen-cing of model plants,such as rice (Oryza sativa L.) and Arabidopsis thaliana,the era of functional plant genomics has arrived which provides a solid basis for the develop-ment of plant proteomics.We review the background and concepts of proteomics,as well as the key techniques which include:(1) separation techniques such as 2-DE (two-dimensional electrophoresis),RP-HPLC (reverse phase high performance liquid chromatography) and SELDI (surface enhanced laser desorption/ionization) protein chip; (2) mass spectrometry such as MALDI-TOF-MS (matrix assisted laser desorption/ionization-time of flight- mass spectrometry) and ESI-MS/MS (elec-trospray ionization mass spectrometry/mass spectro-metry); (3) Peptide sequence tags; (4) databases related to proteomics; (5) quantitative proteome; (6) TAP (tandem affinity purification) and (7) yeast two-hybrid system.In addition,the challenges and prospects of pro-teomics are also discussed.

  11. Proteomics and Mass Spectrometry for Cancer Biomarker Discovery

    Science.gov (United States)

    Lu, Ming; Faull, Kym F.; Whitelegge, Julian P.; He, Jianbo; Shen, Dejun; Saxton, Romaine E.; Chang, Helena R.

    2007-01-01

    Proteomics is a rapidly advancing field not only in the field of biology but also in translational cancer research. In recent years, mass spectrometry and associated technologies have been explored to identify proteins or a set of proteins specific to a given disease, for the purpose of disease detection and diagnosis. Such biomarkers are being investigated in samples including cells, tissues, serum/plasma, and other types of body fluids. When sufficiently refined, proteomic technologies may pave the way for early detection of cancer or individualized therapy for cancer. Mass spectrometry approaches coupled with bioinformatic tools are being developed for biomarker discovery and validation. Understanding basic concepts and application of such technology by investigators in the field may accelerate the clinical application of protein biomarkers in disease management. PMID:19662217

  12. Modern Biotechnology of Phellinus baumii – From Fermentation to Proteomics

    Directory of Open Access Journals (Sweden)

    Hye Jin Hwang

    2007-01-01

    Full Text Available Phellinus baumii is a mushroom used as a folk medicine for a variety of human diseases in several Asian countries. Recently we have reported for the first time about the antidiabetic effect of the crude exopolysaccharides (EPS produced from submerged mycelial culture of P. baumii in streptozotocin (STZ-induced diabetic rats. The diabetic rats study revealed that orally administrated P. baumii EPS lowered the blood glucose levels and stimulated insulin excretion in diabetic rats, and consequently restored the functions of pancreas, liver, and kidney, suggesting that the EPS might be useful for the management of human diabetes mellitus. We undertook proteomic analyses for plasma, pancreas, liver, and kidney of the rats to search for novel biomarkers for monitoring diabetes before and after EPS treatments. In this article, we describe the production of EPS in submerged culture of P. baumii and studies of their hypoglycemic activity. We also explore the issue of proteomic analyses for mining biomarkers of diabetes.

  13. Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts

    Energy Technology Data Exchange (ETDEWEB)

    Tabb, David L.; Wang, Xia; Carr, Steven A.; Clauser, Karl R.; Mertins, Philipp; Chambers, Matthew C.; Holman, Jerry D.; Wang, Jing; Zhang, Bing; Zimmerman, Lisa J.; Chen, Xian; Gunawardena, Harsha P.; Davies, Sherri R.; Ellis, Matthew J. C.; Li, Shunqiang; Townsend, R. Reid; Boja, Emily S.; Ketchum, Karen A.; Kinsinger, Christopher R.; Mesri, Mehdi; Rodriguez, Henry; Liu, Tao; Kim, Sangtae; McDermott, Jason E.; Payne, Samuel H.; Petyuk, Vladislav A.; Rodland, Karin D.; Smith, Richard D.; Yang, Feng; Chan, Daniel W.; Zhang, Bai; Zhang, Hui; Zhang, Zhen; Zhou, Jian-Ying; Liebler, Daniel C.

    2016-03-04

    The NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) employed a pair of reference xenograft proteomes for initial platform validation and ongoing quality control of its data collection for The Cancer Genome Atlas (TCGA) tumors. These two xenografts, representing basal and luminal-B human breast cancer, were fractionated and analyzed on six mass spectrometers in a total of 46 replicates divided between iTRAQ and label-free technologies, spanning a total of 1095 LC-MS/MS experiments. These data represent a unique opportunity to evaluate the stability of proteomic differentiation by mass spectrometry over many months of time for individual instruments or across instruments running dissimilar workflows. We evaluated iTRAQ reporter ions, label-free spectral counts, and label-free extracted ion chromatograms as strategies for data interpretation. From these assessments we found that differential genes from a single replicate were confirmed by other replicates on the same instrument from 61-93% of the time. When comparing across different instruments and quantitative technologies, differential genes were reproduced by other data sets from 67-99% of the time. Projecting gene differences to biological pathways and networks increased the similarities. These overlaps send an encouraging message about the maturity of technologies for proteomic differentiation.

  14. Effects of lead and mercury on the blood proteome of children

    OpenAIRE

    Birdsall, Robert E.; Kiley, Michael P.; Segu, Zaneer M.; Christopher D. Palmer; Madera, Milan; Gump, Brooks B.; MacKenzie, James A.; Parsons,Patrick J.; Mechref, Yehia; Novotny, Milos V.; Bendinskas, Kestutis G.

    2010-01-01

    Heavy metal exposure in children has been associated with a variety of physiological and neurological problems. The goal of this study was to utilize proteomics to enhance the understanding of biochemical interactions responsible for the health problems related to lead and mercury exposure at concentrations well below CDC guidelines. Blood plasma and serum samples from 34 children were ...

  15. Proteomic Analysis of Chinese Hamster Ovary Cells

    DEFF Research Database (Denmark)

    Baycin-Hizal, Deniz; Tabb, David L.; Chaerkady, Raghothama;

    2012-01-01

    To complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells including the cellular proteome, secretome, and glycoproteome using tandem mass spectrometry (MS/MS) of multiple fractions obtained from gel electrophoresis, multidimens......To complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells including the cellular proteome, secretome, and glycoproteome using tandem mass spectrometry (MS/MS) of multiple fractions obtained from gel electrophoresis...

  16. Perfluorooctanoic acid for shotgun proteomics.

    Directory of Open Access Journals (Sweden)

    Chandra Sekhar Rao Kadiyala

    Full Text Available Here, we describe the novel use of a volatile surfactant, perfluorooctanoic acid (PFOA, for shotgun proteomics. PFOA was found to solubilize membrane proteins as effectively as sodium dodecyl sulfate (SDS. PFOA concentrations up to 0.5% (w/v did not significantly inhibit trypsin activity. The unique features of PFOA allowed us to develop a single-tube shotgun proteomics method that used all volatile chemicals that could easily be removed by evaporation prior to mass spectrometry analysis. The experimental procedures involved: 1 extraction of proteins in 2% PFOA; 2 reduction of cystine residues with triethyl phosphine and their S-alkylation with iodoethanol; 3 trypsin digestion of proteins in 0.5% PFOA; 4 removal of PFOA by evaporation; and 5 LC-MS/MS analysis of the resulting peptides. The general applicability of the method was demonstrated with the membrane preparation of photoreceptor outer segments. We identified 75 proteins from 1 µg of the tryptic peptides in a single, 1-hour, LC-MS/MS run. About 67% of the proteins identified were classified as membrane proteins. We also demonstrate that a proteolytic (18O labeling procedure can be incorporated after the PFOA removal step for quantitative proteomic experiments. The present method does not require sample clean-up devices such as solid-phase extractions and membrane filters, so no proteins/peptides are lost in any experimental steps. Thus, this single-tube shotgun proteomics method overcomes the major drawbacks of surfactant use in proteomic experiments.

  17. Proteomic approaches to bacterial differentiation

    Energy Technology Data Exchange (ETDEWEB)

    Norbeck, Angela D.; Callister, Stephen J.; Monroe, Matthew E.; Jaitly, Navdeep; Elias, Dwayne A.; Lipton, Mary S.; Smith, Richard D.

    2006-12-01

    While genomic approaches have been applied for the detection and identification of individual bacteria within microbial communities, analogous proteomics approaches have been effectively precluded due to their inherent complexity. An in silico assessment of peptides that could potentially be present in the proteomes of artificial simple and complex communities was performed to evaluate the effect of proteome complexity on species detection. A mass spectrometry-based proteomics approach was employed to experimentally detect and validate the predicted tryptic peptides initially identified as distinctive within the simple community. An assessment of peptide distinctiveness and the potential for mapping to a particular bacterium within a community was made throughout each step of the study. A second in silico assessment of peptide distinctiveness for a complex community of 25 microorganisms was conducted to investigate the levels of instrumental performance that would be required to experimentally detect these peptides, as well as how performance varied with complexity (e.g., the number of different microorganisms). The experimental data for a simple community showed that it is feasible to predict, observe, and to quantify distinctive peptides from one organism in the presence of at least a 100-fold greater abundance of another, thus yielding putative markers for identifying a bacterium of interest. This work represents a first step towards quantitative proteomic characterization of complex microbial communities and the possible development of community wide markers of perturbations to such communities.

  18. Proteomics Study of Cotton Fiber Cells

    Institute of Scientific and Technical Information of China (English)

    LIU Jin-yuan

    2008-01-01

    @@ A comparative proteomic analysis was applied to explore the mechanism of fiber cell development in cotton.Initially,an efficient protein preparation method was established for proteomic analysis of developing cotton fibers by two-dimensional gel electrophoresis,and a microwave enhanced ink staining technique also was created for fast and sensitive protein quantification in proteomic studies.

  19. Proteomics of Eosinophil Activation

    Directory of Open Access Journals (Sweden)

    Deane F. Mosher

    2017-09-01

    Full Text Available We recently identified and quantified >7,000 proteins in non-activated human peripheral blood eosinophils using liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS and described phosphoproteomic changes that accompany acute activation of eosinophils by interleukin-5 (IL5 (1. These data comprise a treasure trove of information about eosinophils. We illustrate the power of label-free LC–MS/MS quantification by considering four examples: complexity of eosinophil STATs, contribution of immunoproteasome subunits to eosinophil proteasomes, complement of integrin subunits, and contribution of platelet proteins originating from platelet–eosinophil complexes to the overall proteome. We describe how isobaric labeling enables robust sample-to-sample comparisons and relate the 220 phosphosites that changed significantly upon treatment with IL5 to previous studies of eosinophil activation. Finally, we review previous attempts to leverage the power of mass spectrometry to discern differences between eosinophils of healthy subjects and those with eosinophil-associated conditions and point out features of label-free quantification and isobaric labeling that are important in planning future mass spectrometric studies.

  20. Structural Proteomics of Herpesviruses

    Directory of Open Access Journals (Sweden)

    Baptiste Leroy

    2016-02-01

    Full Text Available Herpesviruses are highly prevalent viruses associated with numerous pathologies both in animal and human populations. Until now, most of the strategies used to prevent or to cure these infections have been unsuccessful because these viruses have developed numerous immune evasion mechanisms. Therefore, a better understanding of their complex lifecycle is needed. In particular, while the genome of numerous herpesviruses has been sequenced, the exact composition of virions remains unknown for most of them. Mass spectrometry has recently emerged as a central method and has permitted fundamental discoveries in virology. Here, we review mass spectrometry-based approaches that have recently allowed a better understanding of the composition of the herpesvirus virion. In particular, we describe strategies commonly used for proper sample preparation and fractionation to allow protein localization inside the particle but also to avoid contamination by nonstructural proteins. A collection of other important data regarding post-translational modifications or the relative abundance of structural proteins is also described. This review also discusses the poorly studied importance of host proteins in herpesvirus structural proteins and the necessity to develop a quantitative workflow to better understand the dynamics of the structural proteome. In the future, we hope that this collaborative effort will assist in the development of new strategies to fight these infections.

  1. SciDAC Fusiongrid Project--A National Collaboratory to Advance the Science of High Temperature Plasma Physics for Magnetic Fusion

    Energy Technology Data Exchange (ETDEWEB)

    SCHISSEL, D.P.; ABLA, G.; BURRUSS, J.R.; FEIBUSH, E.; FREDIAN, T.W.; GOODE, M.M.; GREENWALD, M.J.; KEAHEY, K.; LEGGETT, T.; LI, K.; McCUNE, D.C.; PAPKA, M.E.; RANDERSON, L.; SANDERSON, A.; STILLERMAN, J.; THOMPSON, M.R.; URAM, T.; WALLACE, G.

    2006-08-31

    This report summarizes the work of the National Fusion Collaboratory (NFC) Project funded by the United States Department of Energy (DOE) under the Scientific Discovery through Advanced Computing Program (SciDAC) to develop a persistent infrastructure to enable scientific collaboration for magnetic fusion research. A five year project that was initiated in 2001, it built on the past collaborative work performed within the U.S. fusion community and added the component of computer science research done with the USDOE Office of Science, Office of Advanced Scientific Computer Research. The project was a collaboration itself uniting fusion scientists from General Atomics, MIT, and PPPL and computer scientists from ANL, LBNL, Princeton University, and the University of Utah to form a coordinated team. The group leveraged existing computer science technology where possible and extended or created new capabilities where required. Developing a reliable energy system that is economically and environmentally sustainable is the long-term goal of Fusion Energy Science (FES) research. In the U.S., FES experimental research is centered at three large facilities with a replacement value of over $1B. As these experiments have increased in size and complexity, there has been a concurrent growth in the number and importance of collaborations among large groups at the experimental sites and smaller groups located nationwide. Teaming with the experimental community is a theoretical and simulation community whose efforts range from applied analysis of experimental data to fundamental theory (e.g., realistic nonlinear 3D plasma models) that run on massively parallel computers. Looking toward the future, the large-scale experiments needed for FES research are staffed by correspondingly large, globally dispersed teams. The fusion program will be increasingly oriented toward the International Thermonuclear Experimental Reactor (ITER) where even now, a decade before operation begins, a large

  2. Tissue Specific Labeling in Proteomics

    Directory of Open Access Journals (Sweden)

    Evelyn Ramberger

    2017-07-01

    Full Text Available Mass spectrometry-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples. While it is routinely used for the characterization of simple cell line systems, the analysis of the cell specific proteome in multicellular organisms and tissues poses a significant challenge. Isolating a subset of cells from tissues requires mechanical and biochemical separation or sorting, a process which can alter cellular signaling, and thus, the composition of the proteome. Recently, several approaches for cell selective labeling of proteins, that include bioorthogonal amino acids, biotinylating enzymes, and genetic tools, have been developed. These tools facilitate the selective labeling of proteins, their interactome, or of specific cell types within a tissue or an organism, while avoiding the difficult and contamination-prone biochemical separation of cells from the tissue. In this review, we give an overview of existing techniques and their application in cell culture models and whole animals.

  3. Proteomics characterization of exosome cargo.

    Science.gov (United States)

    Schey, Kevin L; Luther, J Matthew; Rose, Kristie L

    2015-10-01

    Characterization of exosomal cargo is of significant interest because this cargo can provide clues to exosome biogenesis, targeting, and cellular effects and may be a source of biomarkers for disease diagnosis, prognosis and response to treatment. With recent improvements in proteomics technologies, both qualitative and quantitative characterization of exosomal proteins is possible. Here we provide a brief review of exosome proteomics studies and provide detailed protocols for global qualitative, global quantitative, and targeted quantitative analysis of exosomal proteins. In addition, we provide an example application of a standard global quantitative analysis followed by validation via a targeted quantitative analysis of urine exosome samples from human patients. Advantages and limitations of each method are discussed as well as future directions for exosome proteomics analysis.

  4. Proteomic analysis of protein profiles in some pathological stages of the human organism

    Directory of Open Access Journals (Sweden)

    Barbara Kossowska

    2009-11-01

    Full Text Available Two-dimensional gel electrophoresis (2-DE is a widely used method for seperation of the proteins of a proteome and it enables their detection in a large concentration range. Sample preparation for isoelectric focusing and SDS-PAGE electrophoresis as well as spot visualization determines the quality of the obtained protein maps. Computer analysis of the proteome maps allows comparison and detection differences in protein profiles. In combination with mass spectrometry (MS it enables the identification of a single protein. Low-abundance proteins of physiological body fluids are considered as the potential source of diagnostic biomarkers. These are obtained by such techniques as affinity chromatography, immunoaffinity, and ultrafiltration. A combination of proteomic and metabonomic analysis provides a collection of new markers which are helpful in modern medical diagnostics.The combination of the 2-DE technique and 1H MRS enables monitoring mild cognitive impairment (MCI and the evolution of Alzheimer disease (AD. Proteome analysis of the liver and red blood cells of patients with diagnosed schizophrenia indicates the importance of analyzing external tissue, not only cerebrospinal fluid, in the diagnosis of this disease. Proteomic techniques enable the identification of new biomarkers in rheumatic disease by analyzing plasma, articular fluid and tissues. New protein biomarkers (in plasma, serum, pancreatic juice, urine enable earlier cancer diagnosis and disease monitoring. Proteome analysis of maternal serum and amniotic fluid creates the possibility detection of protein markers in prenatal tests diagnosing Down’s syndrome. Proteomic studies enable assessment of the influence of environmental contamination on the immunological system.

  5. Advances of Proteomic Sciences in Dentistry.

    Science.gov (United States)

    Khurshid, Zohaib; Zohaib, Sana; Najeeb, Shariq; Zafar, Muhammad Sohail; Rehman, Rabia; Rehman, Ihtesham Ur

    2016-05-13

    Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed.

  6. Advances of Proteomic Sciences in Dentistry

    Science.gov (United States)

    Khurshid, Zohaib; Zohaib, Sana; Najeeb, Shariq; Zafar, Muhammad Sohail; Rehman, Rabia; Rehman, Ihtesham Ur

    2016-01-01

    Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed. PMID:27187379

  7. Centennial paper: Proteomics in animal science.

    Science.gov (United States)

    Lippolis, J D; Reinhardt, T A

    2008-09-01

    Proteomics holds significant promise as a method for advancing animal science research. The use of this technology in animal science is still in its infancy. The ability of proteomics to simultaneously identify and quantify potentially thousands of proteins is unparalleled. In this review, we will discuss basic principles of doing a proteomic experiment. In addition, challenges and limitations of proteomics will be considered, stressing those that are unique to animal sciences. The current proteomic research in animal sciences will be discussed, and the potential uses for this technology will be highlighted.

  8. Proteomic classification of breast cancer.

    LENUS (Irish Health Repository)

    Kamel, Dalia

    2012-11-01

    Being a significant health problem that affects patients in various age groups, breast cancer has been extensively studied to date. Recently, molecular breast cancer classification has advanced significantly with the availability of genomic profiling technologies. Proteomic technologies have also advanced from traditional protein assays including enzyme-linked immunosorbent assay, immunoblotting and immunohistochemistry to more comprehensive approaches including mass spectrometry and reverse phase protein lysate arrays (RPPA). The purpose of this manuscript is to review the current protein markers that influence breast cancer prediction and prognosis and to focus on novel advances in proteomic classification of breast cancer.

  9. The Potato Tuber Mitochondrial Proteome

    DEFF Research Database (Denmark)

    Salvato, Fernanda; Havelund, Jesper F; Chen, Mingjie

    2014-01-01

    manner using normalized spectral counts including as many as 5-fold more “extreme” proteins (low mass, high isoelectric point, hydrophobic) than previous mitochondrial proteome studies. We estimate that this compendium of proteins represents a high coverage of the potato tuber mitochondrial proteome...... that more than 50% of the identified proteins harbor at least one modification. The most prominently observed class of posttranslational modifications was oxidative modifications. This study reveals approximately 500 new or previously unconfirmed plant mitochondrial proteins and outlines a facile strategy...... for unbiased, near-comprehensive identification of mitochondrial proteins and their modified forms....

  10. 金黄色葡萄球菌乳房炎奶牛血浆的比较蛋白质组研究%Differential Proteomics Analysis of Plasma Protein from Staphylococcus aureus Mastitic and Healthy Dairy Cows

    Institute of Scientific and Technical Information of China (English)

    杨永新; 曹随忠; 张勇; 程广龙; 赵辉玲; 赵兴绪

    2011-01-01

    为了分析金黄色葡萄球菌(Staphylococcus aureus)自然感染引起的隐性乳房炎奶牛血浆蛋白的表达变化,经细菌培养分离鉴定了乳中金黄色葡萄球菌,选择其感染的奶牛.采用二维凝胶电泳技术分离了临床健康奶牛和乳房炎奶牛的血浆蛋白,考马斯亮蓝G-250染色后PDQuest 8.0软件检测差异表达蛋白点,高效液相色谱串联离子阱质谱鉴定.结果发现,金黄色葡萄球菌乳房炎奶牛血浆中有10个蛋白点的表达量发生改变,其中6个蛋白点经质谱鉴定为结合珠蛋白、转甲状腺素蛋白和α1酸性糖蛋白等4种蛋白.金黄色葡萄球菌感染可造成奶牛血浆结合珠蛋白、α1酸性糖蛋白和血清淀粉样蛋白A的表达量增加.ELISA法测定血浆结合珠蛋白的结果也发现,金黄色葡萄球菌感染奶牛血浆结合珠蛋白水平显著高于健康牛(P<0.01).结果提示乳房炎奶牛血浆蛋白的变化可为揭示金黄色葡萄球菌感染乳腺炎症的应答提供依据.%The purpose of our study was to investigate the changes of plasma protein from the cows infected with Staphylococcus aureus. Dairy cows shown to be S. aureus-positive on bacteriological culture of milk from all 4 quarters, were classified as S. aureus subclinical mastitis. Two-dimensional gel electrophoresis was used to separate plasma protein from S. aureus subclinical mastitis and healthy dairy cows, and stained with Coomassie Blue G-250 solution. Differential expression proteins were detected by PDQuest 8.0 software and identified by ion trap mass spectrometer. The results showed that the ten protein spots were changed in cows subclinically infected with S. aureus mastitis, and six spots were identified as four proteins including haptoglobin, alpha 1 acid glycoprotein, transthyretin and serum amyloid protein A. Haptoglobin, alpha 1 acid glycoprotein, and serum amyloid protein A were up-regulated in plasma from S. aureus infected cows. ELISA detection of

  11. Liver proteomics in progressive alcoholic steatosis

    Energy Technology Data Exchange (ETDEWEB)

    Fernando, Harshica [Department of Pathology, The University of Texas Medical Branch, Galveston, TX 77555 (United States); Wiktorowicz, John E.; Soman, Kizhake V. [Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555 (United States); Kaphalia, Bhupendra S.; Khan, M. Firoze [Department of Pathology, The University of Texas Medical Branch, Galveston, TX 77555 (United States); Shakeel Ansari, G.A., E-mail: sansari@utmb.edu [Department of Pathology, The University of Texas Medical Branch, Galveston, TX 77555 (United States)

    2013-02-01

    Fatty liver is an early stage of alcoholic and nonalcoholic liver disease (ALD and NALD) that progresses to steatohepatitis and other irreversible conditions. In this study, we identified proteins that were differentially expressed in the livers of rats fed 5% ethanol in a Lieber–DeCarli diet daily for 1 and 3 months by discovery proteomics (two-dimensional gel electrophoresis and mass spectrometry) and non-parametric modeling (Multivariate Adaptive Regression Splines). Hepatic fatty infiltration was significantly higher in ethanol-fed animals as compared to controls, and more pronounced at 3 months of ethanol feeding. Discovery proteomics identified changes in the expression of proteins involved in alcohol, lipid, and amino acid metabolism after ethanol feeding. At 1 and 3 months, 12 and 15 different proteins were differentially expressed. Of the identified proteins, down regulation of alcohol dehydrogenase (− 1.6) at 1 month and up regulation of aldehyde dehydrogenase (2.1) at 3 months could be a protective/adaptive mechanism against ethanol toxicity. In addition, betaine-homocysteine S-methyltransferase 2 a protein responsible for methionine metabolism and previously implicated in fatty liver development was significantly up regulated (1.4) at ethanol-induced fatty liver stage (1 month) while peroxiredoxin-1 was down regulated (− 1.5) at late fatty liver stage (3 months). Nonparametric analysis of the protein spots yielded fewer proteins and narrowed the list of possible markers and identified D-dopachrome tautomerase (− 1.7, at 3 months) as a possible marker for ethanol-induced early steatohepatitis. The observed differential regulation of proteins have potential to serve as biomarker signature for the detection of steatosis and its progression to steatohepatitis once validated in plasma/serum. -- Graphical abstract: The figure shows the Hierarchial cluster analysis of differentially expressed protein spots obtained after ethanol feeding for 1 (1–3

  12. What is Proteomics? - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The term "proteome" refers to the entire complement of proteins, including the modifications made to a particular set of proteins, produced by an organism or a cellular system. This will vary with time and distinct requirements, such as stresses, that a cell or organism undergoes.

  13. Mass Spectrometry-based Proteomics in Acute Respiratory Distress Syndrome: A Powerful Modality for Pulmonary Precision Medicine

    Institute of Scientific and Technical Information of China (English)

    Xue-Feng Xu; Hua-Ping Dai; Yan-Ming Li; Fei Xiao; Chen Wang

    2016-01-01

    Objective:Acute respiratory distress syndrome (ARDS) is an acute and lethal clinical syndrome that is characterized by hypoxemic respiratory failure and diffuse alveolar inflammatory damage.This review aimed to search and discuss the mass spectrometry (MS)-based proteomic studies on different subsets of ARDS patients.Data Sources:Original research articles were collected from the PubMed database published in English up to December 2015.Study Selection:The literature search was done using the term "(acute lung injury OR acute respiratory distress syndrome)AND (proteomics OR proteome OR mass spectrum OR differential in-gel electrophoresis OR two-dimensional polyacrylamide gel electrophoresis)".Related original research articles were included and were carefully analyzed.Results:Eight original proteomic researches on ARDS patients were found.The common proteomic modalities were two-dimensional (2D)high-performance liquid chromatography-based electronic spray ion-MS/MS and 2D-polyacrylamide gel electrophoresis/differential in-gel electrophoresis-based matrix-assisted laser desorption ionization-time of flight/MS.They compared the proteome between ARDS patients and normal controls and analyzed the dynamic changes ofproteome at different ARDS stages or severity.The disturbed proteome in ARDS patients includes plasma acute-phase proteins,inflammatory/immune-associated proteins,and coagulation proteins.Conclusions:Although several previous studies have provided some useful information about the lung proteome in ARDS patients and gained several interesting disease-associated biomarkers,clinical proteomic studies in ARDS patients are still in the initial stage.An increased cooperation is still needed to establish a global and faithful database containing disease-specific proteome from the largest ARDS subsets.

  14. Bioinformatics Resources for In Silico Proteome Analysis

    Directory of Open Access Journals (Sweden)

    Pruess Manuela

    2003-01-01

    Full Text Available In the growing field of proteomics, tools for the in silico analysis of proteins and even of whole proteomes are of crucial importance to make best use of the accumulating amount of data. To utilise this data for healthcare and drug development, first the characteristics of proteomes of entire species—mainly the human—have to be understood, before secondly differentiation between individuals can be surveyed. Specialised databases about nucleic acid sequences, protein sequences, protein tertiary structure, genome analysis, and proteome analysis represent useful resources for analysis, characterisation, and classification of protein sequences. Different from most proteomics tools focusing on similarity searches, structure analysis and prediction, detection of specific regions, alignments, data mining, 2D PAGE analysis, or protein modelling, respectively, comprehensive databases like the proteome analysis database benefit from the information stored in different databases and make use of different protein analysis tools to provide computational analysis of whole proteomes.

  15. Sensitivity of whole-body CT and MRI versus projection radiography in the detection of osteolyses in patients with monoclonal plasma cell disease

    Energy Technology Data Exchange (ETDEWEB)

    Wolf, Maya B., E-mail: m.mueller-wolf@dkfz.de [Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Im Neuenheimer Feld 110, 69120 Heidelberg Germany (Germany); Department of Radiology, German Cancer Research Center (Dkfz), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany); Murray, Fritz, E-mail: fritz.murray@hotmail.de [Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Im Neuenheimer Feld 110, 69120 Heidelberg Germany (Germany); Kilk, Kerstin, E-mail: k_fechtner@hotmail.com [Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Im Neuenheimer Feld 110, 69120 Heidelberg Germany (Germany); Hillengass, Jens, E-mail: jens.hillengass@med.uni-heidelberg.de [Department of Haematology, Oncology, Rheumatology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg (Germany); Delorme, Stefan, E-mail: s.delorme@dkfz-heidelberg.de [Department of Radiology, German Cancer Research Center (Dkfz), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany); Heiss, Christiane, E-mail: c.heiss@dkfz-heidelberg.de [Department of Biostatistics, German Cancer Research Center (Dkfz), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany); Neben, Kai, E-mail: k.neben@klinikum-mittelbaden.de [Department of Haematology, Oncology, Rheumatology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg (Germany); Goldschmidt, Hartmut, E-mail: hartmut.goldschmidt@med.uni-heidelberg.de [Department of Haematology, Oncology, Rheumatology, University Hospital Heidelberg and National Center for Tumour Diseases, Im Neuenheimer Feld 410, 69120 Heidelberg (Germany); Kauczor, Hans-Ulrich, E-mail: hu.kauczor@med.uni-heidelberg.de [Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Im Neuenheimer Feld 110, 69120 Heidelberg Germany (Germany); and others

    2014-07-15

    Purpose: To compare sensitivity of whole-body Computed Tomography (wb-CT) and whole-body Magnetic Resonance Imaging (wb-MRI) with Projection Radiography (PR) regarding each method's ability to detect osteolyses in patients with monoclonal plasma cell disease. Patients and methods: The bone status of 171 patients was evaluated. All patients presented with multiple myeloma (MM) of all stages, monoclonal gammopathy of unknown significance (MGUS) or solitary plasmacytoma. Two groups were formed. Group A consisted of 52 patients (26 females, 26 males) with an average age of 62 years (range, 45–89 years) who received, both, PR and wb-CT as part of their diagnostic work-up. Group B comprised 119 patients (58 females, 61 males) averaging 57 years of age (range, 20–80 years) who received, both, PR and wb-MRI. Two experienced radiologists were blinded regarding the disease status and assessed the number and location of osteolyses in consensus. A distinction was made between axial and extra-axial lesions. Results: In group A, wb-CT revealed osteolyses in 12 patients (23%) that were not detected in PR. CT was superior in detecting lesions in patients with osteopenia and osteoporosis. Compared with PR, wb-CT was significantly more sensitive in detecting osteolyses than PR (p < 0.001). This was particularly true for axial lesions. Additionally, CT revealed clinically relevant incidental findings in 33 patients (63%). In group B, wb-MRI revealed lesions in 19 patients (16%) that were not detected in PR. All lesions detected by PR were also detected by wb-MRI and wb-CT. Wb-MRI and wb-CT are each superior to PR in detecting axial lesions. Conclusion: Wb-CT can detect 23% more focal lesions than PR, especially in the axial skeleton. Therefore, this imaging method should be preferred over PR in the diagnostic work-up and staging of patients with monoclonal plasma cell disease.

  16. Proteomic analysis of the shistosome tegument and its surface membranes

    Directory of Open Access Journals (Sweden)

    Simon Braschi

    2006-10-01

    Full Text Available The tegument surface of the adult schistosome, bounded by a normal plasma membrane overlain by a secreted membranocalyx, holds the key to understanding how schistosomes evade host immune responses. Recent advances in mass spectrometry (MS, and the sequencing of the Schistosoma mansoni transcriptome/genome, have facilitated schistosome proteomics. We detached the tegument from the worm body and enriched its surface membranes by differential extraction, before subjecting the preparation to liquid chromatography-based proteomics to identify its constituents. The most exposed proteins on live worms were labelled with impearmeant biotinylation reagents, and we also developed methods to isolate the membranocalyx for analysis. We identified transporters for sugars, amino acids, inorganic ions and water, which confirm the importance of the tegument plasma membrane in nutrient acquisition and solute balance. Enzymes, including phosphohydrolases, esterases and carbonic anhydrase were located with their catalytic domains external to the plasma membrane, while five tetraspanins, annexin and dysferlin were implicated in membrane architecture. In contrast, few parasite proteins could be assigned to the membranocalyx but mouse immune response proteins, including three immunoglobulins and two complement factors, were detected, plus host membrane proteins such as CD44, integrin and a complement regulatory protein, testifying to the acquisitive properties of the secreted bilayer.

  17. Establishment of Membrane Proteomics Platform with Two-dimensional Electrophoresis for Preparing Identifying Plasma Membrane Proteins from Atractylodes lancea%茅苍术质膜蛋白的制备及其双向电泳蛋白质组学平台的构建

    Institute of Scientific and Technical Information of China (English)

    陈飞; 周彤; 魏宇佳; 杨晶; 戴传超

    2016-01-01

    In order to understand related metabolic pathways of secondary metabolites and carry on metabolic regulation of active medical ingredients in endangered medicinal plant Atractylodes lancea,the method of plasma membrane proteomics was studied in this paper. Purified plasma membrane proteins were respectively extracted and purified from root,stem,and leaf of A. lancea using ultracentrifugation combined with aqueous two-phase partitioning. Moreover,the conditions for two-dimensional electrophoresis(2DE)analysis were optimized,and partial proteins in the latter were identified. The results showed that treating the ultra-centrifuged crude membrane compositions with the aqueous two-phase system of 6.4%,6.3%,and 6.1% Dextran T-500/PEG 3350(w/w)respectively,the high- purity plasma membrane proteins of 92.1%(root),91.5%(stem)and 90.8%(leaf)were obtained. The plasma membrane proteins were decomposed by 2% CHAPS and 2%Triton X-100 as the comprehensive detergents,loaded in the amount of 100 μg and resolved by IEF of 80 000 Vhs and 12.5%-15% SDS-PAGE gradient gel,and total 267,297 and 248 protein spots in the plasma membrane protein profiles of root,stem and leave respectively were detected by the Image Master 2D Platinum 7.0 software. And similarities and differences of 3 tissue proteins were further comparatively analyzed.At last,5 proteins were selected and successfully identified by MALDI-TOF-MS. Conclusively,a complete proteomics technology platform for preparing high-purity plasma membrane proteins from varied tissues of root,stem and leave of A. lancea and identifying the mass spectrometry of membrane protein is established.%探讨濒危药用植物茅苍术的质膜蛋白质组方法,旨在达到了解其次级代谢物的代谢途径,并对相关药用活性成分进行代谢调控的目的。以茅苍术的根、茎、叶为实验材料,确定了超速离心结合双水相法作为提取、纯化其质膜蛋白的方法;进而对这些质膜蛋白的双向

  18. Advancing cell biology through proteomics in space and time (PROSPECTS)

    DEFF Research Database (Denmark)

    Lamond, A.I.; Uhlen, M.; Horning, S.

    2012-01-01

    a range of sensitive and quantitative approaches for measuring protein structures and dynamics that promise to revolutionize our understanding of cell biology and molecular mechanisms in both human cells and model organisms. The Proteomics Specification in Time and Space (PROSPECTS) Network is a unique EU......-funded project that brings together leading European research groups, spanning from instrumentation to biomedicine, in a collaborative five year initiative to develop new methods and applications for the functional analysis of cellular proteins. This special issue of Molecular and Cellular Proteomics presents 16...... research papers reporting major recent progress by the PROSPECTS groups, including improvements to the resolution and sensitivity of the Orbitrap family of mass spectrometers, systematic detection of proteins using highly characterized antibody collections, and new methods for absolute as well as relative...

  19. Unravelling the nuclear matrix proteome

    DEFF Research Database (Denmark)

    Albrethsen, Jakob; Knol, Jaco C; Jimenez, Connie R

    2009-01-01

    The nuclear matrix (NM) model posits the presence of a protein/RNA scaffold that spans the mammalian nucleus. The NM proteins are involved in basic nuclear function and are a promising source of protein biomarkers for cancer. Importantly, the NM proteome is operationally defined as the proteins...

  20. Proteomic interrogation of human chromatin.

    Directory of Open Access Journals (Sweden)

    Mariana P Torrente

    Full Text Available Chromatin proteins provide a scaffold for DNA packaging and a basis for epigenetic regulation and genomic maintenance. Despite understanding its functional roles, mapping the chromatin proteome (i.e. the "Chromatome" is still a continuing process. Here, we assess the biological specificity and proteomic extent of three distinct chromatin preparations by identifying proteins in selected chromatin-enriched fractions using mass spectrometry-based proteomics. These experiments allowed us to produce a chromatin catalog, including several proteins ranging from highly abundant histone proteins to less abundant members of different chromatin machinery complexes. Using a Normalized Spectral Abundance Factor approach, we quantified relative abundances of the proteins across the chromatin enriched fractions giving a glimpse into their chromosomal abundance. The large-scale data sets also allowed for the discovery of a variety of novel post-translational modifications on the identified chromatin proteins. With these comparisons, we find one of the probed methods to be qualitatively superior in specificity for chromatin proteins, but inferior in proteomic extent, evidencing a compromise that must be made between biological specificity and broadness of characterization. Additionally, we attempt to identify proteins in eu- and heterochromatin, verifying the enrichments by characterizing the post-translational modifications detected on histone proteins from these chromatin regions. In summary, our results provide insights into the value of different methods to extract chromatin-associated proteins and provide starting points to study the factors that may be involved in directing gene expression and other chromatin-related processes.

  1. The potato tuber mitochondrial proteome

    DEFF Research Database (Denmark)

    Møller, Ian Max; Salvato, Fernanda; Havelund, Jesper

    proteome was characterized in depth by a combination of gel electrophoresis prefractionation of proteins and liquid chromatography-tandem mass spectrometry of ensuing peptides from in-gel digestion. The results indicate that we have a close to complete coverage. The presence and absence of a number...

  2. Periodontal Proteomics: Wonders Never Cease!

    Directory of Open Access Journals (Sweden)

    Harpreet Singh Grover

    2013-01-01

    Full Text Available Proteins are vital parts of living organisms, as they are integral components of the physiological metabolic pathways of cells. Periodontal tissues comprise multicompartmental groups of interacting cells and matrices that provide continuous support, attachment, proprioception, and physical protection for the teeth. The proteome map, that is, complete catalogue of the matrix and cellular proteins expressed in alveolar bone, cementum, periodontal ligament, and gingiva, is to be explored for more in-depth understanding of periodontium. The ongoing research to understand the signalling pathways that allow cells to divide, differentiate, and die in controlled manner has brought us to the era of proteomics. Proteomics is defined as the study of all proteins including their relative abundance, distribution, posttranslational modifications, functions, and interactions with other macromolecules, in a given cell or organism within a given environment and at a specific stage in the cell cycle. Its application to periodontal science can be used to monitor health status, disease onset, treatment response, and outcome. Proteomics can offer answers to critical, unresolved questions such as the biological basis for the heterogeneity in gingival, alveolar bone, and cemental cell populations.

  3. Proteomic approaches to bacterial differentiation

    Energy Technology Data Exchange (ETDEWEB)

    Norbeck, Angela D.; Callister, Stephen J.; Monroe, Matthew E.; Jaitly, Navdeep; Elias, Dwayne A.; Lipton, Mary S.; Smith, Richard D.

    2006-01-02

    While genomic approaches have been applied to the detection and identification of individual bacteria within microbial communities, analogous proteomics approaches have been effectively precluded due to the inherent complexity. An in silico assessment of peptides derived from artificial simple and complex communities was performed to evaluate the effect of proteome complexity on species detection. Detection and validation of predicted peptides initially identified as distinctive within the simple community was experimentally performed using a mass spectrometry-based proteomics approach. An assessment of peptide distinctiveness and the potential for mapping to a particular bacterium within a community was made throughout each step of the study. A second assessment performed in silico of peptide distinctiveness for a complex community of 25 microorganisms was also conducted. The experimental data for a simple community, and the in silico data for a complex community revealed that it is feasible to predict, observe, and quantify distinctive peptides from one organism in the presence of at least a 100-fold greater abundance of another, thus yielding putative markers for the identification of a bacterium of interest. This work represents a first step towards quantitative proteomic characterization of complex microbial communities.

  4. Microbial proteomics using mass spectrometry.

    Science.gov (United States)

    Hines, Harry B

    2012-01-01

    Proteomic analyses involve a series of intricate, interdependent steps involving approaches and technical issues that must be fully coordinated to obtain the optimal amount of required information about the test subject. Fortunately, many of these steps are common to most test subjects, requiring only modifications to or, in some cases, substitution of some of the steps to ensure they are relevant to the desired objective of a study. This fortunate occurrence creates an essential core of proteomic approaches and techniques that are consistently available for most studies, regardless of test subject. In this chapter, an overview of some of these core approaches, techniques, and mass spectrometric instrumentation is given, while indicating how such steps are useful for and applied to bacterial investigations. To exemplify how such proteomic concepts and techniques are applicable to bacterial investigations, a practical, quantitative method useful for bacterial proteomic analysis is presented with a discussion of possibilities, pitfalls, and some emerging technology to provide a compilation of information from the diverse literature that is intermingled with experimental experience.

  5. Mass Spectrometry Instrumentation in Proteomics

    DEFF Research Database (Denmark)

    Sprenger, Richard Remko; Roepstorff, Peter

    2012-01-01

    Mass spectrometry has evolved into a crucial technology for the field of proteomics, enabling the comprehensive study of proteins in biological systems. Innovative developments have yielded flexible and versatile mass spectrometric tools, including quadrupole time-of-flight, linear ion trap...

  6. Myelin proteomics: molecular anatomy of an insulating sheath.

    Science.gov (United States)

    Jahn, Olaf; Tenzer, Stefan; Werner, Hauke B

    2009-08-01

    Fast-transmitting vertebrate axons are electrically insulated with multiple layers of nonconductive plasma membrane of glial cell origin, termed myelin. The myelin membrane is dominated by lipids, and its protein composition has historically been viewed to be of very low complexity. In this review, we discuss an updated reference compendium of 342 proteins associated with central nervous system myelin that represents a valuable resource for analyzing myelin biogenesis and white matter homeostasis. Cataloging the myelin proteome has been made possible by technical advances in the separation and mass spectrometric detection of proteins, also referred to as proteomics. This led to the identification of a large number of novel myelin-associated proteins, many of which represent low abundant components involved in catalytic activities, the cytoskeleton, vesicular trafficking, or cell adhesion. By mass spectrometry-based quantification, proteolipid protein and myelin basic protein constitute 17% and 8% of total myelin protein, respectively, suggesting that their abundance was previously overestimated. As the biochemical profile of myelin-associated proteins is highly reproducible, differential proteome analyses can be applied to material isolated from patients or animal models of myelin-related diseases such as multiple sclerosis and leukodystrophies.

  7. In-depth proteomic analyses of direct expressed prostatic secretions.

    Science.gov (United States)

    Drake, Richard R; Elschenbroich, Sarah; Lopez-Perez, Orlay; Kim, Yunee; Ignatchenko, Vladimir; Ignatchenko, Alex; Nyalwidhe, Julius O; Basu, Gaurav; Wilkins, Christopher E; Gjurich, Breanne; Lance, Raymond S; Semmes, O John; Medin, Jeffrey A; Kislinger, Thomas

    2010-05-07

    It is expected that clinically obtainable fluids that are proximal to organs contain a repertoire of secreted proteins and shed cells reflective of the physiological state of that tissue and thus represent potential sources for biomarker discovery, investigation of tissue-specific biology, and assay development. The prostate gland secretes many proteins into a prostatic fluid that combines with seminal vesicle fluids to promote sperm activation and function. Proximal fluids of the prostate that can be collected clinically are seminal plasma and expressed prostatic secretion (EPS) fluids. In the current study, MudPIT-based proteomics was applied to EPS obtained from nine men with prostate cancer and resulted in the confident identification of 916 unique proteins. Systematic bioinformatics analyses using publicly available microarray data of 21 human tissues (Human Gene Atlas), the Human Protein Atlas database, and other published proteomics data of shed/secreted proteins were performed to systematically analyze this comprehensive proteome. Therefore, we believe this data will be a valuable resource for the research community to study prostate biology and potentially assist in the identification of novel prostate cancer biomarkers. To further streamline this process, the entire data set was deposited to the Tranche repository for use by other researchers.

  8. The Proteome of the Murine Presynaptic Active Zone

    Directory of Open Access Journals (Sweden)

    Melanie Laßek

    2014-04-01

    Full Text Available The proteome of the presynaptic active zone controls neurotransmitter release and the short- and long-term structural and functional dynamics of the nerve terminal. The proteinaceous inventory of the presynaptic active zone has recently been reported. This review will evaluate the subcellular fractionation protocols and the proteomic approaches employed. A breakthrough for the identification of the proteome of the presynaptic active zone was the successful employment of antibodies directed against a cytosolic epitope of membrane integral synaptic vesicle proteins for the immunopurification of synaptic vesicles docked to the presynaptic plasma membrane. Combining immunopurification and subsequent analytical mass spectrometry, hundreds of proteins, including synaptic vesicle proteins, components of the presynaptic fusion and retrieval machinery, proteins involved in intracellular and extracellular signaling and a large variety of adhesion molecules, were identified. Numerous proteins regulating the rearrangement of the cytoskeleton are indicative of the functional and structural dynamics of the presynapse. This review will critically discuss both the experimental approaches and prominent protein candidates identified. Many proteins have not previously been assigned to the presynaptic release sites and may be directly involved in the short- and long-term structural modulation of the presynaptic compartment. The identification of proteinaceous constituents of the presynaptic active zone provides the basis for further analyzing the interaction of presynaptic proteins with their targets and opens novel insights into the functional role of these proteins in neuronal communication.

  9. Recent advances in yeast organelle and membrane proteomics.

    Science.gov (United States)

    Premsler, Thomas; Zahedi, René Peiman; Lewandrowski, Urs; Sickmann, Albert

    2009-10-01

    Yeast proteome research comprises two different aspects: with respect to systemic fungal infections (fungemias), invasive candidiasis, for instance by Candida albicans, is among the most common causes of morbidity and mortality particularly in the expanding population of immunocompromised patients, which rises a high medical and pharmaceutical interest in this facultative pathogenic organism. Apart from its clinical relevance, yeast research moreover provides an indispensable source of knowledge regarding fundamental biochemical processes of eukaryotic cells. In this context, the budding yeast Saccharomyces cerevisiae is, in addition to its multiple industrial applications, one of the most extensively used microorganisms and serves as the best understood eukaryotic model system so far. Consequently, numerous studies have focused on gaining insight into the yeast proteome, with protein MS providing a very efficient technology to cope with this task since it enables both protein identification and differential quantification of cellular material. In this review we present an overview of recent advances in yeast organelle and membrane proteomics focusing on the cell wall, plasma membrane, mitochondria and vacuole.

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

    Science.gov (United States)

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

    2015-12-16

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

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

    Directory of Open Access Journals (Sweden)

    Joanna Hajduk

    2015-12-01

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

  12. Seven-Signal Proteomic Signature for Detection of Operable Pancreatic Ductal Adenocarcinoma and Their Discrimination from Autoimmune Pancreatitis

    Directory of Open Access Journals (Sweden)

    Kiyoshi Yanagisawa

    2012-01-01

    Full Text Available There is urgent need for biomarkers that provide early detection of pancreatic ductal adenocarcinoma (PDAC as well as discrimination of autoimmune pancreatitis, as current clinical approaches are not suitably accurate for precise diagnosis. We used mass spectrometry to analyze protein profiles of more than 300 plasma specimens obtained from PDAC, noncancerous pancreatic diseases including autoimmune pancreatitis patients and healthy subjects. We obtained 1063 proteomic signals from 160 plasma samples in the training cohort. A proteomic signature consisting of 7 mass spectrometry signals was used for construction of a proteomic model for detection of PDAC patients. Using the test cohort, we confirmed that this proteomic model had discrimination power equal to that observed with the training cohort. The overall sensitivity and specificity for detection of cancer patients were 82.6% and 90.9%, respectively. Notably, 62.5% of the stage I and II cases were detected by our proteomic model. We also found that 100% of autoimmune pancreatitis patients were correctly assigned as noncancerous individuals. In the present paper, we developed a proteomic model that was shown able to detect early-stage PDAC patients. In addition, our model appeared capable of discriminating patients with autoimmune pancreatitis from those with PDAC.

  13. Plasma accelerator experiments in Yugoslavia

    Science.gov (United States)

    Purić, J.; Astashynski, V. M.; Kuraica, M. M.; Dojčinovié, I. P.

    2002-12-01

    An overview is given of the results obtained in the Plasma Accelerator Experiments in Belgrade, using quasi-stationary high current plasma accelerators constructed within the framework of the Yugoslavia-Belarus Joint Project. So far, the following plasma accelerators have been realized: Magnetoplasma Compressor type (MPC); MPC Yu type; one stage Erosive Plasma Dynamic System (EPDS) and, in final stage of construction two stage Quasi-Stationary High Current Plasma Accelerator (QHPA).

  14. Proteomic Studies on Human and Experimental Cerebral Malaria

    KAUST Repository

    Moussa, Ehab

    2012-07-01

    Cerebral malaria (CM) is a severe neurological complication of malaria infection that results from interrelated pathologies. Despite extensive research efforts, the mechanism of the disease is not completely understood. Clinical studies, postmortem analysis, and animal models have been the main research arenas in CM. In this thesis, shotgun proteomics approach was used to further understand the pathology of human and experimental CM. The mechanism by which CM turns fatal is yet to be identified. A clinical proteomics study was conducted on pooled plasma samples from children with reversible or fatal CM from the Gambia. The results show that depletion of coagulation factors and increased levels of circulating proteasomes are associated with fatal pediatric CM. This data suggests that the ongoing coagulation during CM might be a disseminated intravascular coagulation state that eventually causes depletion of the coagulation factors leading to petechial hemorrhages. In addition, the mechanism(s) by which blood transfusion benefits CM in children was investigated. To that end, the concentration and multimerization pattern of von-willebrand factor, and the concentration of haptoglobin in the plasma of children with CM who received blood transfusions were measured. In addition to clinical studies, experimental cerebral malaria (ECM) in mice has been long used as a model for the disease. A shotgun proteomics workflow was optimized to identify the proteomic signature of the brain tissue of mice with ECM.Because of the utmost importance of membrane proteins in the pathology of the disease, sample fractionation and filter aided sample preparation were used to recover them. The proteomic signature of the brains of mice infected with P. berghei ANKA that developed neurological syndrome, mice infected with P. berghei NK56 that developed severe malaria but without neurological signs, and non-infected mice, were compared to identify CM specific proteins. Among the differentially

  15. A final report to the Laboratory Directed Research and Development committee on Project 93-ERP-075: ``X-ray laser propagation and coherence: Diagnosing fast-evolving, high-density laser plasmas using X-ray lasers``

    Energy Technology Data Exchange (ETDEWEB)

    Wan, A.S.; Cauble, R.; Da Silva, L.B.; Libby, S.B.; Moreno, J.C.

    1996-02-01

    This report summarizes the major accomplishments of this three-year Laboratory Directed Research and Development (LDRD) Exploratory Research Project (ERP) entitled ``X-ray Laser Propagation and Coherence: Diagnosing Fast-evolving, High-density Laser Plasmas Using X-ray Lasers,`` tracking code 93-ERP-075. The most significant accomplishment of this project is the demonstration of a new laser plasma diagnostic: a soft x-ray Mach-Zehnder interferometer using a neonlike yttrium x-ray laser at 155 {angstrom} as the probe source. Detailed comparisons of absolute two-dimensional electron density profiles obtained from soft x-ray laser interferograms and profiles obtained from radiation hydrodynamics codes, such as LASNEX, will allow us to validate and benchmark complex numerical models used to study the physics of laser-plasma interactions. Thus the development of soft x-ray interferometry technique provides a mechanism to probe the deficiencies of the numerical models and is an important tool for, the high-energy density physics and science-based stockpile stewardship programs. The authors have used the soft x-ray interferometer to study a number of high-density, fast evolving, laser-produced plasmas, such as the dynamics of exploding foils and colliding plasmas. They are pursuing the application of the soft x-ray interferometer to study ICF-relevant plasmas, such as capsules and hohlraums, on the Nova 10-beam facility. They have also studied the development of enhanced-coherence, shorter-pulse-duration, and high-brightness x-ray lasers. The utilization of improved x-ray laser sources can ultimately enable them to obtain three-dimensional holographic images of laser-produced plasmas.

  16. PatternLab for proteomics: a tool for differential shotgun proteomics

    Directory of Open Access Journals (Sweden)

    Yates John R

    2008-07-01

    Full Text Available Abstract Background A goal of proteomics is to distinguish between states of a biological system by identifying protein expression differences. Liu et al. demonstrated a method to perform semi-relative protein quantitation in shotgun proteomics data by correlating the number of tandem mass spectra obtained for each protein, or "spectral count", with its abundance in a mixture; however, two issues have remained open: how to normalize spectral counting data and how to efficiently pinpoint differences between profiles. Moreover, Chen et al. recently showed how to increase the number of identified proteins in shotgun proteomics by analyzing samples with different MS-compatible detergents while performing proteolytic digestion. The latter introduced new challenges as seen from the data analysis perspective, since replicate readings are not acquired. Results To address the open issues above, we present a program termed PatternLab for proteomics. This program implements existing strategies and adds two new methods to pinpoint differences in protein profiles. The first method, ACFold, addresses experiments with less than three replicates from each state or having assays acquired by different protocols as described by Chen et al. ACFold uses a combined criterion based on expression fold changes, the AC test, and the false-discovery rate, and can supply a "bird's-eye view" of differentially expressed proteins. The other method addresses experimental designs having multiple readings from each state and is referred to as nSVM (natural support vector machine because of its roots in evolutionary computing and in statistical learning theory. Our observations suggest that nSVM's niche comprises projects that select a minimum set of proteins for classification purposes; for example, the development of an early detection kit for a given pathology. We demonstrate the effectiveness of each method on experimental data and confront them with existing strategies

  17. Proteomics Data on UCSC Genome Browser - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium scientists are working together with the University of California, Santa Cruz (UCSC) Genomics Institute to provide public access to cancer proteomics data.

  18. Data for chicken semen proteome and label free quantitative analyses displaying sperm quality biomarkers.

    Science.gov (United States)

    Labas, Valérie; Grasseau, Isabelle; Cahier, Karine; Gargaros, Audrey; Harichaux, Grégoire; Teixeira-Gomes, Ana-Paula; Alves, Sabine; Bourin, Marie; Gérard, Nadine; Blesbois, Elisabeth

    2014-12-01

    Understanding of biology of the avian male gamete is essential to improve the conservation of genetic resources and performances in farming. In this study, the semen proteome of the main domestic avian species (Gallus gallus) and evaluation of the molecular phenotype related to sperm quality were investigated using GeLC-MS/MS approach and label-free quantitative proteomic based on Spectral Counting (SC) and extracted ion chromatograms (XIC) methods. Here we describe in details the peptide/protein inventory of chicken ejaculated spermatozoa (SPZ) and seminal plasma (SP). We also show differential analyses of chicken semen (SPZ and corresponding SP) from 11 males demonstrating different levels of fertilizing capacity and sperm motility. The interpretation and description of these data can be found in a research article published by Labas and colleagues in the Journal of Proteomics in 2014 [1]. This is a new resource for exploring the molecular mechanisms involved in fertilizing capacity and to reveal new sets of fertility biomarkers.

  19. Isolation of cell surface proteins for mass spectrometry-based proteomics.

    Science.gov (United States)

    Elschenbroich, Sarah; Kim, Yunee; Medin, Jeffrey A; Kislinger, Thomas

    2010-02-01

    Defining the cell surface proteome has profound importance for understanding cell differentiation and cell-cell interactions, as well as numerous pathogenic abnormalities. Owing to their hydrophobic nature, plasma membrane proteins that reside on the cell surface pose analytical challenges and, despite efforts to overcome difficulties, remain under-represented in proteomic studies. Limitations in the classically employed ultracentrifugation-based approaches have led to the invention of more elaborate techniques for the purification of cell surface proteins. Three of these methods--cell surface coating with cationic colloidal silica beads, biotinylation and chemical capture of surface glycoproteins--allow for marked enrichment of this subcellular proteome, with each approach offering unique advantages and characteristics for different experiments. In this article, we introduce the principles of each purification method and discuss applications from the recent literature.

  20. A proteomic and ultrastructural characterization of Aspergillus fumigatus' conidia adaptation at different culture ages.

    Science.gov (United States)

    Anjo, Sandra I; Figueiredo, Francisco; Fernandes, Rui; Manadas, Bruno; Oliveira, Manuela

    2017-03-29

    The airborne fungus Aspergillus fumigatus is one of the most common agents of human fungal infections with a remarkable impact on public health. However, A. fumigatus conidia atmospheric resistance and longevity mechanisms are still unknown. Therefore, in this work, the processes underlying conidial adaptation were studied by a time course evaluation of the proteomics and ultrastructural changes of A. fumigatus' conidia at three time-points selected according to relevant changes previously established in conidial survival rates. The proteomics characterization revealed that conidia change from a highly active metabolic to a dormant state, culminating in cell autolysis as revealed by the increased levels of hydrolytic enzymes. Structural characterization corroborates the proteomics data, with noticeable changes observed in mitochondria, nucleus and plasma membrane ultrastructure, accompanied by the formation of autophagic vacuoles. These changes are consistent with both apoptotic and autophagic processes and indicate that the changes in protein levels may anticipate those in cell morphology.

  1. Evolution of Clinical Proteomics and its Role in Medicine | Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    NCI's Office of Cancer Clinical Proteomics Research authored a review of the current state of clinical proteomics in the peer-reviewed Journal of Proteome Research. The review highlights outcomes from the CPTC program and also provides a thorough overview of the different technologies that have pushed the field forward. Additionally, the review provides a vision for moving the field forward through linking advances in genomic and proteomic analysis to develop new, molecularly targeted interventions.

  2. Proteomics in Discovery of Hepatocellular Carcinoma Biomarkers

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Objective: To discover new proteomic biomarkers of hepatocellular carcinoma. Methods: Surface enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry was used to discover biomarkers for differentiating hepatocellular carcinoma and chronic liver disease. A population of 50 patients with hepatocellular carcinoma and 33 patients with chronic liver disease was studied. Results: Twelve proteomic biomarkers of hepatocellular carcinoma were detected in this study. Three proteomic biomarkers were highly expressed in hepatocellular carcinoma and nine proteomic biomarkers were highly expressed in chronic liver disease. The most valuable proteomic biomarker with m/z=11498 had no similar diagnostic value as α-fetoprotein. Conclusion:Some of the twelve proteomic biomarkers may become new biomarkers of hepatocellular carcinoma.

  3. Proteomic approaches in research of cyanobacterial photosynthesis.

    Science.gov (United States)

    Battchikova, Natalia; Angeleri, Martina; Aro, Eva-Mari

    2015-10-01

    Oxygenic photosynthesis in cyanobacteria, algae, and plants is carried out by a fabulous pigment-protein machinery that is amazingly complicated in structure and function. Many different approaches have been undertaken to characterize the most important aspects of photosynthesis, and proteomics has become the essential component in this research. Here we describe various methods which have been used in proteomic research of cyanobacteria, and demonstrate how proteomics is implemented into on-going studies of photosynthesis in cyanobacterial cells.

  4. Evolutionary conservation of the mature oocyte proteome

    Directory of Open Access Journals (Sweden)

    Tamar Lotan

    2014-06-01

    Significance: The current study provides the first proteomic profile of an oocyte of a cnidarian organism the starlet sea anemone N. vectensis and gives new insights on the ancient origin of an oocyte proteome template. The comparative analysis with a chordate oocyte suggests that the oocyte proteome predates the divergence of the cnidarian and bilaterian lineages. In addition, the data generated in the study will serve as a valuable resource for further developmental and evolutional studies.

  5. Application of high-throughput technologies to a structural proteomics-type analysis of Bacillus anthracis

    NARCIS (Netherlands)

    Au, K.; Folkers, G.E.; Kaptein, R.

    2006-01-01

    A collaborative project between two Structural Proteomics In Europe (SPINE) partner laboratories, York and Oxford, aimed at high-throughput (HTP) structure determination of proteins from Bacillus anthracis, the aetiological agent of anthrax and a biomedically important target, is described. Based up

  6. Integrated transcriptomic and proteomic evaluation of gentamicin nephrotoxicity in rats

    Energy Technology Data Exchange (ETDEWEB)

    Com, Emmanuelle, E-mail: emmanuelle.com@univ-rennes1.fr [sanofi-aventis R and D, Disposition Safety and Animal Research, Vitry-sur-Seine (France); INSERM U625, Proteomics Core Facility Biogenouest, Rennes (France); Boitier, Eric; Marchandeau, Jean-Pierre [sanofi-aventis R and D, Disposition Safety and Animal Research, Vitry-sur-Seine (France); Brandenburg, Arnd [Genedata AG, Basel (Switzerland); Schroeder, Susanne [Nycomed GmbH, Barsbüttel (Germany); Hoffmann, Dana; Mally, Angela [University of Würzburg, Department of Toxicology, University of Würzburg, Würzburg (Germany); Gautier, Jean-Charles [sanofi-aventis R and D, Disposition Safety and Animal Research, Vitry-sur-Seine (France)

    2012-01-01

    Gentamicin is an aminoglycoside antibiotic, which induces renal tubular necrosis in rats. In the context of the European InnoMed PredTox project, transcriptomic and proteomic studies were performed to provide new insights into the molecular mechanisms of gentamicin-induced nephrotoxicity. Male Wistar rats were treated with 25 and 75 mg/kg/day subcutaneously for 1, 3 and 14 days. Histopathology observations showed mild tubular degeneration/necrosis and regeneration and moderate mononuclear cell infiltrate after long-term treatment. Transcriptomic data indicated a strong treatment-related gene expression modulation in kidney and blood cells at the high dose after 14 days of treatment, with the regulation of 463 and 3241 genes, respectively. Of note, the induction of NF-kappa B pathway via the p38 MAPK cascade in the kidney, together with the activation of T-cell receptor signaling in blood cells were suggestive of inflammatory processes in relation with the recruitment of mononuclear cells in the kidney. Proteomic results showed a regulation of 163 proteins in kidney at the high dose after 14 days of treatment. These protein modulations were suggestive of a mitochondrial dysfunction with impairment of cellular energy production, induction of oxidative stress, an effect on protein biosynthesis and on cellular assembly and organization. Proteomic results also provided clues for potential nephrotoxicity biomarkers such as AGAT and PRBP4 which were strongly modulated in the kidney. Transcriptomic and proteomic data turned out to be complementary and their integration gave a more comprehensive insight into the putative mode of nephrotoxicity of gentamicin which was in accordance with histopathological findings. -- Highlights: ► Gentamicin induces renal tubular necrosis in rats. ► The mechanisms of gentamicin nephrotoxicity remain still elusive. ► Transcriptomic and proteomic analyses were performed to study this toxicity in rats. ► Transcriptomic and proteomic

  7. Analysis of mass spectrometry data in proteomics

    DEFF Research Database (Denmark)

    Matthiesen, Rune; Jensen, Ole N

    2008-01-01

    that in turn allow protein identification, annotation of secondary modifications, and determination of the absolute or relative abundance of individual proteins. Advances in mass spectrometry-driven proteomics rely on robust bioinformatics tools that enable large-scale data analysis. This chapter describes......The systematic study of proteins and protein networks, that is, proteomics, calls for qualitative and quantitative analysis of proteins and peptides. Mass spectrometry (MS) is a key analytical technology in current proteomics and modern mass spectrometers generate large amounts of high-quality data...... some of the basic concepts and current approaches to the analysis of MS and MS/MS data in proteomics....

  8. Farm animal proteomics - A review

    DEFF Research Database (Denmark)

    Bendixen, Emøke; Danielsen, Marianne; Hollung, Kristin

    2011-01-01

    in large-scale operations, with the aim to obtain animal products for human consumption. Hence, understanding the biological traits that impact yield and quality of these products is the specific aim of much biological experimentation. However, most of the data gathered from experiments on e.g. swine......In agricultural sciences as in all other areas of life science, the implementation of proteomics and other post-genomic tools is an important step towards more detailed understanding of the complex biological systems that control physiology and pathology of living beings. Farm animals are raised...... and cattle are relevant not only for farm animal sciences, but also for adding to our understanding of complex biological mechanisms of health and disease in humans. The aim of this review is to present an overview of the specific topics of interest within farm animal proteomics, and to highlight some...

  9. Plasmasol, photovoltaic effect in a solar photo plasma. Final report of the project. Concerted action energy - 2003; Plasmasol, effet photovoltaique dans un photoplasma solaire. Rapport final du Projet. Action Concertee Energie - 2003 CNRS-MRNT

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2004-07-01

    The aim of this project was to study the feasibility of the solar energy photovoltaic conversion from the photo-ionization of a gaseous medium constituted of metallic vapors. After a bibliography and a recall of based physical data the report presents the absorption of the solar radiation by the cesium vapor, a simplified model of the photovoltaic effect in a photo-plasma, the experimental device and the results. (A.L.B.)

  10. Project and analysis of the toroidal magnetic field production circuits and the plasma formation of the ETE (Spherical Tokamak Experiment) tokamak; Projeto e analise dos circuitos de producao de campo magnetico toroidal e de formacao do plasma do Tokamak ETE (Experimento Tokamak Esferico)

    Energy Technology Data Exchange (ETDEWEB)

    Barbosa, Luis Filipe F.P.W.; Bosco, Edson del

    1994-12-31

    This report presents the project and analysis of the circuit for production of the toroidal magnetic field in the Tokamak ETE (Spherical Tokamak Experiment). The ETE is a Tokamak with a small-aspect-ratio parameter to be used for studying the plasma physics for the research on thermonuclear fusion. This machine is being constructed at the Laboratorio Associado de Plasma (LAP) of the Instituto Nacional de Pesquisas Espaciais (INPE) in Sao Jose dos Campos, SP, Brazil. (author). 20 refs., 39 figs., 4 tabs.

  11. Ozone inhalation modifies the rat liver proteome

    Directory of Open Access Journals (Sweden)

    Whitney S. Theis

    2014-01-01

    Full Text Available Ozone (O3 is a serious public health concern. Recent findings indicate that the damaging health effects of O3 extend to multiple systemic organ systems. Herein, we hypothesize that O3 inhalation will cause downstream alterations to the liver. To test this, male Sprague-Dawley rats were exposed to 0.5 ppm O3 for 8 h/day for 5 days. Plasma liver enzyme measurements showed that 5 day O3 exposure did not cause liver cell death. Proteomic and mass spectrometry analysis identified 10 proteins in the liver that were significantly altered in abundance following short-term O3 exposure and these included several stress responsive proteins. Glucose-regulated protein 78 and protein disulfide isomerase increased, whereas glutathione S-transferase M1 was significantly decreased by O3 inhalation. In contrast, no significant changes were detected for the stress response protein heme oxygenase-1 or cytochrome P450 2E1 and 2B in liver of O3 exposed rats compared to controls. In summary, these results show that an environmentally-relevant exposure to inhaled O3 can alter the expression of select proteins in the liver. We propose that O3 inhalation may represent an important unrecognized factor that can modulate hepatic metabolic functions.

  12. A visual approach to proteomics.

    Science.gov (United States)

    Nickell, Stephan; Kofler, Christine; Leis, Andrew P; Baumeister, Wolfgang

    2006-03-01

    Cryo-electron tomography is an emerging imaging technique that has unique potential for molecular cell biology. At the present resolution of 4-5 nm, large supramolecular structures can be studied in unperturbed cellular environments and, in the future, it will become possible to map molecular landscapes inside cells in a more comprehensive manner. 'Visual proteomics' aims to complement and extend mass-spectrometry-based inventories, and to provide a quantitative description of the macromolecular interactions that underlie cellular functions.

  13. The proteome of human retina.

    Science.gov (United States)

    Zhang, Pingbo; Dufresne, Craig; Turner, Randi; Ferri, Sara; Venkatraman, Vidya; Karani, Rabia; Lutty, Gerard A; Van Eyk, Jennifer E; Semba, Richard D

    2015-02-01

    The retina is a delicate tissue that detects light, converts photochemical energy into neural signals, and transmits the signals to the visual cortex of the brain. A detailed protein inventory of the proteome of the normal human eye may provide a foundation for new investigations into both the physiology of the retina and the pathophysiology of retinal diseases. To provide an inventory, proteins were extracted from five retinas of normal eyes and fractionated using SDS-PAGE. After in-gel digestion, peptides were analyzed in duplicate using LC-MS/MS on an Orbitrap Elite mass spectrometer. A total of 3436 nonredundant proteins were identified in the human retina, including 20 unambiguous protein isoforms, of which eight have not previously been demonstrated to exist at the protein level. The proteins identified in the retina included most of the enzymes involved in the visual cycle and retinoid metabolism. One hundred and fifty-eight proteins that have been associated with age-related macular degeneration were identified in the retina. The MS proteome database of the human retina may serve as a valuable resource for future investigations of retinal biology and disease. All MS data have been deposited in the ProteomeXchange with identifier PXD001242 (http://proteomecentral.proteomexchange.org/dataset/PXD001242).

  14. Human saliva proteome: an overview

    Science.gov (United States)

    Griffin, Timothy J.

    2014-06-01

    Human saliva contains a rich mixture of biomolecules. Proteins are a major component of this mixture. Given their role as the molecular effectors within biological systems, ranging from catalysis to transport to structure, proteins have great potential as biomarkers of health and disease. The ability to collect these salivary biomarkers easily using non-invasive means makes saliva proteins even more attractive for diagnostic applications. Thousands of proteins are now to be known to be present in human saliva - discovered using proteomic technologies. Emerging technologies are now making it possible to go beyond large-scale cataloging of salivary proteins. These include approaches to catalog protein contributions from the community of microorganisms residing in the oral cavity (metaproteomics) that may reflect the health state of the human host. New mass spectrometry-based proteomics methods are also emerging, shifting the emphasis from large-scale discovery experiments to hypothesis-driven assays for profiling proteins of interest within saliva, enabling validation of their association with specific health conditions. This paper provides a brief overview of efforts to catalog the proteome of human saliva. Recent developments making possible characterization of the metaproteome of human saliva will be discussed, and technologies driving new mass spectrometry-based assays for targeted analysis of proteins within complex samples, such as saliva.

  15. The Tokamak Fusion Test Reactor decontamination and decommissioning project and the Tokamak Physics Experiment at the Princeton Plasma Physics Laboratory. Environmental Assessment

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-05-27

    If the US is to meet the energy needs of the future, it is essential that new technologies emerge to compensate for dwindling supplies of fossil fuels and the eventual depletion of fissionable uranium used in present-day nuclear reactors. Fusion energy has the potential to become a major source of energy for the future. Power from fusion energy would provide a substantially reduced environmental impact as compared with other forms of energy generation. Since fusion utilizes no fossil fuels, there would be no release of chemical combustion products to the atmosphere. Additionally, there are no fission products formed to present handling and disposal problems, and runaway fuel reactions are impossible due to the small amounts of deuterium and tritium present. The purpose of the TPX Project is to support the development of the physics and technology to extend tokamak operation into the continuously operating (steady-state) regime, and to demonstrate advances in fundamental tokamak performance. The purpose of TFTR D&D is to ensure compliance with DOE Order 5820.2A ``Radioactive Waste Management`` and to remove environmental and health hazards posed by the TFTR in a non-operational mode. There are two proposed actions evaluated in this environmental assessment (EA). The actions are related because one must take place before the other can proceed. The proposed actions assessed in this EA are: the decontamination and decommissioning (D&D) of the Tokamak Fusion Test Reactor (TFTR); to be followed by the construction and operation of the Tokamak Physics Experiment (TPX). Both of these proposed actions would take place primarily within the TFTR Test Cell Complex at the Princeton Plasma Physics Laboratory (PPPL). The TFTR is located on ``D-site`` at the James Forrestal Campus of Princeton University in Plainsboro Township, Middlesex County, New Jersey, and is operated by PPPL under contract with the United States Department of Energy (DOE).

  16. Proteomics--a blessing or a curse? Application of proteomics technology to transplant medicine.

    Science.gov (United States)

    Kienzl-Wagner, Katrin; Pratschke, Johann; Brandacher, Gerald

    2011-09-15

    Proteomics has emerged as a powerful tool in clinical biomarker research. In the field of transplantation, proteomics aims not only at developing noninvasive tools for immune monitoring and identifying biomarkers of allograft rejection but also to gain mechanistic insights into the pathophysiology of an alloimmune response and hence defining new therapeutic targets. A basic knowledge of proteomic technology is a prerequisite to appreciate the complex data generated and required for critical evaluation/interpretation of proteomic-driven studies. This review provides an overview of proteomic approaches and its underlying concepts and discusses the advantages, clinical implications, challenges, and limitations of this exciting modality in transplantation.

  17. Princeton Plasma Physics Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    1990-01-01

    This report discusses the following topics: principal parameters achieved in experimental devices fiscal year 1990; tokamak fusion test reactor; compact ignition tokamak; Princeton beta experiment- modification; current drive experiment-upgrade; international collaboration; x-ray laser studies; spacecraft glow experiment; plasma processing: deposition and etching of thin films; theoretical studies; tokamak modeling; international thermonuclear experimental reactor; engineering department; project planning and safety office; quality assurance and reliability; technology transfer; administrative operations; PPPL patent invention disclosures for fiscal year 1990; graduate education; plasma physics; graduate education: plasma science and technology; science education program; and Princeton Plasma Physics Laboratory reports fiscal year 1990.

  18. Integrating cell biology and proteomic approaches in plants.

    Science.gov (United States)

    Takáč, Tomáš; Šamajová, Olga; Šamaj, Jozef

    2017-04-22

    Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science. Cell biology approaches are most frequently used in proteomic studies investigating subcellular and developmental proteomes, however, they were also employed in proteomic studies exploring abiotic and biotic stress responses, vesicular transport, cytoskeleton and protein posttranslational modifications. They are used either for detailed cellular or ultrastructural characterization of the object subjected to proteomic study, validation of proteomic results or to expand proteomic data. In this respect, a broad spectrum of methods is employed to support proteomic studies including ultrastructural electron microscopy studies, histochemical staining, immunochemical localization, in vivo imaging of fluorescently tagged proteins and visualization of protein-protein interactions. Thus, cell biological observations on fixed or living cell compartments, cells, tissues and organs are feasible, and in some cases fundamental for the validation and complementation of proteomic data. Validation of proteomic data by independent experimental methods requires development of new complementary approaches. Benefits of cell biology methods and techniques are not sufficiently highlighted in current proteomic studies. This encouraged us to review most popular cell biology methods used in proteomic studies and to evaluate their relevance and potential for proteomic data validation and enrichment of purely proteomic analyses. We also provide examples of

  19. Batch effects correction improves the sensitivity of significance tests in spectral counting-based comparative discovery proteomics.

    Science.gov (United States)

    Gregori, Josep; Villarreal, Laura; Méndez, Olga; Sánchez, Alex; Baselga, José; Villanueva, Josep

    2012-07-16

    Shotgun proteomics has become the standard proteomics technique for the large-scale measurement of protein abundances in biological samples. Despite quantitative proteomics has been usually performed using label-based approaches, label-free quantitation offers advantages related to the avoidance of labeling steps, no limitation in the number of samples to be compared, and the gain in protein detection sensitivity. However, since samples are analyzed separately, experimental design becomes critical. The exploration of spectral counting quantitation based on LC-MS presented here gathers experimental evidence of the influence of batch effects on comparative proteomics. The batch effects shown with spiking experiments clearly interfere with the biological signal. In order to minimize the interferences from batch effects, a statistical correction is proposed and implemented. Our results show that batch effects can be attenuated statistically when proper experimental design is used. Furthermore, the batch effect correction implemented leads to a substantial increase in the sensitivity of statistical tests. Finally, the applicability of our batch effects correction is shown on two different biomarker discovery projects involving cancer secretomes. We think that our findings will allow designing and executing better comparative proteomics projects and will help to avoid reaching false conclusions in the field of proteomics biomarker discovery. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. An individual urinary proteome analysis in normal human beings to define the minimal sample number to represent the normal urinary proteome

    National Research Council Canada - National Science Library

    Liu, Xuejiao; Shao, Chen; Wei, Lilong; Duan, Jindan; Wu, Shuzhen; Li, Xuewang; Li, Mingxi; Sun, Wei

    2012-01-01

    The urinary proteome has been widely used for biomarker discovery. A urinary proteome database from normal humans can provide a background for discovery proteomics and candidate proteins/peptides for targeted proteomics...

  1. Modification-specific proteomics in plant biology

    DEFF Research Database (Denmark)

    Ytterberg, A Jimmy; Jensen, Ole N

    2010-01-01

    and proteomics. In general, methods for PTM characterization are developed to study yeast and mammalian biology and later adopted to investigate plants. Our point of view is that it is advantageous to enrich for PTMs on the peptide level as part of a quantitative proteomics strategy to not only identify the PTM...

  2. Intestinal proteome changes during infant necrotizing enterocolitis

    DEFF Research Database (Denmark)

    Jiang, Pingping; Smith, Birgitte; Qvist, Niels;

    2013-01-01

    Background: Changes in the intestinal and colonic proteome in patients with necrotizing enterocolitis (NEC) may help to characterize the disease pathology and identify new biomarkers and treatment targets for NEC. Methods: Using gel-based proteomics, proteins in NEC-affected intestinal and coloni...

  3. Dynamic Proteomic Insights of Seed Germination

    Institute of Scientific and Technical Information of China (English)

    Marc Galland; Romain Huguet; Erwann Arc; Gwendal Cueff; Dominique Job; Lo(i)c Rajjou

    2012-01-01

    Proteome analysis,which involves the identification and characterization of expressed proteins,is a powerful tool for determining the biological roles and functions of individual proteins.Furthermore,by providing a systematic and without any a priori mean for large-scale identification of cellular proteins,proteomics is expected to accelerate discoveries in complex processes such as plant development.Our research activity is mainly focused on the "Functional proteomics" approach in the field of seed biology.We are developing a proteome analysis of the model plant,Arabidopsis thaliana,in order to investigate seed development,dormancy,germination and longevity and identify related changes in the seed proteome.Combined approaches associating classical 2D gel-based proteome and dynamic radiolabeled proteome disclosed data regarding protein turnover and protein stability (http://www.seed-proteome.com).The selective translation of mRNAs emerges as an important mechanism regulating molecular functions involved in the control of seed germination.

  4. Proteomics: Protein Identification Using Online Databases

    Science.gov (United States)

    Eurich, Chris; Fields, Peter A.; Rice, Elizabeth

    2012-01-01

    Proteomics is an emerging area of systems biology that allows simultaneous study of thousands of proteins expressed in cells, tissues, or whole organisms. We have developed this activity to enable high school or college students to explore proteomic databases using mass spectrometry data files generated from yeast proteins in a college laboratory…

  5. Proteomic Biomarkers for Spontaneous Preterm Birth

    DEFF Research Database (Denmark)

    Kacerovsky, Marian; Lenco, Juraj; Musilova, Ivana

    2014-01-01

    This review aimed to identify, synthesize, and analyze the findings of studies on proteomic biomarkers for spontaneous preterm birth (PTB). Three electronic databases (Medline, Embase, and Scopus) were searched for studies in any language reporting the use of proteomic biomarkers for PTB published...

  6. Applications of proteomics in hepatic diseases research

    Institute of Scientific and Technical Information of China (English)

    SUN; Wei; HE; Fuchu

    2004-01-01

    Proteomics has become an important part in the leading research area and been widely used in the disease-associated study. In hepatic research field, proteomics could be applied in study of hepatic diseases including liver cancer, cirrhosis and hepatotoxicities, etc. Significant proteins could be identified as biomarkers, drug targets and clues for pathogenesis illumination.

  7. Proteomics: Protein Identification Using Online Databases

    Science.gov (United States)

    Eurich, Chris; Fields, Peter A.; Rice, Elizabeth

    2012-01-01

    Proteomics is an emerging area of systems biology that allows simultaneous study of thousands of proteins expressed in cells, tissues, or whole organisms. We have developed this activity to enable high school or college students to explore proteomic databases using mass spectrometry data files generated from yeast proteins in a college laboratory…

  8. Statistical data processing in clinical proteomics

    NARCIS (Netherlands)

    S. Smit

    2009-01-01

    The subject of this thesis is the analysis of data in clinical proteomics studies aimed at the discovery of biomarkers. The data sets produced in proteomics studies are huge, characterized by a small number of samples in which many proteins and peptides are measured. The studies described in this th

  9. Embryology in the era of proteomics.

    Science.gov (United States)

    Katz-Jaffe, Mandy G; McReynolds, Susanna

    2013-03-15

    Proteomic technologies have begun providing evidence that viable embryos possess unique protein profiles. Some of these potential protein biomarkers have been identified as extracellular and could be used in the development of a noninvasive quantitative method for embryo assessment. The field of assisted reproductive technologies would benefit from defining the human embryonic proteome and secretome, thereby expanding our current knowledge of embryonic cellular processes.

  10. GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data.

    Science.gov (United States)

    Rigbolt, Kristoffer T G; Vanselow, Jens T; Blagoev, Blagoy

    2011-08-01

    Recent technological advances have made it possible to identify and quantify thousands of proteins in a single proteomics experiment. As a result of these developments, the analysis of data has become the bottleneck of proteomics experiment. To provide the proteomics community with a user-friendly platform for comprehensive analysis, inspection and visualization of quantitative proteomics data we developed the Graphical Proteomics Data Explorer (GProX)(1). The program requires no special bioinformatics training, as all functions of GProX are accessible within its graphical user-friendly interface which will be intuitive to most users. Basic features facilitate the uncomplicated management and organization of large data sets and complex experimental setups as well as the inspection and graphical plotting of quantitative data. These are complemented by readily available high-level analysis options such as database querying, clustering based on abundance ratios, feature enrichment tests for e.g. GO terms and pathway analysis tools. A number of plotting options for visualization of quantitative proteomics data is available and most analysis functions in GProX create customizable high quality graphical displays in both vector and bitmap formats. The generic import requirements allow data originating from essentially all mass spectrometry platforms, quantitation strategies and software to be analyzed in the program. GProX represents a powerful approach to proteomics data analysis providing proteomics experimenters with a toolbox for bioinformatics analysis of quantitative proteomics data. The program is released as open-source and can be freely downloaded from the project webpage at http://gprox.sourceforge.net.

  11. Tools for the Validation of Genomes and Transcriptomes with Proteomics data

    DEFF Research Database (Denmark)

    Pang, Chi Nam Ignatius; Aya, Carlos; Tay, Aidan

    Aims With the large amount of genomics and proteomics data currently available, there remains a lack of tools to integrate data from these two fields. This project aims to provide a ‘nexus’ for integrating genomics and transcriptomics data generated from next-generation sequencing with proteomics...... data generated from protein mass spectrometry. We are developing a set of tools which allow users to: •Co-visualise genomics, transcriptomics, and proteomics data using the Integrated Genomics Viewer (IGV).1 •Validate the existence of genes and mRNAs using peptides identified from mass spectrometry...... experiments. •Validate alternatively spliced mRNA isoforms by searching for peptides that span across exon-exon junctions....

  12. Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome

    DEFF Research Database (Denmark)

    Grassl, Niklas; Kulak, Nils Alexander; Pichler, Garwin

    2016-01-01

    , disruptions in saliva secretion and changes in the oral microbiome contribute to conditions such as tooth decay and respiratory tract infections. Here we set out to quantitatively map the saliva proteome in great depth with a rapid and in-depth mass spectrometry-based proteomics workflow. METHODS: We used...... with next-generation sequencing data from the Human Microbiome Project as well as a comparison to MALDI-TOF mass spectrometry on microbial cultures revealed strong agreement. The oral microbiome differs between individuals and changes drastically upon eating and tooth brushing. CONCLUSION: Rapid shotgun...... and robust technology can now simultaneously characterize the human and microbiome contributions to the proteome of a body fluid and is therefore a valuable complement to genomic studies. This opens new frontiers for the study of host-pathogen interactions and clinical saliva diagnostics....

  13. Urine sample preparation and fractionation for global proteome profiling by LC-MS.

    Science.gov (United States)

    Court, Magali; Garin, Jérôme; Masselon, Christophe D

    2015-01-01

    Urine has garnered tremendous interest over the past decade as a potential source of protein biomarkers for various pathologies. However, due to its low protein concentration and the presence of interfering compounds, urine constitutes a challenging analyte in proteomics. In the context of a project aimed at the discovery and evaluation of new candidate biomarkers of bladder cancer in urine, our laboratory has implemented and evaluated an array of preparation techniques for urinary proteome analysis. We present here the protocol that, in our hands, yielded the best overall proteome coverage with the lowest analytical effort. It begins with protein precipitation using trichloroacetic acid, in solution digestion and RP-C18 cartridge desalting of the resulting peptides mixture, and is followed by peptide fractionation by gel-free isoelectric focusing, and nano-LC-MS/MS for database compilation.

  14. Multidimensional protein fractionation using ProteomeLab PF 2D™ for profiling amyotrophic lateral sclerosis immunity: A preliminary report

    Directory of Open Access Journals (Sweden)

    Mosley R Lee

    2008-09-01

    Full Text Available Abstract Background The ProteomeLab™ PF 2D platform is a relatively new approach to global protein profiling. Herein, it was used for investigation of plasma proteome changes in amyotrophic lateral sclerosis (ALS patients before and during immunization with glatiramer acetate (GA in a clinical trial. Results The experimental design included immunoaffinity depletion of 12 most abundant proteins from plasma samples with the ProteomeLab™ IgY-12 LC10 column kit as first dimension separation, also referred to as immuno-partitioning. Second and third dimension separations of the enriched proteome were performed on the PF 2D platform utilizing 2D isoelectric focusing and RP-HPLC with the resulting fractions collected for analysis. 1D gel electrophoresis was added as a fourth dimension when sufficient protein was available. Protein identification from collected fractions was performed using nano-LC-MS/MS approach. Analysis of differences in the resulting two-dimensional maps of fractions obtained from the PF 2D and the ability to identify proteins from these fractions allowed sensitivity threshold measurements. Masked proteins in the PF 2D fractions are discussed. Conclusion We offer some insight into the strengths and limitations of this emerging proteomic platform.

  15. Mass spectrometry-based serum proteome pattern analysis in molecular diagnostics of early stage breast cancer

    Directory of Open Access Journals (Sweden)

    Stobiecki Maciej

    2009-07-01

    .0003 increased level of osteopontin in blood of the group of cancer patients studied (however, the plasma level of osteopontin classified cancer samples with 88% sensitivity but only 28% specificity. Conclusion MALDI-ToF spectrometry of serum has an obvious potential to differentiate samples between early breast cancer patients and healthy controls. Importantly, a classifier built on MS-based serum proteome patterns outperforms available protein biomarkers analyzed in blood by immunoassays.

  16. 转乙型肝炎病毒表面抗原基因小鼠肝细胞质膜蛋白质组学研究%Proteomic analysis of liver plasma membrane from hepatitis B surface antigen transgenic mice

    Institute of Scientific and Technical Information of China (English)

    贾小芳; 李春洪; 彭霞; 尹林; 冯艳玲; 马芳; 张丽军

    2012-01-01

    Objective To explore the differential liver plasma membrane (PM) proteins that may be related to the occurrence,development and reversal process of hepatitis and to understand the pathogenesis of hepatitis and the new drug targets by performing a comparative proteomics research of liver PM between hepatitis B surface antigen (HBsAg) transgenic mice and wild-type C57 mice.Methods A 6-month-old HBsAg transgenic mouse model was established.The pathological examination was performed to observe the pathological changes of transgenic mice and wild-type C57 mice.The PM from liver tissue of 6-month-old transgenic mouse and the control mouse were purified through twice sucrose density grade centrifugation combined with second antibody magnetic bead enrichment.The purity of extracted PM was verified by Western blot.Differential proteome expression analysis was performed by using two-dimensional electrophoresis (2-DE) and ImageMaster software analysis.The differentially expressed proteins were lysed by trypsin and identified by liquid chromatography combined with tandem mass spectrometry (LC-MS/MS) analysis.Results The pathological examination results showed that hepatitis was observed in the transgenic mouse group,while no abnormity was found in the controls.The PM was successfully enriched and the mitochondria contamination was reduced by sucrose density grade centrifugation combined with second antibody magnetic bead purification treatment.Thirty differential mice liver PM protein spots were visualized,in which 11 non-redundant proteins were successfully identified by LC-MS/MS in transgenic mouse group,including 9 up regulated protein spots and 2 down-regulated protein spots.These differentially expressed proteins included keratin,cardiac Ca2+ release channel,cytochrome B5,ATP synthase subunit alpha,etc.Conclusions A batch of HBsAg gene expression related differential proteins are identified in mouse liver plasma.These proteins might be new drug targets for anti

  17. A Novel Strategy for Proteome-wide Ligand Screening Using Cross-linked Phage Matrices*

    OpenAIRE

    Qian, Chen; LIU, Jian-ning; Tang, Fengyuan; Yuan, Dawen; Guo, Zhigang; Zhang, Jing

    2010-01-01

    To find a suitable ligand from a complex antigen system is still a mission to be accomplished. Here we have explored a novel “library against proteome” panning strategy for ligand screening and antigen purification from a complex system using phage-displayed antibody technology. Human plasma proteome was targeted for phage library panning. During the process, the panning was carried out in solution, using a biotin/streptavidin beads separation system, for three rounds. Nine monoclonal phages,...

  18. Toward defining the anatomo-proteomic puzzle of the human brain: An integrative analysis.

    Science.gov (United States)

    Fernandez-Irigoyen, Joaquín; Labarga, Alberto; Zabaleta, Aintzane; de Morentin, Xabier Martínez; Perez-Valderrama, Estela; Zelaya, María Victoria; Santamaria, Enrique

    2015-10-01

    The human brain is exceedingly complex, constituted by billions of neurons and trillions of synaptic connections that, in turn, define ∼900 neuroanatomical subdivisions in the adult brain (Hawrylycz et al. An anatomically comprehensive atlas of the human brain transcriptome. Nature 2012, 489, 391-399). The human brain transcriptome has revealed specific regional transcriptional signatures that are regulated in a spatiotemporal manner, increasing the complexity of the structural and molecular organization of this organ (Kang et al. Spatio-temporal transcriptome of the human brain. Nature 2011, 478, 483-489). During the last decade, neuroproteomics has emerged as a powerful approach to profile neural proteomes using shotgun-based MS, providing complementary information about protein content and function at a global level. Here, we revise recent proteome profiling studies performed in human brain, with special emphasis on proteome mapping of anatomical macrostructures, specific subcellular compartments, and cerebrospinal fluid. Moreover, we have performed an integrative functional analysis of the protein compilation derived from these large-scale human brain proteomic studies in order to obtain a comprehensive view of human brain biology. Finally, we also discuss the potential contribution of our meta-analysis to the Chromosome-centric Human Proteome Project initiative. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Panorama: a targeted proteomics knowledge base.

    Science.gov (United States)

    Sharma, Vagisha; Eckels, Josh; Taylor, Greg K; Shulman, Nicholas J; Stergachis, Andrew B; Joyner, Shannon A; Yan, Ping; Whiteaker, Jeffrey R; Halusa, Goran N; Schilling, Birgit; Gibson, Bradford W; Colangelo, Christopher M; Paulovich, Amanda G; Carr, Steven A; Jaffe, Jacob D; MacCoss, Michael J; MacLean, Brendan

    2014-09-05

    Panorama is a web application for storing, sharing, analyzing, and reusing targeted assays created and refined with Skyline,1 an increasingly popular Windows client software tool for targeted proteomics experiments. Panorama allows laboratories to store and organize curated results contained in Skyline documents with fine-grained permissions, which facilitates distributed collaboration and secure sharing of published and unpublished data via a web-browser interface. It is fully integrated with the Skyline workflow and supports publishing a document directly to a Panorama server from the Skyline user interface. Panorama captures the complete Skyline document information content in a relational database schema. Curated results published to Panorama can be aggregated and exported as chromatogram libraries. These libraries can be used in Skyline to pick optimal targets in new experiments and to validate peak identification of target peptides. Panorama is open-source and freely available. It is distributed as part of LabKey Server,2 an open source biomedical research data management system. Laboratories and organizations can set up Panorama locally by downloading and installing the software on their own servers. They can also request freely hosted projects on https://panoramaweb.org , a Panorama server maintained by the Department of Genome Sciences at the University of Washington.

  20. Subnuclear proteomics in colorectal cancer

    DEFF Research Database (Denmark)

    Albrethsen, Jakob; Knol, Jaco C; Piersma, Sander R

    2010-01-01

    Abnormalities in nuclear phenotype and chromosome structure are key features of cancer cells. Investigation of the protein determinants of nuclear subfractions in cancer may yield molecular insights into aberrant chromosome function and chromatin organization and in addition may yield biomarkers...... for early cancer detection. Here we evaluate a proteomics work flow for profiling protein constituents in subnuclear domains in colorectal cancer tissues and apply this work flow to a comparative analysis of the nuclear matrix fraction in colorectal adenoma and carcinoma tissue samples. First, we...

  1. Synchrotron radiation and structural proteomics

    CERN Document Server

    Pechkova, Eugenia

    2011-01-01

    This book presents an overview of the current state of research in both synchrotron radiation and structural proteomics from different laboratories worldwide. The book presents recent research results in the most advanced methods of synchrotron radiation analysis, protein micro- and nano crystallography, X-ray scattering and X-ray optics, coherent X-Ray diffraction, and laser cutting and contactless sample manipulation are described in details. The book focuses on biological applications and highlights important aspects such as radiation damage and molecular modeling.

  2. The potato tuber mitochondrial proteome

    DEFF Research Database (Denmark)

    Møller, Ian Max; Salvato, Fernanda; Havelund, Jesper

    We are testing the hypothesis that oxidized peptides are released from stressed mitochondria and contribute to retrograde signalling (Møller IM & Sweetlove LJ 2010 Trends Plant Sci 15, 370-374). However, there is a large gap between the number of experimentally verified mitochondrial proteins (~450......) and in silico-predicted mitochondrial proteins (2000-3000). Thus, before starting to look for oxidized peptides, we wanted to expand the current compendium of plant mitochondrial proteins while obtaining what could be termed the "baseline proteome" from our model organelle, the potato tuber mitochondrion. Its...

  3. Longitudinal Bank for Serum, Plasma, and DNA for Detection of Biomarkers

    Energy Technology Data Exchange (ETDEWEB)

    Vogelzang, Nicolas; Fink, Louis

    2007-11-12

    The discovery of genetic or biochemical markers to discriminate malignant cancers from normal or benign disease states, markers to stage cancer or monitor disease progression and markers that provide an early indication of an individual’s response to chemotherapy have become a major research objectives of the oncology community over the past few years. The goal of the project is to create a patient speciment bank of serum, plasma, urine and tissues from approximately 1500 individuals. The collection of samples from individuals on a longitudinal basis provided proteomic and biochemical data to be correlated with clinical endpoints. This greatly enhanced our ability to identify biiomarkers for staging different cancers and to detect patient responsiveness to therapy at an early state in the treatment process.

  4. A Colorimetric Method for Monitoring Tryptic Digestion Prior to Shotgun Proteomics

    Directory of Open Access Journals (Sweden)

    Richard I. Somiari

    2014-01-01

    Full Text Available Tryptic digestion is an important preanalytical step in shotgun proteomics because inadequate or excessive digestion can result in a failed or incomplete experiment. Unfortunately, this step is not routinely monitored before mass spectrometry because methods available for protein digestion monitoring either are time/sample consuming or require expensive equipment. To determine if a colorimetric method (ProDM Kit can be used to identify the extent of tryptic digestion that yields the best proteomics outcome, plasma and serum digested for 8 h and 24 h were screened with ProDM, Bioanalyzer, and LC/MS/MS, and the effect of digestion on the number of proteins identified and sequence coverage was compared. About 6% and 16% less proteins were identified when >50% of proteins were digested in plasma and serum, respectively, compared to when ~46% of proteins were digested. Average sequence coverage for albumin, haptoglobin, and serotransferrin after 2 h, 8 h, and 24 h digestion was 52%, 45%, and 45% for serum and 54%, 47%, and 42% for plasma, respectively. This paper reiterates the importance of optimizing the tryptic digestion step and demonstrates the extent to which ProDM can be used to monitor and standardize protein digestion to achieve better proteomics outcomes.

  5. Predicting Chemical Toxicity from Proteomics and Computational Chemistry

    Science.gov (United States)

    2008-07-30

    cells. Results for the numerical invariants based on proteomics maps from liver tissue from rats exposed to peroxisome proliferators...characterizations of proteomic maps and chemically induced changes to proteomes, K Balasubramanian, K Khokhani and SC Basak, Proteome Res., 5,1133-1142 (2006...for proteomics maps: Application to rodent hepatotoxicity , SC Basak, BD Gute, KT Geiss and FA Witzmann, in Computation in Modern Science and

  6. Age-related differences in plasma proteins: how plasma proteins change from neonates to adults.

    Directory of Open Access Journals (Sweden)

    Vera Ignjatovic

    Full Text Available The incidence of major diseases such as cardiovascular disease, thrombosis and cancer increases with age and is the major cause of mortality world-wide, with neonates and children somehow protected from such diseases of ageing. We hypothesized that there are major developmental differences in plasma proteins and that these contribute to age-related changes in the incidence of major diseases. We evaluated the human plasma proteome in healthy neonates, children and adults using the 2D-DIGE approach. We demonstrate significant changes in number and abundance of up to 100 protein spots that have marked differences in during the transition of the plasma proteome from neonate and child through to adult. These proteins are known to be involved in numerous physiological processes such as iron transport and homeostasis, immune response, haemostasis and apoptosis, amongst others. Importantly, we determined that the proteins that are differentially expressed with age are not the same proteins that are differentially expressed with gender and that the degree of phosphorylation of plasma proteins also changes with age. Given the multi-functionality of these proteins in human physiology, understanding the differences in the plasma proteome in neonates and children compared to adults will make a major contribution to our understanding of developmental biology in humans.

  7. Plasma Proteome Profiling to Assess Human Health and Disease

    DEFF Research Database (Denmark)

    Geyer, Philipp E; Kulak, Nils A; Pichler, Garwin

    2016-01-01

    from 1 μl single finger pricks with 20 min gradients. The apolipoprotein family, inflammatory markers such as C-reactive protein, gender-related proteins, and >40 FDA-approved biomarkers are reproducibly quantified (CV

  8. High-density lipoprotein proteome dynamics in human endotoxemia

    Directory of Open Access Journals (Sweden)

    Stroes Erik SG

    2011-06-01

    Full Text Available Abstract Background A large variety of proteins involved in inflammation, coagulation, lipid-oxidation and lipid metabolism have been associated with high-density lipoprotein (HDL and it is anticipated that changes in the HDL proteome have implications for the multiple functions of HDL. Here, SELDI-TOF mass spectrometry (MS was used to study the dynamic changes of HDL protein composition in a human experimental low-dose endotoxemia model. Ten healthy men with low HDL cholesterol (0.7+/-0.1 mmol/L and 10 men with high HDL cholesterol levels (1.9+/-0.4 mmol/L were challenged with endotoxin (LPS intravenously (1 ng/kg bodyweight. We previously showed that subjects with low HDL cholesterol are more susceptible to an inflammatory challenge. The current study tested the hypothesis that this discrepancy may be related to differences in the HDL proteome. Results Plasma drawn at 7 time-points over a 24 hour time period after LPS challenge was used for direct capture of HDL using antibodies against apolipoprotein A-I followed by subsequent SELDI-TOF MS profiling. Upon LPS administration, profound changes in 21 markers (adjusted p-value Conclusions This study shows that the semi-quantitative differences in the HDL proteome as assessed by SELDI-TOF MS cannot explain why subjects with low HDL cholesterol are more susceptible to a challenge with LPS than those with high HDL cholesterol. Instead the results indicate that hierarchical clustering could be useful to predict HDL functionality in acute phase responses towards LPS.

  9. The proteome response to amyloid protein expression in vivo.

    Directory of Open Access Journals (Sweden)

    Ricardo A Gomes

    Full Text Available Protein misfolding disorders such as Alzheimer, Parkinson and transthyretin amyloidosis are characterized by the formation of protein amyloid deposits. Although the nature and location of the aggregated proteins varies between different diseases, they all share similar molecular pathways of protein unfolding, aggregation and amyloid deposition. Most effects of these proteins are likely to occur at the proteome level, a virtually unexplored reality. To investigate the effects of an amyloid protein expression on the cellular proteome, we created a yeast expression system using human transthyretin (TTR as a model amyloidogenic protein. We used Saccharomyces cerevisiae, a living test tube, to express native TTR (non-amyloidogenic and the amyloidogenic TTR variant L55P, the later forming aggregates when expressed in yeast. Differential proteome changes were quantitatively analyzed by 2D-differential in gel electrophoresis (2D-DIGE. We show that the expression of the amyloidogenic TTR-L55P causes a metabolic shift towards energy production, increased superoxide dismutase expression as well as of several molecular chaperones involved in protein refolding. Among these chaperones, members of the HSP70 family and the peptidyl-prolyl-cis-trans isomerase (PPIase were identified. The latter is highly relevant considering that it was previously found to be a TTR interacting partner in the plasma of ATTR patients but not in healthy or asymptomatic subjects. The small ubiquitin-like modifier (SUMO expression is also increased. Our findings suggest that refolding and degradation pathways are activated, causing an increased demand of energetic resources, thus the metabolic shift. Additionally, oxidative stress appears to be a consequence of the amyloidogenic process, posing an enhanced threat to cell survival.

  10. 2D-electrophoresis and multiplex immunoassay proteomic analysis of different body fluids and cellular components reveal known and novel markers for extended fasting

    Directory of Open Access Journals (Sweden)

    Evelo Chris T

    2011-03-01

    Full Text Available Abstract Background Proteomic technologies applied for profiling human biofluids and blood cells are considered to reveal new biomarkers of exposure or provide insights into novel mechanisms of adaptation. Methods Both a non-targeted (classical 2D-electrophoresis combined with mass spectrometry as well as a targeted proteomic approach (multiplex immunoassay were applied to investigate how fasting for 36 h, as compared to 12 h, affects the proteome of platelets, peripheral blood mononuclear cells (PBMC, plasma, urine and saliva collected from ten healthy volunteers. Results Between-subject variability was highest in the plasma proteome and lowest in the PBMC proteome. Random Forests analysis performed on the entire dataset revealed that changes in the level of the RhoGDI2 protein in PBMC and plasma ApoA4 levels were the two most obvious biomarkers of an extended fasting. Random Forests (RF analysis of the multiplex immunoassay data revealed leptin and MMP-3 as biomarkers for extended fasting. However, high between-subject variability may have masked the extended fasting effects in the proteome of the biofluids and blood cells. Conclusions Identification of significantly changed proteins in biofluids and blood cells using a non-targeted approach, together with the outcome of targeted analysis revealed both known and novel markers for a 36 h fasting period, including the cellular proteins RhoGDI2 and CLIC1, and plasma proteins ApoA4, leptin and MMP-3. The PBMC proteome exhibited the lowest between-subject variability and therefore these cells appear to represent the best biosamples for biomarker discovery in human nutrigenomics.

  11. Network-based analysis of proteomic profiles

    KAUST Repository

    Wong, Limsoon

    2016-01-26

    Mass spectrometry (MS)-based proteomics is a widely used and powerful tool for profiling systems-wide protein expression changes. It can be applied for various purposes, e.g. biomarker discovery in diseases and study of drug responses. Although RNA-based high-throughput methods have been useful in providing glimpses into the underlying molecular processes, the evidences they provide are indirect. Furthermore, RNA and corresponding protein levels have been known to have poor correlation. On the other hand, MS-based proteomics tend to have consistency issues (poor reproducibility and inter-sample agreement) and coverage issues (inability to detect the entire proteome) that need to be urgently addressed. In this talk, I will discuss how these issues can be addressed by proteomic profile analysis techniques that use biological networks (especially protein complexes) as the biological context. In particular, I will describe several techniques that we have been developing for network-based analysis of proteomics profile. And I will present evidence that these techniques are useful in identifying proteomics-profile analysis results that are more consistent, more reproducible, and more biologically coherent, and that these techniques allow expansion of the detected proteome to uncover and/or discover novel proteins.

  12. Proteomic Analysis of Chinese Hamster Ovary Cells

    Science.gov (United States)

    Baycin-Hizal, Deniz; Tabb, David L.; Chaerkady, Raghothama; Chen, Lily; Lewis, Nathan E.; Nagarajan, Harish; Sarkaria, Vishaldeep; Kumar, Amit; Wolozny, Daniel; Colao, Joe; Jacobson, Elena; Tian, Yuan; O'Meally, Robert N.; Krag, Sharon S.; Cole, Robert N.; Palsson, Bernhard O.; Zhang, Hui; Betenbaugh, Michael

    2013-01-01

    In order to complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO including the cellular proteome, secretome, and glycoproteome using tandem mass spectrometry (MS/MS) of multiple fractions obtained from gel electrophoresis, multi-dimensional liquid chromatography, and solid phase extraction of glycopeptides (SPEG). From the 120 different mass spectrometry analyses generating 682,097 MS/MS spectra, 93,548 unique peptide sequences were identified with at most a 0.02 false discovery rate (FDR). A total of 6164 grouped proteins were identified from both glycoproteome and proteome analysis, representing an 8-fold increase in the number of proteins currently identified in the CHO proteome. Furthermore, this is the first proteomic study done using CHO genome exclusively which provides for more accurate identification of proteins. From this analysis, the CHO codon frequency was determined and found to be distinct from humans, which will facilitate expression of human proteins in CHO cells. Analysis of the combined proteomic and mRNA data sets indicated the enrichment of a number of pathways including protein processing and apoptosis but depletion of proteins involved in steroid hormone and glycosphingolipid metabolism. 504 of the detected proteins included N-acetylation modifications and 1292 different proteins were observed to be N-glycosylated. This first large-scale proteomic analysis will enhance the knowledge base about CHO capabilities for recombinant expression and provide information useful in cell engineering efforts aimed at modifying CHO cellular functions. PMID:22971049

  13. Visualizing Meta-Features in Proteomic Maps

    Directory of Open Access Journals (Sweden)

    Lepouras George

    2011-07-01

    Full Text Available Abstract Background The steps of a high-throughput proteomics experiment include the separation, differential expression and mass spectrometry-based identification of proteins. However, the last and more challenging step is inferring the biological role of the identified proteins through their association with interaction networks, biological pathways, analysis of the effect of post-translational modifications, and other protein-related information. Results In this paper, we present an integrative visualization methodology that allows combining experimentally produced proteomic features with protein meta-features, typically coming from meta-analysis tools and databases, in synthetic Proteomic Feature Maps. Using three proteomics analysis scenarios, we show that the proposed visualization approach is effective in filtering, navigating and interacting with the proteomics data in order to address visually challenging biological questions. The novelty of our approach lies in the ease of integration of any user-defined proteomic features in easy-to-comprehend visual representations that resemble the familiar 2D-gel images, and can be adapted to the user's needs. The main capabilities of the developed VIP software, which implements the presented visualization methodology, are also highlighted and discussed. Conclusions By using this visualization and the associated VIP software, researchers can explore a complex heterogeneous proteomics dataset from different perspectives in order to address visually important biological queries and formulate new hypotheses for further investigation. VIP is freely available at http://pelopas.uop.gr/~egian/VIP/index.html.

  14. Legume proteomics: Progress, prospects, and challenges.

    Science.gov (United States)

    Rathi, Divya; Gayen, Dipak; Gayali, Saurabh; Chakraborty, Subhra; Chakraborty, Niranjan

    2016-01-01

    Legumes are the major sources of food and fodder with strong commercial relevance, and are essential components of agricultural ecosystems owing to their ability to carry out endosymbiotic nitrogen fixation. In recent years, legumes have become one of the major choices of plant research. The legume proteomics is currently represented by more than 100 reference maps and an equal number of stress-responsive proteomes. Among the 48 legumes in the protein databases, most proteomic studies have been accomplished in two model legumes, soybean, and barrel medic. This review highlights recent contributions in the field of legume proteomics to comprehend the defence and regulatory mechanisms during development and adaptation to climatic changes. Here, we attempted to provide a concise overview of the progress in legume proteomics and discuss future developments in three broad perspectives: (i) proteome of organs/tissues; (ii) subcellular compartments; and (iii) spatiotemporal changes in response to stress. Such data mining may aid in discovering potential biomarkers for plant growth, in general, apart from essential components involved in stress tolerance. The prospect of integrating proteome data with genome information from legumes will provide exciting opportunities for plant biologists to achieve long-term goals of crop improvement and sustainable agriculture.

  15. Proteomics and the Inner Ear

    Directory of Open Access Journals (Sweden)

    Isolde Thalmann

    2001-01-01

    Full Text Available The inner ear, one of the most complex organs, contains within its bony shell three sensory systems, the evolutionary oldest gravity receptor system, the three semicircular canals for the detection of angular acceleration, and the auditory system - unrivaled in sensitivity and frequency discrimination. All three systems are susceptible to a host of afflictions affecting the quality of life for all of us. In the first part of this review we present an introduction to the milestones of inner ear research to pave the way for understanding the complexities of a proteomics approach to the ear. Minute sensory structures, surrounded by large fluid spaces and a hard bony shell, pose extreme challenges to the ear researcher. In spite of these obstacles, a powerful preparatory technique was developed, whereby precisely defined microscopic tissue elements can be isolated and analyzed, while maintaining the biochemical state representative of the in vivo conditions. The second part consists of a discussion of proteomics as a tool in the elucidation of basic and pathologic mechanisms, diagnosis of disease, as well as treatment. Examples are the organ of Corti proteins OCP1 and OCP2, oncomodulin, a highly specific calcium-binding protein, and several disease entities, Meniere's disease, benign paroxysmal positional vertigo, and perilymphatic fistula.

  16. NIH Common Fund - Disruptive Proteomics Technologies - Challenges and Opportunities | Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    This Request for Information (RFI) is directed toward determining how best to accelerate research in disruptive proteomics technologies. The Disruptive Proteomics Technologies (DPT) Working Group of the NIH Common Fund wishes to identify gaps and opportunities in current technologies and methodologies related to proteome-wide measurements.  For the purposes of this RFI, “disruptive” is defined as very rapid, very significant gains, similar to the "disruptive" technology development that occurred in DNA sequencing technology.

  17. NCI Launches Proteomics Assay Portal | Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    In a paper recently published by the journal Nature Methods, Investigators from the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (NCI-CPTAC) announced the launch of a proteomics Assay Portal for multiple reaction monitoring-mass spectrometry (MRM-MS) assays.  This community web-based repository for well-characterized quantitative proteomic assays currently consists of 456 unique peptide assays to 282 unique proteins and ser

  18. Trends in mass spectrometry instrumentation for proteomics.

    Science.gov (United States)

    Smith, Richard D

    2002-12-01

    Mass spectrometry has become a primary tool for proteomics because of its capabilities for rapid and sensitive protein identification and quantitation. It is now possible to identify thousands of proteins from microgram sample quantities in a single day and to quantify relative protein abundances. However, the need for increased capabilities for proteome measurements is immense and is now driving both new strategies and instrument advances. These developments include those based on integration with multi-dimensional liquid separations and high accuracy mass measurements and promise more than order of magnitude improvements in sensitivity, dynamic range and throughput for proteomic analyses in the near future.

  19. Virion Proteomics of Large DNA Viruses

    Institute of Scientific and Technical Information of China (English)

    Ran-ran WANG; Zhi-hong HU; Hua-lin WANG; Fei DENG

    2009-01-01

    Large DNA viruses normally have complex structures with many of protein components derived from both viral and host origins. The development in proteomics, especially mass spectrometry identification techniques provide powerful tools for analyzing large viruses. In this review, we have summarized the recent achievements on proteomic studies of large DNA viruses, such as herpesvirus, poxvirus, nimavirus and baculoviruse. The proteomics of baculovirus occlusion-derived virions (ODV) were emphasized. Different mass spectrometry techniques used on ,carious baculoviruses were introduced, and the identified structurally associated proteins of baculoviruses are summarized.

  20. A comprehensive compilation of SUMO proteomics

    DEFF Research Database (Denmark)

    Hendriks, Ivo A; Vertegaal, Alfred C O

    2016-01-01

    Small ubiquitin-like modifiers (SUMOs) are essential for the regulation of several cellular processes and are potential therapeutic targets owing to their involvement in diseases such as cancer and Alzheimer disease. In the past decade, we have witnessed a rapid expansion of proteomic approaches...... for identifying sumoylated proteins, with recent advances in detecting site-specific sumoylation. In this Analysis, we combined all human SUMO proteomics data currently available into one cohesive database. We provide proteomic evidence for sumoylation of 3,617 proteins at 7,327 sumoylation sites, and insight...

  1. Plasma turbulence

    Energy Technology Data Exchange (ETDEWEB)

    Horton, W. [Univ. of Texas, Austin, TX (United States). Inst. for Fusion Studies; Hu, G. [Globalstar LP, San Jose, CA (United States)

    1998-07-01

    The origin of plasma turbulence from currents and spatial gradients in plasmas is described and shown to lead to the dominant transport mechanism in many plasma regimes. A wide variety of turbulent transport mechanism exists in plasmas. In this survey the authors summarize some of the universally observed plasma transport rates.

  2. Proteomics and Mass Spectrometry for Cancer Biomarker Discovery

    Directory of Open Access Journals (Sweden)

    Ming Lu

    2007-01-01

    Full Text Available Proteomics is a rapidly advancing field not only in the field of biology but also in translational cancer research. In recent years, mass spectrometry and associated technologies have been explored to identify proteins or a set of proteins specific to a given disease, for the purpose of disease detection and diagnosis. Such biomarkers are being investigated in samples including cells, tissues, serum/plasma, and other types of body fluids. When sufficiently refined, proteomic technologies may pave the way for early detection of cancer or individualized therapy for cancer. Mass spectrometry approaches coupled with bioinformatic tools are being developed for biomarker discovery and validation. Understanding basic concepts and application of such technology by investigators in the field may accelerate the clinical application of protein biomarkers in disease management.Abbreviations: 2DE: two-dimensional gel electrophoresis; ABPP: activity-based protein profiling; CEA: carcinoembryonic antigen; CI: confidence interval; ESI: electrospray ionization; FP: fluorophosphonate; HPLC: high performance liquid chromatography; ICAT: isotope coded affi nitytags; IEF: isoelectric focusing; iTRAQ: isobaric tags for relative and absolute quantification; LCMS: combined liquid chromatography-mass spectrometry; LCMSMS: liquid chromatography tandem mass spectrometry; LOD: limit of detection; m/z: mass to charge ratio; MALDI: matrix-assisted laser desorption ionization; MS: mass spectrometry; MUDPIT: multidimensional protein identification technology; NAF: nipple aspirate fluid; PMF: peptide mass fingerprinting; PSA: prostate specifi c antigen; PTMs: post-translational modifications; RPMA: reverse phase protein microarray; SELDI: surface enhanced laser desorption ionization; TOF: time-of-flight.

  3. Identification and proteomic analysis of osteoblast-derived exosomes.

    Science.gov (United States)

    Ge, Min; Ke, Ronghu; Cai, Tianyi; Yang, Junyi; Mu, Xiongzheng

    2015-11-01

    Exosomes are nanometer-sized vesicles with the function of intercellular communication, and they are released by various cell types. To reveal the knowledge about the exosomes from osteoblast, and explore the potential functions of osteogenesis, we isolated microvesicles from supernatants of mouse Mc3t3 by ultracentrifugation, characterized exosomes by electron microscopy and immunoblotting and presented the protein profile by proteomic analysis. The result demonstrated that microvesicles were between 30 and 100 nm in diameter, round shape with cup-like concavity and expressed exosomal marker tumor susceptibility gene (TSG) 101 and flotillin (Flot) 1. We identified a total number of 1069 proteins among which 786 proteins overlap with ExoCarta database. Gene Oncology analysis indicated that exosomes mostly derived from plasma membrane and mainly involved in protein localization and intracellular signaling. The Ingenuity Pathway Analysis showed pathways are mostly involved in exosome biogenesis, formation, uptake and osteogenesis. Among the pathways, eukaryotic initiation factor 2 pathways played an important role in osteogenesis. Our study identified osteoblast-derived exosomes, unveiled the content of them, presented potential osteogenesis-related proteins and pathways and provided a rich proteomics data resource that will be valuable for further studies of the functions of individual proteins in bone diseases.

  4. Establishing the proteome of normal human cerebrospinal fluid.

    Directory of Open Access Journals (Sweden)

    Steven E Schutzer

    Full Text Available BACKGROUND: Knowledge of the entire protein content, the proteome, of normal human cerebrospinal fluid (CSF would enable insights into neurologic and psychiatric disorders. Until now technologic hurdles and access to true normal samples hindered attaining this goal. METHODS AND PRINCIPAL FINDINGS: We applied immunoaffinity separation and high sensitivity and resolution liquid chromatography-mass spectrometry to examine CSF from healthy normal individuals. 2630 proteins in CSF from normal subjects were identified, of which 56% were CSF-specific, not found in the much larger set of 3654 proteins we have identified in plasma. We also examined CSF from groups of subjects previously examined by others as surrogates for normals where neurologic symptoms warranted a lumbar puncture but where clinical laboratory were reported as normal. We found statistically significant differences between their CSF proteins and our non-neurological normals. We also examined CSF from 10 volunteer subjects who had lumbar punctures at least 4 weeks apart and found that there was little variability in CSF proteins in an individual as compared to subject to subject. CONCLUSIONS: Our results represent the most comprehensive characterization of true normal CSF to date. This normal CSF proteome establishes a comparative standard and basis for investigations into a variety of diseases with neurological and psychiatric features.

  5. Diagnostic Proteomics: Serum Proteomic Patterns for the Detection of Early Stage Cancers

    Directory of Open Access Journals (Sweden)

    Li-Rong Yu

    2004-01-01

    Full Text Available The ability to interrogate thousands of proteins found in complex biological samples using proteomic technologies has brought the hope of discovering novel disease-specific biomarkers. While most proteomic technologies used to discover diagnostic biomarkers are quite sophisticated, "proteomic pattern analysis" has emerged as a simple, yet potentially revolutionary, method for the early diagnosis of diseases. Utilizing this technology, hundreds of clinical samples can be analyzed per day and several preliminary studies suggest proteomic pattern analysis has the potential to be a novel, highly sensitive diagnostic tool for the early detection of cancer.

  6. Proteomics and posttranslational proteomics of seed dormancy and germination.

    Science.gov (United States)

    Rajjou, Loïc; Belghazi, Maya; Catusse, Julie; Ogé, Laurent; Arc, Erwann; Godin, Béatrice; Chibani, Kamel; Ali-Rachidi, Sonia; Collet, Boris; Grappin, Philippe; Jullien, Marc; Gallardo, Karine; Job, Claudette; Job, Dominique

    2011-01-01

    The seed is the dispersal unit of plants and must survive the vagaries of the environment. It is the object of intense genetic and genomic studies because processes related to seed quality affect crop yield and the seed itself provides food for humans and animals. Presently, the general aim of postgenomics analyses is to understand the complex biochemical and molecular processes underlying seed quality, longevity, dormancy, and vigor. Due to advances in functional genomics, the recent past years have seen a tremendous progress in our understanding of several aspects of seed development and germination. Here, we describe the proteomics protocols (from protein extraction to mass spectrometry) that can be used to investigate several aspects of seed physiology, including germination and its hormonal regulation, dormancy release, and seed longevity. These techniques can be applied to the study of both model plants (such as Arabidopsis) and crops.

  7. A Microsomal Proteomics View of H2O2- and ABA-Dependent Responses

    KAUST Repository

    Alquraishi, May Majed

    2017-08-21

    The plant hormone abscisic acid (ABA) modulates a number of plant developmental processes and responses to stress. In planta, ABA has been shown to induce reactive oxygen species (ROS) production through the action of plasma membrane-associated nicotinamide adenine dinucleotide phosphate (NADPH)-oxidases. Although quantitative proteomics studies have been performed to identify ABA- or hydrogen peroxide (H₂O₂)-dependent proteins, little is known about the ABA- and H₂O₂-dependent microsomal proteome changes. Here, we examined the effect of 50 µM of either H₂O₂ or ABA on the Arabidopsis microsomal proteome using tandem mass spectrometry and identified 86 specifically H₂O₂-dependent, and 52 specifically ABA-dependent proteins that are differentially expressed. We observed differential accumulation of proteins involved in the tricarboxylic acid (TCA) cycle notably in response to H₂O₂. Of these, aconitase 3 responded to both H₂O₂ and ABA. Additionally, over 30 proteins linked to RNA biology responded significantly to both treatments. Gene ontology categories such as \\'response to stress\\' and \\'transport\\' were enriched, suggesting that H₂O₂ or ABA directly and/or indirectly cause complex and partly overlapping cellular responses. Data are available via ProteomeXchange with identifier PXD006513.

  8. Technological advances for deciphering the complexity of psychiatric disorders: merging proteomics with cell biology.

    Science.gov (United States)

    Wesseling, Hendrik; Guest, Paul C; Lago, Santiago G; Bahn, Sabine

    2014-08-01

    Proteomic studies have increased our understanding of the molecular pathways affected in psychiatric disorders. Mass spectrometry and two-dimensional gel electrophoresis analyses of post-mortem brain samples from psychiatric patients have revealed effects on synaptic, cytoskeletal, antioxidant and mitochondrial protein networks. Multiplex immunoassay profiling studies have found alterations in hormones, growth factors, transport and inflammation-related proteins in serum and plasma from living first-onset patients. Despite these advances, there are still difficulties in translating these findings into platforms for improved treatment of patients and for discovery of new drugs with better efficacy and side effect profiles. This review describes how the next phase of proteomic investigations in psychiatry should include stringent replication studies for validation of biomarker candidates and functional follow-up studies which can be used to test the impact on physiological function. All biomarker candidates should now be tested in series with traditional and emerging cell biological approaches. This should include investigations of the effects of post-translational modifications, protein dynamics and network analyses using targeted proteomic approaches. Most importantly, there is still an urgent need for development of disease-relevant cellular models for improved translation of proteomic findings into a means of developing novel drug treatments for patients with these life-altering disorders.

  9. Alternative profiling platform based on MELDI and its applicability in clinical proteomics.

    Science.gov (United States)

    Najam-ul-Haq, Muhammad; Rainer, Matthias; Trojer, Lukas; Feuerstein, Isabel; Vallant, Rainer Markus; Huck, Christian W; Bakry, Rania; Bonn, Günther Karl

    2007-08-01

    The presence of numerous proteomics data and their results in literature reveal the importance and influence of proteins and peptides on human cell cycle. For instance, the proteomic profiling of biological samples, such as serum, plasma or cells, and their organelles, carried out by surface-enhanced laser desorption/ionization mass spectrometry, has led to the discovery of numerous key proteins involved in many biological disease processes. However, questions still remain regarding the reproducibility, bioinformatic artifacts and cross-validations of such experimental set-ups. The authors have developed a material-based approach, termed material-enhanced laser desorption/ionization mass spectrometry (MELDI-MS), to facilitate and improve the robustness of large-scale proteomic experiments. MELDI-MS includes a fully automated protein-profiling platform, from sample preparation and analysis to data processing involving state-of-the-art methods, which can be further improved. Multiplexed protein pattern analysis, based on material morphology, physical characteristics and chemical functionalities provides a multitude of protein patterns and allows prostate cancer samples to be distinguished from non-prostate cancer samples. Furthermore, MELDI-MS enables not only the analysis of protein signatures, but also the identification of potential discriminating peaks via capillary liquid chromatography mass spectrometry. The optimized MELDI approach offers a complete proteomics platform with improved sensitivity, selectivity and short sample preparation times.

  10. Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

    Directory of Open Access Journals (Sweden)

    Rong-Xia Li

    Full Text Available BACKGROUND: Recent advances in proteomics have shed light to discover serum proteins or peptides as biomarkers for tracking the progression of diabetes as well as understanding molecular mechanisms of the disease. RESULTS: In this work, human serum of non-diabetic and diabetic cohorts was analyzed by proteomic approach. To analyze total 1377 high-confident serum-proteins, we developed a computing strategy called localized statistics of protein abundance distribution (LSPAD to calculate a significant bias of a particular protein-abundance between these two cohorts. As a result, 68 proteins were found significantly over-represented in the diabetic serum (p<0.01. In addition, a pathway-associated analysis was developed to obtain the overall pathway bias associated with type 2 diabetes, from which the significant over-representation of complement system associated with type 2 diabetes was uncovered. Moreover, an up-stream activator of complement pathway, ficolin-3, was observed over-represented in the serum of type 2 diabetic patients, which was further validated with statistic significance (p = 0.012 with more clinical samples. CONCLUSIONS: The developed LSPAD approach is well fit for analyzing proteomic data derived from biological complex systems such as plasma proteome. With LSPAD, we disclosed the comprehensive distribution of the proteins associated with diabetes in different abundance levels and the involvement of ficolin-related complement activation in diabetes.

  11. Individual variability in the venom proteome of juvenile Bothrops jararaca specimens.

    Science.gov (United States)

    Dias, Gabriela S; Kitano, Eduardo S; Pagotto, Ana H; Sant'anna, Sávio S; Rocha, Marisa M T; Zelanis, André; Serrano, Solange M T

    2013-10-04

    Snake venom proteomes/peptidomes are highly complex and subject to ontogenetic changes. Individual variation in the venom proteome of juvenile snakes is poorly known. We report the proteomic analysis of venoms from 21 juvenile specimens of Bothrops jararaca of different geographical origins and correlate it with the evaluation of important venom features. Individual venoms showed similar caseinolytic activities; however, their amidolytic activities were significantly different. Rather intriguingly, plasma coagulant activity showed remarkable variability among the venoms but not the prothrombin-activating activity. LC-MS analysis showed significant differences between venoms; however, an interesting finding was the ubiquitous presence of the tripeptide ZKW, an endogenous inhibitor of metalloproteinases. Electrophoretic profiles of proteins submitted to reduction showed significant variability in total proteins, glycoproteins, and in the subproteomes of proteinases. Moreover, identification of differential bands revealed variation in most B. jararaca toxin classes. Profiles of venoms analyzed under nonreducing conditions showed less individual variability and identification of proteins in a conserved band revealed the presence of metalloproteinases and l-amino acid oxidase as common components of these venoms. Taken together, our findings suggest that individual venom proteome variability in B. jararaca exists from a very early animal age and is not a result of ontogenetic and diet changes.

  12. Applications of urinary proteomics in renal disease research using animal models.

    Science.gov (United States)

    Lv, Yang; Cai, Guangyan; Chen, Xiangmei

    2015-01-01

    Animal models of renal disease are essential tools in research on kidney disease and have provided valuable insights into pathogenesis. Use of animal models minimises inter-individual differences, allows specific pathological changes to be examined, and facilitates collection of tissue samples. Thus, mechanistic research and identification of biomarkers are possible. Various animal models manifesting specific pathological lesions can be used to investigate acute or chronic kidney disease (CKD). Urine, a terminal metabolic product, is produced via glomerular filtration, reabsorption, and excretion in the tubular and collecting ducts, reflecting the functions of glomeruli or tubular tissue stimulated in various ways or subject to disease. Almost 70 % of urinary proteins originate from the kidney (the other 30 % come from plasma), and urinary sampling is important to noninvasively detect renal disease. Proteomics is powerful when used to screen urine components. Increasingly, urine proteomics is used to explore the pathogenesis of kidney disease in animals and to identify novel biomarkers of renal disease. In this section, we will introduce the field of urinary proteomics as applied in different models of animal renal disease and the valuable role played by proteomics in noninvasive diagnosis and rational treatment of human renal disease.

  13. No Evidence for Statin-induced Proteinuria in Healthy Volunteers as Assessed by Proteomic Analysis

    Directory of Open Access Journals (Sweden)

    Anja Verhulst

    2011-01-01

    Full Text Available In clinical studies of statins (class of drugs lowering plasma cholesterol levels, transient low-molecular-weight proteinuria was observed. The causes of statin-induced proteinuria in the patient background of those studies (cardiovascular and kidney disease are multifactorial and, therefore, a matter of debate. In light of this, it seemed interesting to investigate the effect of statins on the urinary protein concentration and proteome in healthy volunteers. Six healthy volunteers were randomly treated with rosuvastatin (40 mg/day or pravastatin (80 mg/day in a double-blinded cross-over study. Total urinary protein concentration and the concentration of albumin/retinol-binding protein were analysed, after which the urinary proteome was investigated. From the results described in this study, it was concluded that statins do not induce major changes in the urinary protein concentration/proteome. High variability in the baseline urinary proteome/proteins among volunteers, however, made it very difficult to find subtle (possibly isolated to individuals effects of statins.

  14. Monitoring the native phosphorylation state of plasma membrane proteins from a single mouse cerebellum

    DEFF Research Database (Denmark)

    Schindler, J.; Ye, J. Y.; Jensen, Ole Nørregaard

    2013-01-01

    Neuronal processing in the cerebellum involves the phosphorylation and dephosphorylation of various plasma membrane proteins such as AMPA or NMDA receptors. Despite the importance of changes in phosphorylation pattern, no global phospho-proteome analysis has yet been performed. As plasma membrane...

  15. Proteome-Wide Quantitation by SILAC

    DEFF Research Database (Denmark)

    Rigbolt, Kristoffer T G; Blagoev, Blagoy

    2010-01-01

    isotope labeling by amino acids in cell culture (SILAC) has emerged as a powerful and versatile approach for proteome-wide quantitation by mass spectrometry. SILAC utilizes the cells' own metabolism to incorporate isotopically labeled amino acids into its proteome which can be mixed with the proteome...... detailed procedure for performing SILAC-based experiment for proteome-wide quantitation, including a protocol for optimizing SILAC labeling. We also provide an update on the most recent developments of this technique....... of unlabeled cells and differences in protein expression can easily be read out by comparing the abundance of the labeled versus unlabeled proteins. SILAC has been applied to numerous different cell lines and the technique has been adapted for a wide range of experimental procedures. In this chapter we provide...

  16. New Methods for Clinical Proteomics in Allergy

    Directory of Open Access Journals (Sweden)

    Zenichiro Kato

    2005-01-01

    Full Text Available Recent genomic studies have revealed many kinds of genetic polymorphisms. Some genetic polymorphisms have a correlation with allergic phenotypes, however there is only a statistical association without a precise molecular mechanism being demonstrated. Analysis of the molecular mechanisms from a proteomic perspective should contribute to a better understanding of diseases and indicate possible therapeutic approaches. Recent advances in identification and characterization of many immunological molecules have led to a shift to profiling research, clinical proteomics, of already known factors. However, analysis of such biomarkers in allergies requires methodological improvements because allergic reactions can be greatly influenced by subtle changes of factors. These subtle changes cannot be detected by conventional techniques such as 2D-PAGE, and the grammar behind the system is not well recognized by conventional proteomics. Examples of innovative methods useful for proteomic approaches to allergies are discussed here ; especially high throughput screening and structural methods for allergy targeting.

  17. Clinical proteomics in obstetrics and neonatology.

    Science.gov (United States)

    Klein, Julie; Buffin-Meyer, Benedicte; Mullen, William; Carty, David M; Delles, Christian; Vlahou, Antonia; Mischak, Harald; Decramer, Stéphane; Bascands, Jean-Loup; Schanstra, Joost P

    2014-02-01

    Clinical proteomics has been applied to the identification of biomarkers of obstetric and neonatal disease. We will discuss a number of encouraging studies that have led to potentially valid biomarkers in the context of Down's syndrome, preterm birth, amniotic infections, preeclampsia, intrauterine growth restriction and obstructive uropathies. Obtaining noninvasive biomarkers (e.g., from the maternal circulation, urine or cervicovaginal fluid) may be more feasible for obstetric diseases than for diseases of the fetus, for which invasive methods are required (e.g., amniotic fluid, fetal urine). However, studies providing validated proteomics-identified biomarkers are limited. Efforts should be made to save well-characterized samples of these invasive body fluids so that many valid biomarkers of pregnancy-related diseases will be identified in the coming years using proteomics based analysis upon adoption of 'clinical proteomics guidelines'.

  18. Proteomics of aluminum tolerance in plants.

    Science.gov (United States)

    Zheng, Lu; Lan, Ping; Shen, Ren Fang; Li, Wen Feng

    2014-03-01

    Aluminum (Al) toxicity is a major constraint for plant root development and growth as well as crop yield in acidic soils, which constitute approximately 40% of the potentially arable lands worldwide. The mechanisms of Al tolerance in plants are not well understood. As a whole systems approach, proteomic techniques have proven to be crucial as a complementary strategy to explore the mechanism in Al toxicity. Review here focuses on the potential of proteomics to unravel the common and plant species-specific changes at proteome level under Al stress, via comparative analysis of the Al-responsive proteins uncovered by recent proteomic studies using 2DE. Understanding the mechanisms of Al tolerance in plants is critical to generate Al resistance crops for developing sustainable agriculture practices, thereby contributing to food security worldwide.

  19. Proteomics in the genome engineering era.

    Science.gov (United States)

    Vandemoortele, Giel; Gevaert, Kris; Eyckerman, Sven

    2016-01-01

    Genome engineering experiments used to be lengthy, inefficient, and often expensive, preventing a widespread adoption of such experiments for the full assessment of endogenous protein functions. With the revolutionary clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 technology, genome engineering became accessible to the broad life sciences community and is now implemented in several research areas. One particular field that can benefit significantly from this evolution is proteomics where a substantial impact on experimental design and general proteome biology can be expected. In this review, we describe the main applications of genome engineering in proteomics, including the use of engineered disease models and endogenous epitope tagging. In addition, we provide an overview on current literature and highlight important considerations when launching genome engineering technologies in proteomics workflows.

  20. Distinct proteome pathology of circulating microparticles in systemic lupus erythematosus

    DEFF Research Database (Denmark)

    Østergaard, Ole; Nielsen, Christoffer Tandrup; Tanassi, Julia Tanas

    2017-01-01

    BACKGROUND: The pathogenesis of systemic lupus erythematosus (SLE) is poorly understood but has been linked to defective clearance of subcellular particulate material from the circulation. This study investigates the origin, formation, and specificity of circulating microparticles (MPs) in patients...... with SLE based on comprehensive MP proteome profiling using patients with systemic sclerosis (SSc) and healthy donors (HC) as controls. METHODS: We purified MPs from platelet-poor plasma using differential centrifugation of samples from SLE (n = 45), SSc (n = 38), and two sets of HC (n = 35, n = 25). MP......-MPs (which we propose to call luposomes) are highly specific for SLE, i.e. not found in MP preparations from HC or patients with another autoimmune, systemic disease, SSc. In SLE-MPs platelet proteins and mitochondrial proteins are significantly diminished, cytoskeletal proteins deranged, and glycolytic...

  1. Integrated multifunctional microfluidics for automated proteome analyses.

    Science.gov (United States)

    Osiri, John K; Shadpour, Hamed; Witek, Małgorzata A; Soper, Steven A

    2011-01-01

    Proteomics is a challenging field for realizing totally integrated microfluidic systems for complete proteome processing due to several considerations, including the sheer number of different protein types that exist within most proteomes, the large dynamic range associated with these various protein types, and the diverse chemical nature of the proteins comprising a typical proteome. For example, the human proteome is estimated to have >10(6) different components with a dynamic range of >10(10). The typical processing pipeline for proteomics involves the following steps: (1) selection and/or extraction of the particular proteins to be analyzed; (2) multidimensional separation; (3) proteolytic digestion of the protein sample; and (4) mass spectral identification of either intact proteins (top-down proteomics) or peptide fragments generated from proteolytic digestions (bottom-up proteomics). Although a number of intriguing microfluidic devices have been designed, fabricated and evaluated for carrying out the individual processing steps listed above, work toward building fully integrated microfluidic systems for protein analysis has yet to be realized. In this chapter, information will be provided on the nature of proteomic analysis in terms of the challenges associated with the sample type and the microfluidic devices that have been tested to carry out individual processing steps. These include devices such as those for multidimensional electrophoretic separations, solid-phase enzymatic digestions, and solid-phase extractions, all of which have used microfluidics as the functional platform for their implementation. This will be followed by an in-depth review of microfluidic systems, which are defined as units possessing two or more devices assembled into autonomous systems for proteome processing. In addition, information will be provided on the challenges involved in integrating processing steps into a functional system and the approaches adopted for device

  2. Quantitative proteomics of Chlorobaculum tepidum

    DEFF Research Database (Denmark)

    Falkenby, Lasse Gaarde; Szymanska, Monika; Holkenbrink, Carina;

    2011-01-01

    two different growth conditions. Wild-type cells growing on thiosulfate had an increased abundance of periplasmic cytochrome c-555 and proteins of the periplasmic thiosulfate-oxidizing SOX enzyme system when compared with cells growing on sulfide. A dsrM mutant of Cba. tepidum, which lacks......Chlorobaculum (Cba.) tepidum is a green sulfur bacterium that oxidizes sulfide, elemental sulfur, and thiosulfate for photosynthetic growth. To gain insight into the sulfur metabolism, the proteome of Cba. tepidum cells sampled under different growth conditions has been quantified using a rapid gel......-free, filter-aided sample preparation (FASP) protocol with an in-solution isotopic labeling strategy. Among the 2245 proteins predicted from the Cba. tepidum genome, approximately 970 proteins were detected in unlabeled samples, whereas approximately 630-640 proteins were detected in labeled samples comparing...

  3. Bioinformatic analysis of proteomics data.

    Science.gov (United States)

    Schmidt, Andreas; Forne, Ignasi; Imhof, Axel

    2014-01-01

    Most biochemical reactions in a cell are regulated by highly specialized proteins, which are the prime mediators of the cellular phenotype. Therefore the identification, quantitation and characterization of all proteins in a cell are of utmost importance to understand the molecular processes that mediate cellular physiology. With the advent of robust and reliable mass spectrometers that are able to analyze complex protein mixtures within a reasonable timeframe, the systematic analysis of all proteins in a cell becomes feasible. Besides the ongoing improvements of analytical hardware, standardized methods to analyze and study all proteins have to be developed that allow the generation of testable new hypothesis based on the enormous pre-existing amount of biological information. Here we discuss current strategies on how to gather, filter and analyze proteomic data sates using available software packages.

  4. Plasma harmonics

    CERN Document Server

    Ganeev, Rashid A

    2014-01-01

    Preface; Why plasma harmonics? A very brief introduction Early stage of plasma harmonic studies - hopes and frustrations New developments in plasma harmonics studies: first successes Improvements of plasma harmonics; Theoretical basics of plasma harmonics; Basics of HHG Harmonic generation in fullerenes using few-cycle pulsesVarious approaches for description of observed peculiarities of resonant enhancement of a single harmonic in laser plasmaTwo-colour pump resonance-induced enhancement of odd and even harmonics from a tin plasmaCalculations of single harmonic generation from Mn plasma;Low-o

  5. Collaboration - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    Despite great strides in proteomics and the growing number of articles citing the discovery of potential biomarkers, the actual rate of introduction of Food and Drug Administration (FDA) approved protein analytes has been relatively unchanged over the past 10 years. One of reasons for the lack of new protein-based biomarkers approved has been a lack of information and understanding by the proteomics research community to the regulatory process used by the FDA.

  6. Proteomic evaluation of sheep serum proteins

    OpenAIRE

    Chiaradia Elisabetta; Avellini Luca; Tartaglia Micaela; Gaiti Alberto; Just Ingo; Scoppetta Fausto; Czentnar Zoltan; Pich Andreas

    2012-01-01

    Abstract Background The applications of proteomic strategies to ovine medicine remain limited. The definition of serum proteome may be a good tool to identify useful protein biomarkers for recognising sub-clinical conditions and overt disease in sheep. Findings from bovine species are often directly translated for use in ovine medicine. In order to characterize normal protein patterns and improve knowledge of molecular species-specific characteristics, we generated a two-dimensional reference...

  7. Plasma degradome affected by variable storage of human blood

    NARCIS (Netherlands)

    Kaisar, Maria; Van Dullemen, Leon F. A.; Thezenas, Marie-Laetitia; Akhtar, M. Zeeshan; Huang, Honglei; Rendel, Sandrine; Charles, Philip D.; Fischer, Roman; Ploeg, Rutger J.; Kessler, Benedikt M.

    2016-01-01

    Background: The successful application of-omics technologies in the discovery of novel biomarkers and targets of therapeutic interventions is facilitated by large collections of well curated clinical samples stored in bio banks. Mining the plasma proteome holds promise to improve our understanding o

  8. Proteomics boosts translational and clinical microbiology.

    Science.gov (United States)

    Del Chierico, F; Petrucca, A; Vernocchi, P; Bracaglia, G; Fiscarelli, E; Bernaschi, P; Muraca, M; Urbani, A; Putignani, L

    2014-01-31

    The application of proteomics to translational and clinical microbiology is one of the most advanced frontiers in the management and control of infectious diseases and in the understanding of complex microbial systems within human fluids and districts. This new approach aims at providing, by dedicated bioinformatic pipelines, a thorough description of pathogen proteomes and their interactions within the context of human host ecosystems, revolutionizing the vision of infectious diseases in biomedicine and approaching new viewpoints in both diagnostic and clinical management of the patient. Indeed, in the last few years, many laboratories have matured a series of advanced proteomic applications, aiming at providing individual proteome charts of pathogens, with respect to their morph and/or cell life stages, antimicrobial or antimycotic resistance profiling, epidemiological dispersion. Herein, we aim at reviewing the current state-of-the-art on proteomic protocols designed and set-up for translational and diagnostic microbiological purposes, from axenic pathogens' characterization to microbiota ecosystems' full description. The final goal is to describe applications of the most common MALDI-TOF MS platforms to advanced diagnostic issues related to emerging infections, increasing of fastidious bacteria, and generation of patient-tailored phylotypes. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

  9. Proteomics: A new perspective for cancer

    Directory of Open Access Journals (Sweden)

    Basavaradhya Sahukar Shruthi

    2016-01-01

    Full Text Available In the past decades, several ground breaking discoveries in life science were made. The completion of sequencing the human genome certainly belongs to the key tasks successfully completed, representing a true milestone in the biomedicine. The accomplishment of the complete genome also brings along a new, even more challenging task for scientists: The characterization of the human proteome. Proteomics, the main tool for proteome research, is a relatively new and extremely dynamically evolving branch of science, focused on the evaluation of gene expression at proteome level. Due to the specific properties of proteins, current proteomics deals with different issues, such as protein identification, quantification, characterization of post-translational modification, structure and function elucidation, and description of possible interactions. This field incorporates technologies that can be applied to serum and tissue in order to extract important biological information in the form of biomarkers to aid clinicians and scientists in understanding the dynamic biology of their system of interest, such as a patient with cancer. The present review article provides a detail description of proteomics and its role in cancer research.

  10. [Progress in stable isotope labeled quantitative proteomics methods].

    Science.gov (United States)

    Zhou, Yuan; Shan, Yichu; Zhang, Lihua; Zhang, Yukui

    2013-06-01

    Quantitative proteomics is an important research field in post-genomics era. There are two strategies for proteome quantification: label-free methods and stable isotope labeling methods which have become the most important strategy for quantitative proteomics at present. In the past few years, a number of quantitative methods have been developed, which support the fast development in biology research. In this work, we discuss the progress in the stable isotope labeling methods for quantitative proteomics including relative and absolute quantitative proteomics, and then give our opinions on the outlook of proteome quantification methods.

  11. Identification of canine platelet proteins separated by differential detergent fractionation for nonelectrophoretic proteomics analyzed by Gene Ontology and pathways analysis

    Directory of Open Access Journals (Sweden)

    Trichler SA

    2014-01-01

    Full Text Available Shauna A Trichler,1,* Sandra C Bulla,1,* Nandita Mahajan,1 Kari V Lunsford,2 Ken Pendarvis,3 Bindu Nanduri,4,5 Fiona M McCarthy,3 Camilo Bulla1 1Department of Pathobiology and Population Medicine, 2Department of Clinical Sciences and Animal Health Center, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 3Department of Veterinary Science and Microbiology, University of Arizona, Tucson, AZ, 4Department of Biological Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 5Institute for Genomics, Biocomputing and Biotechnology, Starkville, MS, USA *These authors contributed equally to this work Abstract: During platelet development, proteins necessary for the many functional roles of the platelet are stored within cytoplasmic granules. Platelets have also been shown to take up and store many plasma proteins into granules. This makes the platelet a potential novel source of biomarkers for many disease states. Approaches to sample preparation for proteomic studies for biomarkers search vary. Compared with traditional two-dimensional polyacrylamide gel electrophoresis systems, nonelectrophoretic proteomics methods that employ offline protein fractionation methods such as the differential detergent fractionation method have clear advantages. Here we report a proteomic survey of the canine platelet proteome using differential detergent fractionation coupled with mass spectrometry and functional modeling of the canine platelet proteins identified. A total of 5,974 unique proteins were identified from platelets, of which only 298 (5% had previous experimental evidence of in vivo expression. The use of offline prefractionation of canine proteins by differential detergent fractionation resulted in greater proteome coverage as compared with previous reports. This initial study contributes to a broader understanding of canine platelet biology and aids functional research

  12. The core proteome and pan proteome of Salmonella Paratyphi A epidemic strains.

    Directory of Open Access Journals (Sweden)

    Li Zhang

    Full Text Available Comparative proteomics of the multiple strains within the same species can reveal the genetic variation and relationships among strains without the need to assess the genomic data. Similar to comparative genomics, core proteome and pan proteome can also be obtained within multiple strains under the same culture conditions. In this study we present the core proteome and pan proteome of four epidemic Salmonella Paratyphi A strains cultured under laboratory culture conditions. The proteomic information was obtained using a Two-dimensional gel electrophoresis (2-DE technique. The expression profiles of these strains were conservative, similar to the monomorphic genome of S. Paratyphi A. Few strain-specific proteins were found in these strains. Interestingly, non-core proteins were found in similar categories as core proteins. However, significant fluctuations in the abundance of some core proteins were also observed, suggesting that there is elaborate regulation of core proteins in the different strains even when they are cultured in the same environment. Therefore, core proteome and pan proteome analysis of the multiple strains can demonstrate the core pathways of metabolism of the species under specific culture conditions, and further the specific responses and adaptations of the strains to the growth environment.

  13. Princeton Plasma Physics Laboratory:

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, C.A. (ed.)

    1986-01-01

    This paper discusses progress on experiments at the Princeton Plasma Physics Laboratory. The projects and areas discussed are: Principal Parameters Achieved in Experimental Devices, Tokamak Fusion Test Reactor, Princeton Large Torus, Princeton Beta Experiment, S-1 Spheromak, Current-Drive Experiment, X-ray Laser Studies, Theoretical Division, Tokamak Modeling, Spacecraft Glow Experiment, Compact Ignition Tokamak, Engineering Department, Project Planning and Safety Office, Quality Assurance and Reliability, and Administrative Operations.

  14. Mark Twain: how to fathom the depth of your pet proteome.

    Science.gov (United States)

    Righetti, Pier Giorgio; Boschetti, Egisto; Candiano, Giovanni

    2012-08-01

    The present review highlights recent progresses in the technique of combinatorial peptide ligand libraries (CPPL), a methodology that has much to offer for the detection of low- to very-low abundance proteins (nanograms/mL scale and below) in any proteome. In particular, advances in exploration of the urinary, plasma and tissue proteomes are discussed and evaluated. It is shown that when treating biological fluids, such as plasma, with CPLLs, the detection sensitivity, which in the control only reaches 10 ng/mL, can be enhanced to as high as 10 pg/mL, with an increment of sensitivity of three orders of magnitude. The possibility of using CPLLs as a two-dimensional pre-fractionation of any proteome is also evaluated: on the charge axis, CPLL capture can be implemented at no less than three different pH values (4.0, 7.2 and 9.3), thus permitting a capture of proteinaceous analytes bearing a net positive or net negative charge, respectively. When capture is performed in the absence of salts or at high levels of salts (of the Hofmeister series), one can favor the capture of hydrophilic vs. hydrophobic proteins, respectively. This would thus be a genuine 2D protocol, working on orthogonal separation principles (charge vs. hydrophobicity). As the horizon of CPLLs is expanding and its use is exponentially growing, we expect major breakthroughs in, e.g., biomarker discovery, a field that has suffered a decade of failures.

  15. Low Mass Blood Peptides Discriminative of Inflammatory Bowel Disease (IBD) Severity: A Quantitative Proteomic Perspective.

    Science.gov (United States)

    Wasinger, Valerie C; Yau, Yunki; Duo, Xizi; Zeng, Ming; Campbell, Beth; Shin, Sean; Luber, Raphael; Redmond, Diane; Leong, Rupert W L

    2016-01-01

    Breakdown of the protective gut barrier releases effector molecules and degradation products into the blood stream making serum and plasma ideal as a diagnostic medium. The enriched low mass proteome is unexplored as a source of differentiators for diagnosing and monitoring inflammatory bowel disease (IBD) activity, that is less invasive than colonoscopy. Differences in the enriched low mass plasma proteome (Peptides differentiating controls from IBD originate from secreted phosphoprotein 24 (SPP24, p = 0.000086, 0.009); whereas those in remission and healthy can be differentiated in UC by SPP24 (p = 0.00023, 0.001), α-1-microglobulin (AMBP, p = 0.006) and CD by SPP24 (p = 0.019, 0.05). UC and CD can be differentiated by Guanylin (GUC2A, p = 0.001), and Secretogranin-1 (CHGB p = 0.035). Active and quiescent disease can also be differentiated in UC and CD by CHGB (p ≤ 0.023) SPP24 (p ≤ 0.023) and AMBP (UC p = 0.046). Five peptides discriminating IBD activity and severity had very little-to-no correlation to erythrocyte sedimentation rate, C-reactive protein, white cell or platelet counts. Three of these peptides were found to be binding partners to SPP24 protein alongside other known matrix proteins. These proteins have the potential to improve diagnosis and evaluate IBD activity, reducing the need for more invasive techniques. Data are available via ProteomeXchange with identifier PXD002821.

  16. Analytical methods for proteome data obtained from SDS-PAGE multi-dimensional separation and mass spectrometry

    Directory of Open Access Journals (Sweden)

    Gun Wook Park

    2010-03-01

    Full Text Available For proteome analysis, various experimental protocols using mass spectrometry have been developed over thelast decade. The different protocols have differing performances and degrees of accuracy. Furthermore, the “best”protocol for a proteomic analysis of a sample depends on the purpose of the analysis, especially in connection withdisease proteomics, including biomarker discovery and therapeutics analyses of human serum or plasma. Theprotein complexity and the wide dynamic range of blood samples require high-dimensional separation technology.In this article, we review proteome analysis protocols in which both Sodium Dodecyl Sulfate-Polyacryl Amide GelElectrophoresis(SDS-PAGE and liquid chromatography are used for peptide and protein separations. Multidimensionalseparation technology supplies a high-quality dataset of tandem mass spectra and reveals signals fromlow-abundance proteins, although it can be time-consuming and laborious work. We survey shotgun proteomicsprotocols using SDS-PAGE and liquid chromatography and introduce bioinformatics tools for the analysis ofproteomics data. We also review efforts toward the biological interpretation of the proteome.

  17. Dusty plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Fortov, Vladimir E; Khrapak, Aleksei G; Molotkov, Vladimir I; Petrov, Oleg F [Institute for High Energy Densities, Associated Institute for High Temperatures, Russian Academy of Sciences, Moscow (Russian Federation); Khrapak, Sergei A [Max-Planck-Institut fur Extraterrestrische Physik, Garching (Germany)

    2004-05-31

    The properties of dusty plasmas - low-temperature plasmas containing charged macroparticles - are considered. The most important elementary processes in dusty plasmas and the forces acting on dust particles are investigated. The results of experimental and theoretical investigations of different states of strongly nonideal dusty plasmas - crystal-like, liquid-like, gas-like - are summarized. Waves and oscillations in dusty plasmas, as well as their damping and instability mechanisms, are studied. Some results on dusty plasma investigated under microgravity conditions are presented. New directions of experimental research and potential applications of dusty plasmas are discussed. (reviews of topical problems)

  18. Optimizing Algorithm Choice for Metaproteomics: Comparing X!Tandem and Proteome Discoverer for Soil Proteomes

    Science.gov (United States)

    Diaz, K. S.; Kim, E. H.; Jones, R. M.; de Leon, K. C.; Woodcroft, B. J.; Tyson, G. W.; Rich, V. I.

    2014-12-01

    The growing field of metaproteomics links microbial communities to their expressed functions by using mass spectrometry methods to characterize community proteins. Comparison of mass spectrometry protein search algorithms and their biases is crucial for maximizing the quality and amount of protein identifications in mass spectral data. Available algorithms employ different approaches when mapping mass spectra to peptides against a database. We compared mass spectra from four microbial proteomes derived from high-organic content soils searched with two search algorithms: 1) Sequest HT as packaged within Proteome Discoverer (v.1.4) and 2) X!Tandem as packaged in TransProteomicPipeline (v.4.7.1). Searches used matched metagenomes, and results were filtered to allow identification of high probability proteins. There was little overlap in proteins identified by both algorithms, on average just ~24% of the total. However, when adjusted for spectral abundance, the overlap improved to ~70%. Proteome Discoverer generally outperformed X!Tandem, identifying an average of 12.5% more proteins than X!Tandem, with X!Tandem identifying more proteins only in the first two proteomes. For spectrally-adjusted results, the algorithms were similar, with X!Tandem marginally outperforming Proteome Discoverer by an average of ~4%. We then assessed differences in heat shock proteins (HSP) identification by the two algorithms by BLASTing identified proteins against the Heat Shock Protein Information Resource, because HSP hits typically account for the majority signal in proteomes, due to extraction protocols. Total HSP identifications for each of the 4 proteomes were approximately ~15%, ~11%, ~17%, and ~19%, with ~14% for total HSPs with redundancies removed. Of the ~15% average of proteins from the 4 proteomes identified as HSPs, ~10% of proteins and spectra were identified by both algorithms. On average, Proteome Discoverer identified ~9% more HSPs than X!Tandem.

  19. Differential Proteomic Analysis of Carbon Ion Radiation in Sheep Sperm

    Institute of Scientific and Technical Information of China (English)

    HE Yu-xuan; LI Hong-yan; ZHANG Yong; HE Jian-hua; ZHANG Hong; ZHAO Xing-xu

    2013-01-01

    This study is first to investigate proteomic changes in sheep sperm induced by carbon ion radiation using two-dimensional electrophoresis (2-DE) analysis in the project of breeding a new variety of sheep. Differential expression proteins were detected using the PDQuest 8.0 software after staining with Coomassie blue. Valid spots were then analyzed through liquid chromatography tandem mass spectrometry (LC-MS/MS). Among the 480 total protein spots displayed in 2-D gels, 6 specific protein spots were observed in sperm gels. A search against protein sequences in the National Center for Biotechnology Information databases (NCBI) indicated that differentially expressed proteins correspond to two proteins, identified to be enolase and transcription factor AP-2-alpha (TFAP-2α). The two proteins were up-regulated in the irradiated sperm. To the best of our knowledge, this study is the first to identify proteomic changes induced by carbon ion radiation in sheep sperm. The analysis of differential expression protein may be useful in identifying new breeding markers in sheep reproduction and in clarifying the mechanisms involved in irradiation or space breeding.

  20. Defining the human gallbladder proteome by transcriptomics and affinity proteomics.

    Science.gov (United States)

    Kampf, Caroline; Mardinoglu, Adil; Fagerberg, Linn; Hallström, Björn M; Danielsson, Angelika; Nielsen, Jens; Pontén, Fredrik; Uhlen, Mathias

    2014-11-01

    Global protein analysis of human gallbladder tissue is vital for identification of molecular regulators and effectors of its physiological activity. Here, we employed a genome-wide deep RNA sequencing analysis in 28 human tissues to identify the genes overrepresented in the gallbladder and complemented it with antibody-based immunohistochemistry in 48 human tissues. We characterized human gallbladder proteins and identified 140 gallbladder-specific proteins with an elevated expression in the gallbladder as compared to the other analyzed tissues. Five genes were categorized as enriched, with at least fivefold higher levels in gallbladder, 60 genes were categorized as group enriched with elevated transcript levels in gallbladder shared with at least one other tissue and 75 genes were categorized as enhanced with higher expression than the average expression in other tissues. We explored the localization of the genes within the gallbladder through cell-type specific antibody-based protein profiling and the subcellular localization of the genes through immunofluorescent-based profiling. Finally, we revealed the biological processes and metabolic functions carried out by these genes through the use of GO, KEGG Pathway, and HMR2.0 that is compilation of the human metabolic reactions. We demonstrated the results of the combined analysis of the transcriptomics and affinity proteomics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Identification and characterization of N-glycosylated proteins using proteomics

    DEFF Research Database (Denmark)

    Selby, David S; Larsen, Martin R; Calvano, Cosima Damiana;

    2008-01-01

    Glycoproteins constitute a large fraction of the proteome. The fundamental role of protein glycosylation in cellular development, growth, and differentiation, tissue development, and in host-pathogen interactions is by now widely accepted. Proteome-wide characterization of glycoproteins...

  2. Inspection, visualisation and analysis of quantitative proteomics data

    OpenAIRE

    Gatto, Laurent

    2016-01-01

    Material Quantitative Proteomics and Data Analysis Course. 4 - 5 April 2016, Queen Hotel, Chester, UK Table D - Inspection, visualisation and analysis of quantitative proteomics data, Laurent Gatto (University of Cambridge)

  3. Progress through Collaboration - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute (NCI), through the Office of Cancer Clinical Proteomics Research (OCCPR), has signed two Memorandums of Understanding (MOUs) in the areas of sharing proteomics reagents and protocols and also in regulatory science.

  4. Director's Update - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (NCI-CPTAC) has recently begun the proteomic interrogation of genomically-characterized tumors from The Cancer Genome Atlas.

  5. Large pore dermal microdialysis and liquid chromatography-tandem mass spectroscopy shotgun proteomic analysis

    DEFF Research Database (Denmark)

    Petersen, Lars J; Sørensen, Mette A; Codrea, Marius C

    2013-01-01

    phases of the study; trauma due to implantation of the dialysis device, a post implantation steady-state period, and after induction of vasodilatation and plasma extravasation. For shotgun proteomics, the proteins were extracted and digested with trypsin. Peptides were separated by capillary and nanoflow...... HPLC systems, followed by tandem mass spectrometry (MS/MS) on a Quadrupole-TOF hybrid instrument. The MS/MS spectra were merged and mapped to a human target protein database to achieve peptide identification and protein inference. ResultsResults showed variation in protein amounts and profiles for each......, and complement factors, make up the major load of proteins in all three test conditions. ConclusionShotgun proteomics allowed the identification of more than 150 proteins in microdialysis samples from human skin. This highlights the opportunities of LC-MS/MS to study the complex molecular interactions...

  6. Qualitative and quantitative peptidomic and proteomic approaches to phenotyping chicken semen.

    Science.gov (United States)

    Labas, Valérie; Grasseau, Isabelle; Cahier, Karine; Gargaros, Audrey; Harichaux, Grégoire; Teixeira-Gomes, Ana-Paula; Alves, Sabine; Bourin, Marie; Gérard, Nadine; Blesbois, Elisabeth

    2015-01-01

    Understanding of the avian male gamete biology is essential to improve the conservation of genetic resources and performance in farming. In this study, the chicken semen peptidome/proteome and the molecular phenotype related to sperm quality were investigated. Spermatozoa (SPZ) and corresponding seminal plasma (SP) from 11 males with different fertilizing capacity were analyzed using three quantitative strategies (fluid and intact cells MALDI-MS, SDS-PAGE combined to LC-MS/MS with spectral counting and XIC methods). Individual MALDI profiling in combination with top-down MS allowed to characterize specific profiles per male and to identify 16 biomolecules (e.g.VMO1, AvBD10 and AvBD9 including polymorphism). Qualitative analysis identified 1165 proteins mainly involved in oxidoreduction mechanisms, energy processes, proteolysis and protein localization. Comparative analyses between the most and the least fertile males were performed. The enzymes involved in energy metabolism, respiratory chain or oxido-reduction activity were over-represented in SPZ of the most fertile males. The SP of the most and the least fertile males differed also on many proteins (e.g. ACE, AvBD10 and AvBD9, NEL precursor, acrosin). Thus proteomic is a "phenomic molecular tool" that may help to discriminate avian males on their reproductive capacity. The data have been deposited with ProteomeXchange (identifiers PXD000287 and PXD001254). This peptidomic and proteomic study i) characterized for the first time the semen protein composition of the main domestic avian species (Gallus gallus) by analysis of ejaculated spermatozoa and corresponding seminal plasma; ii) established a characteristic molecular phenotype distinguishing semen and males at an individual level; and iii) proposedthe first evidence of biomarkers related to fertility. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Urine proteomic profiling of uranium nephrotoxicity

    Energy Technology Data Exchange (ETDEWEB)

    Malard, V.; Gaillard, J.C.; Sage, N. [CEA, DSV, IBEB, SBTN, Laboratoire de Biochimie des Systemes Perturbes (LBSP), Bagnols-sur-Ceze, F-30207 (France); Berenguer, F. [CEA, DSV, IBEB, SBTN, Laboratoire d' Etude des Proteines Cibles (LEPC), Bagnols-sur-Ceze, F-30207 (France); Quemeneur, E. [CEA, DSV, IBEB, SBTN, Bagnols-sur-Ceze, F-30207 (France)

    2009-07-01

    Uranium is used in many chemical forms in civilian and military industries and is a known nephro-toxicant. A key issue in monitoring occupational exposure is to be able to evaluate the potential damage to the body, particularly the kidney. In this study we used innovative proteomic techniques to analyse urinary protein modulation associated with acute uranium exposure in rats. Given that the rat urinary proteome has rarely been studied, we first identified 102 different proteins in normal urine, expanding the current proteome data set for this central animal in toxicology. Rats were exposed intravenously to uranyl nitrate at 2.5 and 5 mg/kg and samples were collected 24 h later. Using two complementary proteomic methods, a classic 2-DE approach and semi-quantitative SDS-PAGE-LC-MS/MS, 14 modulated proteins (7 with increased levels and 7 with decreased levels) were identified in urine after uranium exposure. Modulation of three of them was confirmed by western blot. Some of the modulated proteins corresponded to proteins already described in case of nephrotoxicity, and indicated a loss of glomerular permeability (albumin, alpha-1-anti-proteinase, sero-transferrin). Others revealed tubular damage, such as EGF and vitamin D-binding protein. A third category included proteins never described in urine as being associated with metal stress, such as ceruloplasmin. Urinary proteomics is thus a valuable tool to profile uranium toxicity non-invasively and could be very useful in follow-up in case of accidental exposure to uranium. (authors)

  8. Integrated and Quantitative Proteomics of Human Tumors.

    Science.gov (United States)

    Yakkioui, Y; Temel, Y; Chevet, E; Negroni, L

    2017-01-01

    Quantitative proteomics represents a powerful approach for the comprehensive analysis of proteins expressed under defined conditions. These properties have been used to investigate the proteome of disease states, including cancer. It has become a major subject of studies to apply proteomics for biomarker and therapeutic target identification. In the last decades, technical advances in mass spectrometry have increased the capacity of protein identification and quantification. Moreover, the analysis of posttranslational modification (PTM), especially phosphorylation, has allowed large-scale identification of biological mechanisms. Even so, increasing evidence indicates that global protein quantification is often insufficient for the explanation of biology and has shown to pose challenges in identifying new and robust biomarkers. As a consequence, to improve the accuracy of the discoveries made using proteomics in human tumors, it is necessary to combine (i) robust and reproducible methods for sample preparation allowing statistical comparison, (ii) PTM analyses in addition to global proteomics for additional levels of knowledge, and (iii) use of bioinformatics for decrypting protein list. Herein, we present technical specificities for samples preparation involving isobaric tag labeling, TiO2-based phosphopeptides enrichment and hydrazyde-based glycopeptides purification as well as the key points for the quantitative analysis and interpretation of the protein lists. The method is based on our experience with tumors analysis derived from hepatocellular carcinoma, chondrosarcoma, human embryonic intervertebral disk, and chordoma experiments.

  9. PROTEOMICS in aquaculture: applications and trends.

    Science.gov (United States)

    Rodrigues, Pedro M; Silva, Tomé S; Dias, Jorge; Jessen, Flemming

    2012-07-19

    Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5 million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous growth in production is still expected for decades to come. Aquaculture is, though, a very competitive market, and a global awareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organism through a sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful comparative tool, has therefore been increasingly used over the last decade to address different questions in aquaculture, regarding welfare, nutrition, health, quality, and safety. In this paper we will give an overview of these biological questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue.

  10. Proteome studies of bacterial antibiotic resistance mechanisms.

    Science.gov (United States)

    Vranakis, Iosif; Goniotakis, Ioannis; Psaroulaki, Anna; Sandalakis, Vassilios; Tselentis, Yannis; Gevaert, Kris; Tsiotis, Georgios

    2014-01-31

    Ever since antibiotics were used to help humanity battle infectious diseases, microorganisms straight away fought back. Antibiotic resistance mechanisms indeed provide microbes with possibilities to by-pass and survive the action of antibiotic drugs. Several methods have been employed to identify these microbial resistance mechanisms in an ongoing effort to reduce the steadily increasing number of treatment failures due to multi-drug-resistant microbes. Proteomics has evolved to an important tool for this area of research. Following rapid advances in whole genome sequencing, proteomic technologies have been widely used to investigate microbial gene expression. This review highlights the contribution of proteomics in identifying microbial drug resistance mechanisms. It summarizes different proteomic studies on bacteria resistant to different antibiotic drugs. The review further includes an overview of the methodologies used, as well as lists key proteins identified, thus providing the reader not only a summary of research already done, but also directions for future research. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

  11. Post-harvest proteomics and food security.

    Science.gov (United States)

    Pedreschi, Romina; Lurie, Susan; Hertog, Maarten; Nicolaï, Bart; Mes, Jurriaan; Woltering, Ernst

    2013-06-01

    To guarantee sufficient food supply for a growing world population, efforts towards improving crop yield and plant resistance should be complemented with efforts to reduce post-harvest losses. Post-harvest losses are substantial and occur at different stages of the food chain in developed and developing countries. In recent years, a substantially increasing interest can be seen in the application of proteomics to understand post-harvest events. In the near future post-harvest proteomics will be poised to move from fundamental research to aiding the reduction of food losses. Proteomics research can help in reducing food losses through (i) identification and validation of gene products associated to specific quality traits supporting marker-assisted crop improvement programmes, (ii) delivering markers of initial quality that allow optimisation of distribution conditions and prediction of remaining shelf-life for decision support systems and (iii) delivering early detection tools of physiological or pathogen-related post-harvest problems. In this manuscript, recent proteomics studies on post-harvest and stress physiology are reviewed and discussed. Perspectives on future directions of post-harvest proteomics studies aiming to reduce food losses are presented.

  12. Mass spectrometry in food proteomics: a tutorial.

    Science.gov (United States)

    Cunsolo, Vincenzo; Muccilli, Vera; Saletti, Rosaria; Foti, Salvatore

    2014-09-01

    In the last decades, the continuous and rapid evolution of proteomic approaches has provided an efficient platform for the characterization of food-derived proteins. Particularly, the impressive increasing in performance and versatility of the MS instrumentation has contributed to the development of new analytical strategies for proteins, evidencing how MS arguably represents an indispensable tool in food proteomics. Investigation of protein composition in foodstuffs is helpful for understanding the relationship between the protein content and the nutritional and technological properties of foods, the production of methods for food traceability, the assessment of food quality and safety, including the detection of allergens and microbial contaminants in foods, or even the characterization of genetically modified products. Given the high variety of the food-derived proteins and considering their differences in chemical and physical properties, a single proteomic strategy for all purposes does not exist. Rather, proteomic approaches need to be adapted to each analytical problem, and development of new strategies is necessary in order to obtain always the best results. In this tutorial, the most relevant aspects of MS-based methodologies in food proteomics will be examined, and their advantages and drawbacks will be discussed.

  13. The Coming Age of Complete, Accurate, and Ubiquitous Proteomes

    DEFF Research Database (Denmark)

    Mann, M.; Kulak, N.A.; Nagaraj, N.

    2013-01-01

    High-resolution mass spectrometry (MS)-based proteomics has progressed tremendously over the years. For model organisms like yeast, we can now quantify complete proteomes in just a few hours. Developments discussed in this Perspective will soon enable complete proteome analysis of mammalian cells...

  14. Mitochondrial specialization revealed by single muscle fiber proteomics

    DEFF Research Database (Denmark)

    Schiaffino, S; Reggiani, C; Kostrominova, T Y

    2015-01-01

    We have developed a highly sensitive mass spectrometry-based proteomic workflow to examine the proteome of single muscle fibers. This study revealed significant differences in the mitochondrial proteome of the four major fiber types present in mouse skeletal muscle. Here, we focus on Krebs cycle ...... scavenging capacity to cope with the higher levels of reactive oxygen species production....

  15. Tumor Cold Ischemia - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    In a recently published manuscript in the journal of Molecular and Cellular Proteomics, researchers from the National Cancer Institutes (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigated the effect of cold ischemia on the proteome of fresh frozen tumors.

  16. [Proteomic biomarkers in Parkinson's disease].

    Science.gov (United States)

    Bandrés, Sara; Durán, Raquel; Barrero, Francisco; Ramírez, Manuel; Vives, Francisco

    2014-02-16

    Parkinson's disease (PD) is a neurodegenerative disorder that affects movement and is caused by the death of the dopaminergic neurons in the compact part of the substantia nigra. Its diagnosis is essentially clinical, but although the signs and symptoms of PD are well known, the rate of diagnostic error is relatively high. It is estimated that 10-30% of patients initially diagnosed with PD are later reclassified. This disease has a high prevalence beyond the age of 60, and one of its biggest problems is that it is diagnosed when the degenerative process is already at a very advanced stage. Therefore, it is necessary to look for other biomarkers that make it possible to carry out an early diagnosis of PD, follow up its development, distinguish it from other related pathologies (parkinsonisms) and help monitor the effect of novel therapies. The fact that there are mutations that lead to PD, as well as polygenetic combinations that can act as risk factors, suggests the possibility of measuring the proteins resulting from the expression of these genes in peripheral tissues. And once their sensitivity and specificity have been proved they could be used as biomarkers for PD, even in the early phases of the disease. The aim of this work is to focus on a detailed review of the main candidate proteomic biomarkers researched to date by discussing the most recent literature.

  17. Proteomic Analysis of Hair Follicles

    Science.gov (United States)

    Ishioka, Noriaki; Terada, Masahiro; Yamada, Shin; Seki, Masaya; Takahashi, Rika; Majima, Hideyuki J.; Higashibata, Akira; Mukai, Chiaki

    2013-02-01

    Hair root cells actively divide in a hair follicle, and they sensitively reflect physical conditions. By analyzing the human hair, we can know stress levels on the human body and metabolic conditions caused by microgravity environment and cosmic radiation. The Japan Aerospace Exploration Agency (JAXA) has initiated a human research study to investigate the effects of long-term space flight on gene expression and mineral metabolism by analyzing hair samples of astronauts who stayed in the International Space Station (ISS) for 6 months. During long-term flights, the physiological effects on astronauts include muscle atrophy and bone calcium loss. Furthermore, radiation and psychological effects are important issue to consider. Therefore, an understanding of the effects of the space environment is important for developing countermeasures against the effects experienced by astronauts. In this experiment, we identify functionally important target proteins that integrate transcriptome, mineral metabolism and proteome profiles from human hair. To compare the protein expression data with the gene expression data from hair roots, we developed the protein processing method. We extracted the protein from five strands of hair using ISOGEN reagents. Then, these extracted proteins were analyzed by LC-MS/MS. These collected profiles will give us useful physiological information to examine the effect of space flight.

  18. Prefractionation techniques in proteome analysis.

    Science.gov (United States)

    Righetti, Pier Giorgio; Castagna, Annalisa; Herbert, Ben; Reymond, Frederic; Rossier, Joël S

    2003-08-01

    The present review deals with a number of prefractionation protocols in preparation for two-dimensional map analysis, both in the fields of chromatography and in the field of electrophoresis. In the first case, Fountoulaki's groups has reported just about any chromatographic procedure useful as a prefractionation step, including affinity, ion-exchange, and reversed-phase resins. As a result of the various enrichment steps, several hundred new species, previously undetected in unfractionated samples, could be revealed for the first time. Electrophoretic prefractionation protocols include all those electrokinetic methodologies which are performed in free solution, essentially all relying on isoelectric focusing steps. The devices here reviewed include multichamber apparatus, such as the multicompartment electrolyzer with Immobiline membranes, Off-Gel electrophoresis in a multicup device and the Rotofor, an instrument also based on a multichamber system but exploiting the conventional technique of carrier-ampholyte-focusing. Other instruments of interest are the Octopus, a continuous-flow device for isoelectric focusing in a upward flowing liquid curtain, and the Gradiflow, where different pI cuts are obtained by a multistep passage through two compartments buffered at different pH values. It is felt that this panoply of methods could offer a strong step forward in "mining below the tip of the iceberg" for detecting the "unseen proteome".

  19. Single Electron Transistor Platform for Microgravity Proteomics Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This Phase II program builds from the successful Phase I efforts to demonstrate that Quantum Logic Devices' nanoelectronic platform for biological detection could...

  20. Proteomics in Argentina - limitations and future perspectives: A special emphasis on meat proteomics.

    Science.gov (United States)

    Fadda, Silvina; Almeida, André M

    2015-11-01

    Argentina is one of the most relevant countries in Latin America, playing a major role in regional economics, culture and science. Over the last 80 years, Argentinean history has been characterized by several upward and downward phases that had major consequences on the development of science in the country and most recently on proteomics. In this article, we characterize the evolution of Proteomics sciences in Argentina over the last decade and a half. We describe the proteomics publication output of the country in the framework of the regional and international contexts, demonstrating that Argentina is solidly anchored in a regional context, showing results similar to other emergent and Latin American countries, albeit still far from the European, American or Australian realities. We also provide a case-study on the importance of Proteomics to a specific sector in the area of food science: the use of bacteria of technological interest, highlighting major achievements obtained by Argentinean proteomics scientists. Finally, we provide a general picture of the endeavors being undertaken by Argentinean Proteomics scientists and their international collaborators to promote the Proteomics-based research with the new generation of scientists and PhD students in both Argentina and other countries in the Southern cone.