ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments
Detection of differentially abundant proteins in label-free quantitative shotgun liquid chromatography–tandem mass spectrometry (LC–MS/MS) experiments requires a series of computational steps that identify and quantify LC–MS features. It also requires statistical analyses that distinguish systematic...
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Published in | Journal of proteome research Vol. 16; no. 2; pp. 945 - 957 |
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Main Authors | , , , , , , , , , , , , , |
Format | Journal Article |
Language | English |
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United States
American Chemical Society
03.02.2017
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Abstract | Detection of differentially abundant proteins in label-free quantitative shotgun liquid chromatography–tandem mass spectrometry (LC–MS/MS) experiments requires a series of computational steps that identify and quantify LC–MS features. It also requires statistical analyses that distinguish systematic changes in abundance between conditions from artifacts of biological and technical variation. The 2015 study of the Proteome Informatics Research Group (iPRG) of the Association of Biomolecular Resource Facilities (ABRF) aimed to evaluate the effects of the statistical analysis on the accuracy of the results. The study used LC–tandem mass spectra acquired from a controlled mixture, and made the data available to anonymous volunteer participants. The participants used methods of their choice to detect differentially abundant proteins, estimate the associated fold changes, and characterize the uncertainty of the results. The study found that multiple strategies (including the use of spectral counts versus peak intensities, and various software tools) could lead to accurate results, and that the performance was primarily determined by the analysts’ expertise. This manuscript summarizes the outcome of the study, and provides representative examples of good computational and statistical practice. The data set generated as part of this study is publicly available. |
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AbstractList | Detection of differentially abundant proteins in label-free quantitative shotgun liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments requires a series of computational steps that identify and quantify LC-MS features. It also requires statistical analyses that distinguish systematic changes in abundance between conditions from artifacts of biological and technical variation. The 2015 study of the Proteome Informatics Research Group (iPRG) of the Association of Biomolecular Resource Facilities (ABRF) aimed to evaluate the effects of the statistical analysis on the accuracy of the results. The study used LC-tandem mass spectra acquired from a controlled mixture, and made the data available to anonymous volunteer participants. The participants used methods of their choice to detect differentially abundant proteins, estimate the associated fold changes, and characterize the uncertainty of the results. The study found that multiple strategies (including the use of spectral counts versus peak intensities, and various software tools) could lead to accurate results, and that the performance was primarily determined by the analysts' expertise. This manuscript summarizes the outcome of the study, and provides representative examples of good computational and statistical practice. The data set generated as part of this study is publicly available. |
Author | Lam, Henry Neubert, Thomas A MacLean, Brendan Palmblad, Magnus Colangelo, Christopher Kapp, Eugene A Cottrell, John Eren-Dogu, Zeynep F Vitek, Olga Weintraub, Susan T Hoopmann, Michael R Phinney, Brett S Kim, Sangtae Choi, Meena |
AuthorAffiliation | New York University School of Medicine Walter and Eliza Hall Institute of Medical Research University of California at Davis Department of Chemical and Biomolecular Engineering and Division of Biomedical Engineering Skirball Institute and Department of Biochemistry and Molecular Pharmacology University of Texas Health Science Center at San Antonio The Hong Kong University of Science and Technology Leiden University Medical Center Matrix Science Ltd Institute for Systems Biology Primary Ion, LLC University of Washington Pacific Northwest National Laboratory Center for Proteomics and Metabolomics |
AuthorAffiliation_xml | – name: Center for Proteomics and Metabolomics – name: Walter and Eliza Hall Institute of Medical Research – name: University of Texas Health Science Center at San Antonio – name: Institute for Systems Biology – name: University of Washington – name: Skirball Institute and Department of Biochemistry and Molecular Pharmacology – name: Matrix Science Ltd – name: Pacific Northwest National Laboratory – name: The Hong Kong University of Science and Technology – name: New York University School of Medicine – name: University of California at Davis – name: Primary Ion, LLC – name: Department of Chemical and Biomolecular Engineering and Division of Biomedical Engineering – name: Leiden University Medical Center |
Author_xml | – sequence: 1 givenname: Meena orcidid: 0000-0002-6025-5035 surname: Choi fullname: Choi, Meena – sequence: 2 givenname: Zeynep F surname: Eren-Dogu fullname: Eren-Dogu, Zeynep F – sequence: 3 givenname: Christopher surname: Colangelo fullname: Colangelo, Christopher – sequence: 4 givenname: John surname: Cottrell fullname: Cottrell, John – sequence: 5 givenname: Michael R surname: Hoopmann fullname: Hoopmann, Michael R – sequence: 6 givenname: Eugene A surname: Kapp fullname: Kapp, Eugene A – sequence: 7 givenname: Sangtae surname: Kim fullname: Kim, Sangtae – sequence: 8 givenname: Henry surname: Lam fullname: Lam, Henry – sequence: 9 givenname: Thomas A surname: Neubert fullname: Neubert, Thomas A – sequence: 10 givenname: Magnus surname: Palmblad fullname: Palmblad, Magnus – sequence: 11 givenname: Brett S surname: Phinney fullname: Phinney, Brett S – sequence: 12 givenname: Susan T surname: Weintraub fullname: Weintraub, Susan T – sequence: 13 givenname: Brendan surname: MacLean fullname: MacLean, Brendan – sequence: 14 givenname: Olga orcidid: 0000-0003-1728-1104 surname: Vitek fullname: Vitek, Olga email: o.vitek@neu.edu |
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Snippet | Detection of differentially abundant proteins in label-free quantitative shotgun liquid chromatography–tandem mass spectrometry (LC–MS/MS) experiments requires... Detection of differentially abundant proteins in label-free quantitative shotgun liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments requires... |
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SubjectTerms | Chromatography, Liquid - standards Data Interpretation, Statistical Humans Laboratory Proficiency Testing Professional Competence Proteome - isolation & purification Proteome - standards Proteomics - instrumentation Proteomics - methods Proteomics - standards Reproducibility of Results Tandem Mass Spectrometry - standards Uncertainty |
Title | ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments |
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