title: ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments.
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.
authors.affiliation: Northeastern University , Boston, Massachusetts 02115, United States.
authors.forename: Meena
authors.identifier: 0000-0002-6025-5035
authors.initials: M
authors.lastname: Choi
authors.affiliation: Mugla Sitki Kocman University , 48000 Mugla, Turkey.
authors.forename: Zeynep F
authors.initials: ZF
authors.lastname: Eren-Dogu
authors.affiliation: Primary Ion, LLC , Old Lyme, Connecticut 06371, United States.
authors.forename: Christopher
authors.initials: C
authors.lastname: Colangelo
authors.affiliation: Matrix Science Ltd. , London W1U 7GB, U.K.
authors.forename: John
authors.initials: J
authors.lastname: Cottrell
authors.affiliation: Institute for Systems Biology , Seattle, Washington 98109, United States.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Hoopmann
authors.affiliation: Walter and Eliza Hall Institute of Medical Research , Melbourne 3052, Australia.
authors.forename: Eugene A
authors.initials: EA
authors.lastname: Kapp
authors.affiliation: Pacific Northwest National Laboratory , Richland, Washington 99354, United States.
authors.forename: Sangtae
authors.initials: S
authors.lastname: Kim
authors.affiliation: Department of Chemical and Biomolecular Engineering and Division of Biomedical Engineering, The Hong Kong University of Science and Technology , Clear Water Bay, Hong Kong.
authors.forename: Henry
authors.initials: H
authors.lastname: Lam
authors.affiliation: Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine , New York, New York 10016, United States.
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Neubert
authors.affiliation: Center for Proteomics and Metabolomics, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands.
authors.forename: Magnus
authors.initials: M
authors.lastname: Palmblad
authors.affiliation: University of California at Davis , Davis, California 95616, United States.
authors.forename: Brett S
authors.initials: BS
authors.lastname: Phinney
authors.affiliation: University of Texas Health Science Center at San Antonio , San Antonio, Texas 78229, United States.
authors.forename: Susan T
authors.initials: ST
authors.lastname: Weintraub
authors.affiliation: University of Washington , Seattle, Washington 98105, United States.
authors.forename: Brendan
authors.initials: B
authors.lastname: MacLean
authors.affiliation: Northeastern University , Boston, Massachusetts 02115, United States.
authors.forename: Olga
authors.identifier: 0000-0003-1728-1104
authors.initials: O
authors.lastname: Vitek
mesh_terms: D002853:Chromatography, Liquid / Q000592:standards*; D003627:Data Interpretation, Statistical; D006801:Humans; D059021:Laboratory Proficiency Testing; D011361:Professional Competence; D020543:Proteome / Q000302:isolation & purification* / Q000592:standards; D040901:Proteomics / Q000295:instrumentation / Q000379:methods / Q000592:standards*; D015203:Reproducibility of Results; D053719:Tandem Mass Spectrometry / Q000592:standards*; D035501:Uncertainty
chemical_list: D020543:Proteome
keywords: LC−MS/MS; bioinformatics; differential abundance; mass spectrometry; quantitative proteomics; statistics