Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0

doi:10.1021/acs.jproteome.9b00542

Authors:

Deutsch, Eric W, Lane, Lydie, Overall, Christopher M, Bandeira, Nuno, Baker, Mark D., Pineau, Charles, Moritz, Robert L, Corrales, Fernando, Orchard, Sandra, van Eyk, Jennifer E, Paik, Young-Ki, Weintraub, Susan T, Vandenbrouck, Yves, Omenn, Gilbert S + 9

Contributors:

Institute for Systems Biology Seattle (ISB), Université de Genève = University of Geneva (UNIGE), University of British Columbia (UBC), University of California San Diego (UC San Diego), University of California (UC), Macquarie University, Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique EHESP (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), École des Hautes Études en Santé Publique EHESP (EHESP), Consejo Superior de Investigaciones Cientificas España = Spanish National Research Council Spain (CSIC), Wellcome Trust, Cedars-Sinai Medical Center, Yonsei University, The University of Texas at San Antonio (UTSA), Etude de la dynamique des protéomes (EDyP ), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes 2016-2019 (UGA 2016-2019 )-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes 2016-2019 (UGA 2016-2019 )-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Michigan Ann Arbor, University of Michigan System, R01GM087221, National Institute of General Medical Sciences, U54ES017885, National Institute of Environmental Health Sciences, National Institute of Mental Health, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Allergy and Infectious Diseases, 148408, Canadian Institutes of Health Research, DBI-1933311, Division of Biological Infrastructure, IOS-1922871, Division of Integrative Organismal Systems, HI13C2098, Ministry of Health and Welfare, ANR-10-INBS-08, Agence Nationale de la Recherche, National Eye Institute, R01LM013115, U.S. National Library of Medicine, U24CA210967, National Cancer Institute, U54EB020406, National Institute of Biomedical Imaging and Bioengineering, R01HL133135, National Heart, Lung, and Blood Institute, U19AG02312, National Institute on Aging, ABI-1759980, National Science Foundation, U24HG007822, National Human Genome Research Institute, ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010) + 41

Published in:

ISSN: 1535-3893

Publisher:

HAL CCSD, American Chemical Society

Abstract

International audience ; The Human Proteome Organization’s (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, we describe an update to these guidelines based on consensus-reaching discussions with the wider HPP community over the past year. The revised 3.0 guidelines address several major and minor identified gaps. We have added guidelines for emerging data independent acquisition (DIA) MS workflows and for use of the new Universal Spectrum Identifier (USI) system being developed by the HUPO Proteomics Standards Initiative (PSI). In addition, we discuss updates to the standard HPP pipeline for collecting MS evidence for all proteins in the HPP, including refinements to minimum evidence. We present a new plan for incorporating MassIVE-KB into the HPP pipeline for the next (HPP 2020) cycle in order to obtain more comprehensive coverage of public MS data sets. The main checklist has been reorganized under headings and subitems, and related guidelines have been grouped. In sum, Version 2.1 of the HPP MS Data Interpretation Guidelines has served well, and this timely update to version 3.0 will aid the HPP as it approaches its goal of collecting and curating MS evidence of translation and expression for all predicted ∼20 000 human proteins encoded by the human genome.