1. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0
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Nuno Bandeira, Yves Vandenbrouck, Fernando J. Corrales, Robert L. Moritz, Eric W. Deutsch, Christopher M. Overall, Charles Pineau, Jennifer E. Van Eyk, Gilbert S. Omenn, Mark S. Baker, Susan T. Weintraub, Sandra Orchard, Lydie Lane, Young Ki Paik, National Institutes of Health (US), Iranian National Science Foundation, Canadian Institutes of Health Research, Ministry of Health and Welfare (South Korea), Ministère de l’Enseignement supérieur et de la Recherche (France), National Eye Institute (US), National Human Genome Research Institute (US), National Heart, Lung, and Blood Institute (US), National Institute of Allergy and Infectious Diseases (US), National Institute of Diabetes and Digestive and Kidney Diseases (US), National Institute of General Medical Sciences (US), National Institute of Mental Health (US), 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 Científicas [Madrid] (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), University of Geneva [Switzerland], University of California, Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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 ), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and 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])
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Proteomics ,Societies, Scientific ,0301 basic medicine ,Standards ,Proteome ,Computer science ,[SDV]Life Sciences [q-bio] ,Guidelines as Topic ,Guidelines ,Mass spectrometry ,Biochemistry ,Article ,03 medical and health sciences ,Human proteome project ,Humans ,Data-independent acquisition ,Human Proteome Project ,Human proteins ,030304 developmental biology ,ddc:616 ,0303 health sciences ,030102 biochemistry & molecular biology ,Proteomics Standards Initiative ,4. Education ,C-HPP ,030302 biochemistry & molecular biology ,Universal Spectrum Identifier (USI) ,Data interpretation ,Signal Processing, Computer-Assisted ,General Chemistry ,Data science ,3. Good health ,030104 developmental biology ,Workflow ,False-discovery rates ,Human genome ,HPP ,B/D-HPP ,Unicity checker - Abstract
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., This work was funded in part by the National Institutes of Health grants R01GM087221 (EWD/RLM), R24GM127667 (EWD), U54EB020406 (EWD), R01HL133135 (RLM), U19AG02312 (RLM), U54ES017885 (GSO), U24CA210967-01 (GSO), R01LM013115 (NB) and P41GM103484 (NB); National Science Foundation grants ABI-1759980 (NB), DBI-1933311 (EWD), and IOS-1922871 (EWD); Canadian Institutes of Health Research 148408 (CMO); Korean Ministry of Health and Welfare HI13C2098 (YKP); French Ministry of Higher Education, Research and Innovation, ProFI project, ANR-10-INBS-08 (YV); also in part by the National Eye Institute (NEI), National Human Genome Research Institute (NHGRI), National Heart, Lung, and Blood Institute (NHLBI), National Institute of Allergy and Infectious Diseases (NIAID), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institute of General Medical Sciences (NIGMS), and National Institute of Mental Health (NIMH) of the National Institutes of Health under Award Number U24HG007822 (SO) (the content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health).
- Published
- 2019
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