Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0

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

doi:10.1021/acs.jproteome.9b00542

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0

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

Research output: Contribution to journal › Review article › peer-review

50 Citations (Scopus)

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 â 20â »000 human proteins encoded by the human genome.

Original language	English
Pages (from-to)	4108-4116
Number of pages	9
Journal	Journal of Proteome Research
Volume	18
Issue number	12
DOIs	https://doi.org/10.1021/acs.jproteome.9b00542
Publication status	Published - 2019 Dec 6

Bibliographical note

Funding Information:
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).

Publisher Copyright:
Copyright © 2019 American Chemical Society.

All Science Journal Classification (ASJC) codes

Chemistry(all)
Biochemistry

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Deutsch, E. W., Lane, L., Overall, C. M., Bandeira, N., Baker, M. S., Pineau, C., Moritz, R. L., Corrales, F., Orchard, S., Van Eyk, J. E., Paik, Y. K., Weintraub, S. T., Vandenbrouck, Y., & Omenn, G. S. (2019). Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0. Journal of Proteome Research, 18(12), 4108-4116. https://doi.org/10.1021/acs.jproteome.9b00542

@article{7b346272a6ad4c5ab48ddc94596c8ee0,

title = "Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0",

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 {\^a} 20{\^a} »000 human proteins encoded by the human genome.",

author = "Deutsch, {Eric W.} and Lydie Lane and Overall, {Christopher M.} and Nuno Bandeira and Baker, {Mark S.} and Charles Pineau and Moritz, {Robert L.} and Fernando Corrales and Sandra Orchard and {Van Eyk}, {Jennifer E.} and Paik, {Young Ki} and Weintraub, {Susan T.} and Yves Vandenbrouck and Omenn, {Gilbert S.}",

note = "Funding Information: 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). Publisher Copyright: Copyright {\textcopyright} 2019 American Chemical Society.",

year = "2019",

month = dec,

day = "6",

doi = "10.1021/acs.jproteome.9b00542",

language = "English",

volume = "18",

pages = "4108--4116",

journal = "Journal of Proteome Research",

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AU - Deutsch, Eric W.

AU - Lane, Lydie

AU - Overall, Christopher M.

AU - Bandeira, Nuno

AU - Baker, Mark S.

AU - Pineau, Charles

AU - Moritz, Robert L.

AU - Corrales, Fernando

AU - Orchard, Sandra

AU - Van Eyk, Jennifer E.

AU - Paik, Young Ki

AU - Weintraub, Susan T.

AU - Vandenbrouck, Yves

AU - Omenn, Gilbert S.

N1 - Funding Information: 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). Publisher Copyright: Copyright © 2019 American Chemical Society.

PY - 2019/12/6

Y1 - 2019/12/6

N2 - 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 â 20â »000 human proteins encoded by the human genome.

AB - 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 â 20â »000 human proteins encoded by the human genome.

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Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0

Abstract

Bibliographical note

All Science Journal Classification (ASJC) codes

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