Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0
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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.
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The HPP routinely applies high-stringency protein inference analytics generated through the Trans-Proteomic Pipeline.
“The HPP routinely applies high-stringency protein inference analytics10, generated through the Trans-Proteomic Pipeline11.”
From A high-stringency blueprint of the human proteome (2020) · cites this paper as [10]
The current HPP guidelines require at least two uniquely mapping peptides (using neXtProt's Peptide Uniqueness Checker Tool) that are at least nine amino acid residues long, non-nested but may overlap partially so coverage exceeds >18 residues.
“The current HPP guidelines10 require at least two uniquely mapping peptides (using neXtProt’s Peptide Uniqueness Checker Tool12), which are at least nine amino acid residues long. Peptides must be non-nested (i.e., one not fully contained within another) but may overlap partially so coverage exceeds >18 residues.”
From A high-stringency blueprint of the human proteome (2020) · cites this paper as [10]
The HPP requires full declaration of false discovery rate (FDR) calculation procedures at peptide and protein levels, with a maximum allowable protein-level FDR of 1%.
“The HPP also requires full declaration of false discovery rate (FDR) calculation procedures at peptide and protein levels, with a maximum allowable protein-level FDR of 1%.”
From A high-stringency blueprint of the human proteome (2020) · cites this paper as [10]
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- [20]Lane L; Bairoch A; Beavis RC; Deutsch EW; Gaudet P; Lundberg E; Omenn GS Metrics for the Human Proteome Project 2013–2014 and Strategies for Finding Missing Proteins. J. Proteome Res 2014, 13 (1), 15– 20. 10.1021/pr401144x. 24364385 PMC3928647 · DOI · Paper page
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Self-citationA high-stringency blueprint of the human proteome
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Self-citation
- Authors
- 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.
- Affiliations
- Institute for Systems Biology (US)
- University of Geneva (CH)
- University of British Columbia (CA)
- University of California San Diego (US)
- Macquarie University (AU)
- Inserm (FR)
- Instituto de Salud Carlos III (ES)
- European Bioinformatics Institute (GB)
- Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Yonsei University (KR)
- The University of Texas at San Antonio Health Science Center (US)
- University of Michigan (US)
- Corresponding author
- Deutsch, Eric W.
- ORCID
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2019-10-10
- Volume
- 18
- Issue
- 12
- Pages
- 4108-4116
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- PMC
- PMC6986310
- OpenAlex
- W2979860221
- Cited by
- 122
- References
- 49
- Citations by year
- 2026: 14 · 2025: 11 · 2024: 24 · 2023: 21 · 2022: 18 · 2021: 15 · 2020: 15 · 2019: 3
- FWCI
- 5.08
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Journal of Proteome Research (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion, other-oa)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- Funders
- National Institute of Environmental Health Sciences (U54ES017885)
- Division of Integrative Organismal Systems (IOS-1922871)
- Division of Biological Infrastructure (DBI-1933311)
- National Cancer Institute (U24CA210967)
- National Eye Institute
- National Human Genome Research Institute (U24HG007822)
- National Institute of Diabetes and Digestive and Kidney Diseases
- National Heart, Lung, and Blood Institute (R01HL133135)
- National Institute of Allergy and Infectious Diseases
- U.S. National Library of Medicine (R01LM013115)
- National Institute of Biomedical Imaging and Bioengineering (U54EB020406)
- National Institute on Aging (U19AG02312)
- National Institute of Mental Health
- National Institute of General Medical Sciences (P41GM103484, R01GM087221, R24GM127667)
- National Science Foundation (ABI-1759980)
- Canadian Institutes of Health Research (148408)
- Agence Nationale de la Recherche (ANR-10-INBS-08)
- Ministry of Health and Welfare (HI13C2098)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- Human Proteome Project, mass spectral interpretation, protein identification, false positive reduction, data-independent acquisition, MassIVE-KB, human proteome, data curation
- MeSH terms
- Humans, Signal Processing, Computer-Assisted, Societies, Scientific, Mass Spectrometry, Guidelines as Topic, Proteome, Proteomics
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