Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project
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The Human Proteome Project (HPP) annually reports on progress made throughout the field in credibly identifying and characterizing the complete human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2019-01-11 contains 17 694 proteins with strong protein-level evidence (PE1), compliant with HPP Guidelines for Interpretation of MS Data v2.1; these represent 89% of all 19 823 neXtProt predicted coding genes (all PE1,2,3,4 proteins), up from 17 470 one year earlier. Conversely, the number of neXtProt PE2,3,4 proteins, termed the "missing proteins" (MPs), has been reduced from 2949 to 2129 since 2016 through efforts throughout the community, including the chromosome-centric HPP. PeptideAtlas is the source of uniformly reanalyzed raw mass spectrometry data for neXtProt; PeptideAtlas added 495 canonical proteins between 2018 and 2019, especially from studies designed to detect hard-to-identify proteins. Meanwhile, the Human Protein Atlas has released version 18.1 with immunohistochemical evidence of expression of 17 000 proteins and survival plots as part of the Pathology Atlas. Many investigators apply multiplexed SRM-targeted proteomics for quantitation of organ-specific popular proteins in studies of various human diseases. The 19 teams of the Biology and Disease-driven B/D-HPP published a total of 160 publications in 2018, bringing proteomics to a broad array of biomedical research.
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In each of the seven annual HPP metrics papers published to date, PE1,2,3,4,5 entries have been added, deleted, renamed, merged and/or de-merged, indicating ongoing fine-tuning of the HPP reference proteome.
“In each of the seven annual HPP metrics papers published to date (9 and refs therein), PE1,2,3,4,5 entries have been added, deleted, renamed, merged and/or de-merged, indicating ongoing fine-tuning of the HPP reference proteome.”
From A high-stringency blueprint of the human proteome (2020) · cites this paper as [9]
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Self-citationRonci, M., Pieroni, L., Greco, V., Scotti, L., Marini, F., Carregari, V. C., Cunsolo, V., Foti, S., Aceto, A., & Urbani, A. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00422 · Cited by 9 · see citing works
Siddiqui, O., Zhang, H., Guan, Y., & Omenn, G. S. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00442 · Cited by 8 · see citing works
Self-citationYu, K., Lee, M. T., Chen, Y., Ré, C., Kou, S. C., Chiang, J.-H., Snyder, M. P., & Kohane, I. S. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00378 · Cited by 7 · see citing works
Self-citationClemente, L. F., Hernáez, M. L., Ramos-Fernández, A., Ligero, G., Gil, C., Corrales, F. J., & Marcilla, M. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00384 · Cited by 5 · see citing works
Self-citationHuman Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0Preprint
Deutsch, E. W., Lane, L., Overall, C. M., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/733576 · Cited by 2 · see citing works
Self-citation
Flagged first, then by citations
Research works printed but not linked: 2
- [15]Zhang H; Siddiqui O; Guan Y; Omenn GS Chromosome 17: neXt-MP50 challenge completed. J. Proteome Res 2019. PMC6465108 30280577
- [81]Sjostedt E; Sivertsson A; Hikmet Noraddin F; Katona B; Nasstrom A; Vuu J; Kesti D; Oksvold P; Edqvist PH; Olsson I; Uhlen M; Lindskog C Integration of transcriptomics and antibody-based proteomics for exploration of proteins expressed in specialized tissues. J. Proteome Res 2018, 17 (12), 4127– 4137. 30272454
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A high-stringency blueprint of the human proteome
Adhikari, S., Nice, E. C., Deutsch, E. W., Lane, L., Omenn, G. S., Pennington, S. R., Paik, Y.-K., Overall, C. M., Corrales, F. J., Cristea, I. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19045-9 · Cited by 210 · see citing works
Self-citationHuman Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0
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., et al. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00542 · Cited by 122 · see citing works
Self-citation
- Authors
- Omenn, G. S., Lane, L., Overall, C. M., Corrales, F. J., Schwenk, J. M., Paik, Y.-K., Van Eyk, J. E., Liu, S., Pennington, S., Snyder, M. P., Baker, M. S., & Deutsch, E. W.
- Affiliations
- University of Michigan (US)
- University of Geneva (CH)
- University of British Columbia (CA)
- Consejo Superior de Investigaciones Científicas (ES)
- Science for Life Laboratory (SE)
- Yonsei University (KR)
- Advanced Clinical BioSystems Research Institute, Cedars Sinai Precision Biomarker Laboratories, Barbra Streisand Women’s Heart Center, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
- BGI Group (China) (CN)
- University College Dublin (IE)
- Stanford University (US)
- Macquarie University (AU)
- Institute for Systems Biology (US)
- Corresponding author
- Omenn, Gilbert S.
- ORCID
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2019-08-20
- Volume
- 18
- Issue
- 12
- Pages
- 4098-4107
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- PMC
- PMC6898754
- OpenAlex
- W2995467264
- Cited by
- 40
- References
- 83
- Citations by year
- 2026: 1 · 2024: 3 · 2023: 1 · 2022: 5 · 2021: 8 · 2020: 17 · 2019: 5
- FWCI
- 3.48
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Journal of Proteome Research (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- Funders
- Canadian Institutes of Health Research
- Ministry of Health and Welfare (HI16C0257, HI13C22098)
- National Health and Medical Research Council (APP1010303)
- Knut och Alice Wallenbergs Stiftelse
- National Institute of Biomedical Imaging and Bioengineering (U54EB020406)
- Canada Research Chairs
- National Institute on Aging (U19AG023122)
- National Institutes of Health (P30ES017885-01A1, U24CA210967)
- National Institute of General Medical Sciences (R01GM087221, R24GM127667)
- Swiss Institute of Bioinformatics
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced Biosensing Techniques and Applications
- Keywords
- human proteome, Human Proteome Project, protein identification, neXtProt, missing proteins, PeptideAtlas, Human Protein Atlas, targeted proteomics, multi-omics
- MeSH terms
- Chromosomes, Human, Humans, Proteins, Mass Spectrometry, Guidelines as Topic, Proteome, Databases, Protein
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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