Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project

Gilbert S. Omenn; Lydie Lane; Christopher M. Overall; Young Ki Paik; Ileana M. Cristea; Fernando J. Corrales; Cecilia Lindskog; Susan Weintraub; Michael H.A. Roehrl; Siqi Liu; Nuno Bandeira; Sudhir Srivastava; Yu Ju Chen; Ruedi Aebersold; Robert L. Moritz; Eric W. Deutsch

doi:10.1021/acs.jproteome.1c00590

Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project

Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Young Ki Paik, Ileana M. Cristea, Fernando J. Corrales, Cecilia Lindskog, Susan Weintraub, Michael H.A. Roehrl, Siqi Liu, Nuno Bandeira, Sudhir Srivastava, Yu Ju Chen, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch

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

25 Citations (Scopus)

Abstract

The 2021 Metrics of the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 »357 (92.8%) of the 19 »778 predicted proteins coded in the human genome, a gain of 483 since 2020 from reports throughout the world reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 478 to 1421. This represents remarkable progress on the proteome parts list. The utilization of proteomics in a broad array of biological and clinical studies likewise continues to expand with many important findings and effective integration with other omics platforms. We present highlights from the Immunopeptidomics, Glycoproteomics, Infectious Disease, Cardiovascular, Musculo-Skeletal, Liver, and Cancers B/D-HPP teams and from the Knowledgebase, Mass Spectrometry, Antibody Profiling, and Pathology resource pillars, as well as ethical considerations important to the clinical utilization of proteomics and protein biomarkers.

Original language	English
Pages (from-to)	5227-5240
Number of pages	14
Journal	Journal of Proteome Research
Volume	20
Issue number	12
DOIs	https://doi.org/10.1021/acs.jproteome.1c00590
Publication status	Published - 2021 Dec 3

Bibliographical note

Funding Information:
We appreciate the guidance from the HPP Executive Committee and the participation of all HPP investigators. We thank the UniProt groups at SIB, EBI, and PIR for providing high-quality annotations for the human proteins in UniProtKB/Swiss-Prot. The neXtProt server is hosted by VitalIT in Switzerland, ProteomeXchange and PRIDE at the European Bioinformatics Institute in Cambridge, UK, PeptideAtlas at the Institute for Systems Biology in Seattle, and MassIVE at the University of California San Diego. G.S.O. acknowledges support from National Institutes of Health Grants P30ES017885-01A1 and U24CA210967; E.W.D. from National Institutes of Health Grants R01GM087221, R24GM127667, U19AG023122, and from National Science Foundation Grant DBI-1933311; L.L. and neXtProt from the SIB Swiss Institute of Bioinformatics; C.M.O. by Canadian Institutes of Health Research Foundation Grant 148408 and a Canada Research Chair in Protease Proteomics and Systems Biology; M.S.B. by NHMRC Project Grant APP1010303; C.L. by the Knut and Alice Wallenberg Foundation for the Human Protein Atlas; Y.-K.P. by grants from the Korean Ministry of Health and Welfare HI13C22098 and HI16C0257; M.H.R by National Institutes of Health Grants R21 CA263262, U01 CA253217, R21 CA251992, P30 CA008748 (MSKCC CCSG, Pathology Component), NIH-Leidos CPTAC contract 17X173, and Farmer Family Foundation; and I.M.C. from National Institutes of Health Grant R01GM114141.

Publisher Copyright:
© 2021 American Chemical Society.

All Science Journal Classification (ASJC) codes

Chemistry(all)
Biochemistry

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Omenn, G. S., Lane, L., Overall, C. M., Paik, Y. K., Cristea, I. M., Corrales, F. J., Lindskog, C., Weintraub, S., Roehrl, M. H. A., Liu, S., Bandeira, N., Srivastava, S., Chen, Y. J., Aebersold, R., Moritz, R. L., & Deutsch, E. W. (2021). Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project. Journal of Proteome Research, 20(12), 5227-5240. https://doi.org/10.1021/acs.jproteome.1c00590

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title = "Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project",

abstract = "The 2021 Metrics of the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 »357 (92.8%) of the 19 »778 predicted proteins coded in the human genome, a gain of 483 since 2020 from reports throughout the world reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 478 to 1421. This represents remarkable progress on the proteome parts list. The utilization of proteomics in a broad array of biological and clinical studies likewise continues to expand with many important findings and effective integration with other omics platforms. We present highlights from the Immunopeptidomics, Glycoproteomics, Infectious Disease, Cardiovascular, Musculo-Skeletal, Liver, and Cancers B/D-HPP teams and from the Knowledgebase, Mass Spectrometry, Antibody Profiling, and Pathology resource pillars, as well as ethical considerations important to the clinical utilization of proteomics and protein biomarkers.",

author = "Omenn, {Gilbert S.} and Lydie Lane and Overall, {Christopher M.} and Paik, {Young Ki} and Cristea, {Ileana M.} and Corrales, {Fernando J.} and Cecilia Lindskog and Susan Weintraub and Roehrl, {Michael H.A.} and Siqi Liu and Nuno Bandeira and Sudhir Srivastava and Chen, {Yu Ju} and Ruedi Aebersold and Moritz, {Robert L.} and Deutsch, {Eric W.}",

note = "Funding Information: We appreciate the guidance from the HPP Executive Committee and the participation of all HPP investigators. We thank the UniProt groups at SIB, EBI, and PIR for providing high-quality annotations for the human proteins in UniProtKB/Swiss-Prot. The neXtProt server is hosted by VitalIT in Switzerland, ProteomeXchange and PRIDE at the European Bioinformatics Institute in Cambridge, UK, PeptideAtlas at the Institute for Systems Biology in Seattle, and MassIVE at the University of California San Diego. G.S.O. acknowledges support from National Institutes of Health Grants P30ES017885-01A1 and U24CA210967; E.W.D. from National Institutes of Health Grants R01GM087221, R24GM127667, U19AG023122, and from National Science Foundation Grant DBI-1933311; L.L. and neXtProt from the SIB Swiss Institute of Bioinformatics; C.M.O. by Canadian Institutes of Health Research Foundation Grant 148408 and a Canada Research Chair in Protease Proteomics and Systems Biology; M.S.B. by NHMRC Project Grant APP1010303; C.L. by the Knut and Alice Wallenberg Foundation for the Human Protein Atlas; Y.-K.P. by grants from the Korean Ministry of Health and Welfare HI13C22098 and HI16C0257; M.H.R by National Institutes of Health Grants R21 CA263262, U01 CA253217, R21 CA251992, P30 CA008748 (MSKCC CCSG, Pathology Component), NIH-Leidos CPTAC contract 17X173, and Farmer Family Foundation; and I.M.C. from National Institutes of Health Grant R01GM114141. Publisher Copyright: {\textcopyright} 2021 American Chemical Society.",

year = "2021",

month = dec,

day = "3",

doi = "10.1021/acs.jproteome.1c00590",

language = "English",

volume = "20",

pages = "5227--5240",

journal = "Journal of Proteome Research",

issn = "1535-3893",

publisher = "American Chemical Society",

number = "12",

}

Omenn, GS, Lane, L, Overall, CM, Paik, YK, Cristea, IM, Corrales, FJ, Lindskog, C, Weintraub, S, Roehrl, MHA, Liu, S, Bandeira, N, Srivastava, S, Chen, YJ, Aebersold, R, Moritz, RL & Deutsch, EW 2021, 'Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project', Journal of Proteome Research, vol. 20, no. 12, pp. 5227-5240. https://doi.org/10.1021/acs.jproteome.1c00590

TY - JOUR

T1 - Progress Identifying and Analyzing the Human Proteome

T2 - 2021 Metrics from the HUPO Human Proteome Project

AU - Omenn, Gilbert S.

AU - Lane, Lydie

AU - Overall, Christopher M.

AU - Paik, Young Ki

AU - Cristea, Ileana M.

AU - Corrales, Fernando J.

AU - Lindskog, Cecilia

AU - Weintraub, Susan

AU - Roehrl, Michael H.A.

AU - Liu, Siqi

AU - Bandeira, Nuno

AU - Srivastava, Sudhir

AU - Chen, Yu Ju

AU - Aebersold, Ruedi

AU - Moritz, Robert L.

AU - Deutsch, Eric W.

N1 - Funding Information: We appreciate the guidance from the HPP Executive Committee and the participation of all HPP investigators. We thank the UniProt groups at SIB, EBI, and PIR for providing high-quality annotations for the human proteins in UniProtKB/Swiss-Prot. The neXtProt server is hosted by VitalIT in Switzerland, ProteomeXchange and PRIDE at the European Bioinformatics Institute in Cambridge, UK, PeptideAtlas at the Institute for Systems Biology in Seattle, and MassIVE at the University of California San Diego. G.S.O. acknowledges support from National Institutes of Health Grants P30ES017885-01A1 and U24CA210967; E.W.D. from National Institutes of Health Grants R01GM087221, R24GM127667, U19AG023122, and from National Science Foundation Grant DBI-1933311; L.L. and neXtProt from the SIB Swiss Institute of Bioinformatics; C.M.O. by Canadian Institutes of Health Research Foundation Grant 148408 and a Canada Research Chair in Protease Proteomics and Systems Biology; M.S.B. by NHMRC Project Grant APP1010303; C.L. by the Knut and Alice Wallenberg Foundation for the Human Protein Atlas; Y.-K.P. by grants from the Korean Ministry of Health and Welfare HI13C22098 and HI16C0257; M.H.R by National Institutes of Health Grants R21 CA263262, U01 CA253217, R21 CA251992, P30 CA008748 (MSKCC CCSG, Pathology Component), NIH-Leidos CPTAC contract 17X173, and Farmer Family Foundation; and I.M.C. from National Institutes of Health Grant R01GM114141. Publisher Copyright: © 2021 American Chemical Society.

PY - 2021/12/3

Y1 - 2021/12/3

N2 - The 2021 Metrics of the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 »357 (92.8%) of the 19 »778 predicted proteins coded in the human genome, a gain of 483 since 2020 from reports throughout the world reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 478 to 1421. This represents remarkable progress on the proteome parts list. The utilization of proteomics in a broad array of biological and clinical studies likewise continues to expand with many important findings and effective integration with other omics platforms. We present highlights from the Immunopeptidomics, Glycoproteomics, Infectious Disease, Cardiovascular, Musculo-Skeletal, Liver, and Cancers B/D-HPP teams and from the Knowledgebase, Mass Spectrometry, Antibody Profiling, and Pathology resource pillars, as well as ethical considerations important to the clinical utilization of proteomics and protein biomarkers.

AB - The 2021 Metrics of the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 »357 (92.8%) of the 19 »778 predicted proteins coded in the human genome, a gain of 483 since 2020 from reports throughout the world reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 478 to 1421. This represents remarkable progress on the proteome parts list. The utilization of proteomics in a broad array of biological and clinical studies likewise continues to expand with many important findings and effective integration with other omics platforms. We present highlights from the Immunopeptidomics, Glycoproteomics, Infectious Disease, Cardiovascular, Musculo-Skeletal, Liver, and Cancers B/D-HPP teams and from the Knowledgebase, Mass Spectrometry, Antibody Profiling, and Pathology resource pillars, as well as ethical considerations important to the clinical utilization of proteomics and protein biomarkers.

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DO - 10.1021/acs.jproteome.1c00590

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SN - 1535-3893

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Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project

Abstract

Bibliographical note

All Science Journal Classification (ASJC) codes

UN SDGs

Access to Document

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