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 journalReview articlepeer-review

25 Citations (Scopus)


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 languageEnglish
Pages (from-to)5227-5240
Number of pages14
JournalJournal of Proteome Research
Issue number12
Publication statusPublished - 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


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