Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project

Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Fernando J. Corrales, Jochen M. Schwenk, Young Ki Paik, Jennifer E. Van Eyk, Siqi Liu, Stephen Pennington, Michael P. Snyder, Mark S. Baker, Eric W. Deutsch

Research output: Contribution to journalReview articlepeer-review

32 Citations (Scopus)


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 17â »694 proteins with strong protein-level evidence (PE1), compliant with HPP Guidelines for Interpretation of MS Data v2.1; these represent 89% of all 19â »823 neXtProt predicted coding genes (all PE1,2,3,4 proteins), up from 17â »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 17â »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.

Original languageEnglish
Pages (from-to)4098-4107
Number of pages10
JournalJournal of Proteome Research
Issue number12
Publication statusPublished - 2019 Dec 6

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. The PeptideAtlas server is hosted at the Institute for Systems Biology in Seattle. G.S.O. acknowledges grant support from National Institutes of Health grants P30ES017885-01A1 and U24CA210967; E.W.D. from National Institutes of Health grants, R01GM087221, R24GM127667, U54EB020406, and the U19AG023122; L.L. and neXtProt from the SIB Swiss Institute of Bioinformatics; C.M.O. by a Canadian Institutes of Health Research Foundation Grant and a Canada Research Chair in Protease Proteomics and Systems Biology; M.S.B. by NHMRC Project Grant APP1010303; J.M.S. by the Knut and Alice Wallenberg Foundation for the Human Protein Atlas; and Y.-K.P. by grants from the Korean Ministry of Health and Welfare HI13C22098 and HI16C0257.

Publisher Copyright:
Copyright © 2019 American Chemical Society.

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Biochemistry


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