Progress on Identifying and Characterizing the Human Proteome: 2018 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, Michael Snyder, Mark S. Baker, Eric W. Deutsch

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49 Citations (Scopus)


The Human Proteome Project (HPP) annually reports on progress throughout the field in credibly identifying and characterizing the human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2018-01-17, the baseline for this sixth annual HPP special issue of the Journal of Proteome Research, contains 17470 PE1 proteins, 89% of all neXtProt predicted PE1-4 proteins, up from 17008 in release 2017-01-23 and 13975 in release 2012-02-24. Conversely, the number of neXtProt PE2,3,4 missing proteins has been reduced from 2949 to 2579 to 2186 over the past two years. Of the PE1 proteins, 16092 are based on mass spectrometry results, and 1378 on other kinds of protein studies, notably protein-protein interaction findings. PeptideAtlas has 15798 canonical proteins, up 625 over the past year, including 269 from SUMOylation studies. The largest reason for missing proteins is low abundance. Meanwhile, the Human Protein Atlas has released its Cell Atlas, Pathology Atlas, and updated Tissue Atlas, and is applying recommendations from the International Working Group on Antibody Validation. Finally, there is progress using the quantitative multiplex organ-specific popular proteins targeted proteomics approach in various disease categories.

Original languageEnglish
Pages (from-to)4031-4041
Number of pages11
JournalJournal of Proteome Research
Issue number12
Publication statusPublished - 2018 Dec 7

Bibliographical note

Funding Information:
We appreciate the guidance from the HPP Executive Committee and Dr. Amos Bairoch of neXtProt. 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 NIH U24CA210967; E.W.D. from NIH grants R01GM087221, R24GM127667, and U54EB020406; L.L. and neXtProt from the SIB Swiss Institute of Bioinformatics; C.M.O. by a Canadian Institutes of Health Research 7-year 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 the grants from the Korean Ministry of Health and Welfare (HI13C22098 and HI16C0257 to Y.-K.P.).

Publisher Copyright:
Copyright © 2018 American Chemical Society.

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Biochemistry


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