The 2023 Report on the Proteome from the HUPO Human Proteome Project

Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Cecilia Lindskog, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Susan T. Weintraub, Sandra Orchard, Michael H.A. Roehrl, Edouard Nice, Tiannan Guo, Jennifer E. Van Eyk, Siqi Liu, Nuno Bandeira, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch

Research output: Contribution to journalReview articlepeer-review

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Abstract

Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-18, protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1-4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.

Original languageEnglish (US)
Pages (from-to)532-549
Number of pages18
JournalJournal of Proteome Research
Volume23
Issue number2
DOIs
StatePublished - Feb 2 2024

All Science Journal Classification (ASJC) codes

  • General Chemistry
  • Biochemistry

Keywords

  • Biology and Disease-HPP (B/D-HPP)
  • Chromosome-centric HPP (C-HPP)
  • Grand Challenge Project
  • Human Protein Atlas
  • Human Proteome Organization (HUPO)
  • Human Proteome Project (HPP)
  • Mass Spectrometry Interactive Virtual Environment Knowledge Base (MassIVE-KB)
  • PeptideAtlas
  • missing proteins (MP)
  • neXtProt protein existence (PE) metrics
  • non-MS PE1 proteins
  • uncharacterized protein existence 1 (uPE1)

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