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The 2023 Report on the Proteome from the HUPO Human Proteome Project
Univ Michigan, Ann Arbor, MI 48109 USA.;Inst Syst Biol, Seattle, WA 98109 USA..ORCID iD: 0000-0002-8976-6074
SIB Swiss Inst Bioinformat, CALIPHO Grp, CH-1015 Lausanne, Switzerland.;Univ Geneva, CH-1015 Lausanne, Switzerland..ORCID iD: 0000-0002-9818-3030
Univ British Columbia, Vancouver, BC V6T 1Z4, Canada.;Yonsei Univ, Seoul 03722, South Korea..
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Cancer precision medicine.ORCID iD: 0000-0001-5611-1015
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2024 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 23, no 2, p. 532-549Article, review/survey (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2024. Vol. 23, no 2, p. 532-549
Keywords [en]
Human Proteome Organization (HUPO), Human Proteome Project (HPP), neXtProt protein existence (PE) metrics, missing proteins (MP), non-MS PE1 proteins, uncharacterizedprotein existence 1 (uPE1), Chromosome-centric HPP (C-HPP), Biology and Disease-HPP (B/D-HPP), PeptideAtlas, Mass Spectrometry Interactive Virtual Environment Knowledge Base (MassIVE-KB), Human Protein Atlas, Grand Challenge Project
National Category
Biochemistry Molecular Biology Bioinformatics and Computational Biology
Identifiers
URN: urn:nbn:se:uu:diva-523979DOI: 10.1021/acs.jproteome.3c00591ISI: 001157566300001PubMedID: 38232391OAI: oai:DiVA.org:uu-523979DiVA, id: diva2:1841089
Funder
Knut and Alice Wallenberg FoundationNIH (National Institutes of Health), P30ES017885-11-S1NIH (National Institutes of Health), U24CA271037NIH (National Institutes of Health), R01GM087221NIH (National Institutes of Health), R24GM127667NIH (National Institutes of Health), U19AG023122NIH (National Institutes of Health), S10OD026936NIH (National Institutes of Health), R01LM013115NIH (National Institutes of Health), R21CA263262NIH (National Institutes of Health), U01CA253217NIH (National Institutes of Health), R21CA251992NIH (National Institutes of Health), P30CA008748NIH (National Institutes of Health), U01CA263986Available from: 2024-02-27 Created: 2024-02-27 Last updated: 2025-02-20Bibliographically approved

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Lindskog, Cecilia

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