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J Proteome Res. 2019 Sep 13. doi: 10.1021/acs.jproteome.9b00434. [Epub ahead of print]

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

Author information

1
Department of Computational Medicine and Bioinformatics , University of Michigan , 100 Washtenaw Avenue , Ann Arbor , Michigan 48109-2218 , United States.
2
Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5263 , United States.
3
CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine , University of Geneva , CMU, Michel-Servet 1 , 1211 Geneva 4 , Switzerland.
4
Life Sciences Institute, Faculty of Dentistry , University of British Columbia , 2350 Health Sciences Mall, Room 4.401 , Vancouver , British Columbia V6T 1Z3 , Canada.
5
Centro Nacional de Biotecnologia (CSIC) , Darwin 3 , 28049 Madrid , Spain.
6
Science for Life Laboratory , KTH Royal Institute of Technology , Tomtebodavägen 23A , 17165 Solna , Sweden.
7
Yonsei Proteome Research Center , Yonsei University , Room 425, Building #114, 50 Yonsei-ro , Seodaemoon-ku , Seoul 120-749 , South Korea.
8
Advanced Clinical BioSystems Research Institute, Cedars Sinai Precision Biomarker Laboratories, Barbra Streisand Women's Heart Center , Cedars-Sinai Medical Center , Los Angeles , California 90048 , United States.
9
BGI Group-Shenzhen , Yantian District , Shenzhen 518083 , China.
10
School of Medicine , University College Dublin , Conway Institute Belfield , Dublin 4 , Ireland.
11
Department of Genetics , Stanford University , Alway Building, 300 Pasteur Drive and 3165 Porter Drive , Palo Alto , California 94304 , United States.
12
Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , 75 Talavera Road , North Ryde , NSW 2109 , Australia.

Abstract

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 17 694 proteins with strong protein-level evidence (PE1), compliant with HPP Guidelines for Interpretation of MS Data v2.1; these represent 89% of all 19 823 neXtProt predicted coding genes (all PE1,2,3,4 proteins), up from 17 470 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 17 000 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.

KEYWORDS:

Biology and Disease-HPP (B/D-HPP); Chromosome-centric HPP (C-HPP); Human Protein Atlas; Human Proteome Project (HPP) Guidelines 3.0; PeptideAtlas; missing proteins (MPs); neXt-MP50 and CP50 challenges; neXtProt protein existence metrics; unannotated protein existence 1 (uPE1)

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