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J Proteome Res. 2018 Dec 7;17(12):4031-4041. doi: 10.1021/acs.jproteome.8b00441. Epub 2018 Aug 23.

Progress on Identifying and Characterizing the Human Proteome: 2018 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 , BC 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 , 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
Department of Molecular Biology , University of Texas Southwestern Medical Center , Dallas , Texas 75390-9148 , United States.
10
Department of Genetics , Stanford University , Alway Building, 300 Pasteur Drive, 3165 Porter Drive , Palo Alto , California 94304 , United States.
11
Department of Biomedical Sciences , Macquarie University , North Ryde , NSW 2109 , Australia.

Abstract

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 17 470 PE1 proteins, 89% of all neXtProt predicted PE1-4 proteins, up from 17 008 in release 2017-01-23 and 13 975 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, 16 092 are based on mass spectrometry results, and 1378 on other kinds of protein studies, notably protein-protein interaction findings. PeptideAtlas has 15 798 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.

KEYWORDS:

Biology and Disease-driven HPP (B/D-HPP); Chromosome-centric HPP (C-HPP); HPP Guidelines; Human Proteome Organization (HUPO); Human Proteome Project (HPP); PeptideAtlas; metrics; missing proteins; neXtProt

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