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J Proteome Res. 2017 Dec 1;16(12):4281-4287. doi: 10.1021/acs.jproteome.7b00375. Epub 2017 Oct 9.

Progress on the HUPO Draft Human Proteome: 2017 Metrics of the 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 Human Protein Science, University of Geneva , CMU, Michel-Servet 1, 1211 Geneva 4, Switzerland.
4
SciLifeLab Stockholm and School of Biotechnology, KTH, Karolinska Institutet Science Park , Tomtebodavägen 23, SE-171 65 Solna, Sweden.
5
Life Sciences Institute, Faculty of Dentistry, University of British Columbia , 2350 Health Sciences Mall, Room 4.401, Vancouver, British Columbia V6T 1Z3, Canada.

Abstract

The Human Proteome Organization (HUPO) Human Proteome Project (HPP) continues to make progress on its two overall goals: (1) completing the protein parts list, with an annual update of the HUPO draft human proteome, and (2) making proteomics an integrated complement to genomics and transcriptomics throughout biomedical and life sciences research. neXtProt version 2017-01-23 has 17 008 confident protein identifications (Protein Existence [PE] level 1) that are compliant with the HPP Guidelines v2.1 ( https://hupo.org/Guidelines ), up from 13 664 in 2012-12 and 16 518 in 2016-04. Remaining to be found by mass spectrometry and other methods are 2579 "missing proteins" (PE2+3+4), down from 2949 in 2016. PeptideAtlas 2017-01 has 15 173 canonical proteins, accounting for nearly all of the 15 290 PE1 proteins based on MS data. These resources have extensive data on PTMs, single amino acid variants, and splice isoforms. The Human Protein Atlas v16 has 10 492 highly curated protein entries with tissue and subcellular spatial localization of proteins and transcript expression. Organ-specific popular protein lists have been generated for broad use in quantitative targeted proteomics using SRM-MS or DIA-SWATH-MS studies of biology and disease.

KEYWORDS:

Human Proteome Project (HPP); PeptideAtlas; guidelines; long noncoding RNAs (lncRNAs); metrics; missing proteins; neXtProt

PMID:
28853897
PMCID:
PMC5872831
DOI:
10.1021/acs.jproteome.7b00375
[Indexed for MEDLINE]
Free PMC Article

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