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J Proteome Res. 2015 Sep 4;14(9):3452-60. doi: 10.1021/acs.jproteome.5b00499. Epub 2015 Jul 30.

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification.

Author information

1
Department of Computational Medicine and Bioinformatics, University of Michigan , 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States.
2
CALIPHO Group, Swiss Institute of Bioinformatics , Michel-Servet 1, 1211 Geneva 4, Switzerland.
3
SciLifeLab Stockholm and School of Biotechnology, KTH , Karolinska Institutet Science Park, Tomtebodavägen 23, SE-171 65 Solna, Sweden.
4
Biochemistry & Medical Genetics, University of Manitoba , Winnipeg, MB, Canada R3T 2N2.
5
Pathology Department, University of Michigan , Medical Science Building 1, M4237, Ann Arbor, Michigan 48109-5602, United States.
6
Institute for Systems Biology , 401 Terry Avenue North, Seattle, Washington 98109-5263, United States.

Abstract

Remarkable progress continues on the annotation of the proteins identified in the Human Proteome and on finding credible proteomic evidence for the expression of "missing proteins". Missing proteins are those with no previous protein-level evidence or insufficient evidence to make a confident identification upon reanalysis in PeptideAtlas and curation in neXtProt. Enhanced with several major new data sets published in 2014, the human proteome presented as neXtProt, version 2014-09-19, has 16,491 unique confident proteins (PE level 1), up from 13,664 at 2012-12 and 15,646 at 2013-09. That leaves 2948 missing proteins from genes classified having protein existence level PE 2, 3, or 4, as well as 616 dubious proteins at PE 5. Here, we document the progress of the HPP and discuss the importance of assessing the quality of evidence, confirming automated findings and considering alternative protein matches for spectra and peptides. We provide guidelines for proteomics investigators to apply in reporting newly identified proteins.

KEYWORDS:

Global Proteome Machine database (GPMDB); HPP metrics; Human Protein Atlas; Human Proteome Project; PeptideAtlas; guidelines; high-confidence protein identifications; missing proteins; neXtProt; novel proteins

PMID:
26155816
PMCID:
PMC4755311
DOI:
10.1021/acs.jproteome.5b00499
[Indexed for MEDLINE]
Free PMC Article

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