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Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification
KTH, School of Biotechnology (BIO). Karolinska Inst, KTH, SciLifeLab.ORCID iD: 0000-0001-7034-0850
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2015 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 14, no 9, 3452-3460 p.Article in journal (Refereed) Published
Abstract [en]

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 I), 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.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2015. Vol. 14, no 9, 3452-3460 p.
Keyword [en]
Human Proteome Project, HPP metrics, guidelines, high-confidence protein identifications, neXtProt, PeptideAtlas, Human Protein Atlas, Global Proteome Machine database (GPMDB), missing proteins, novel proteins
National Category
Bioinformatics and Systems Biology Bioinformatics (Computational Biology) Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-174931DOI: 10.1021/acs.jproteome.5b00499ISI: 000361087100005PubMedID: 26155816Scopus ID: 2-s2.0-84941057782OAI: oai:DiVA.org:kth-174931DiVA: diva2:862475
Funder
EU, FP7, Seventh Framework Programme, 260558Knut and Alice Wallenberg Foundation
Note

QC 20151022

Available from: 2015-10-22 Created: 2015-10-09 Last updated: 2017-12-01Bibliographically approved

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Lundberg, Emma K.

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