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Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications
dataset
posted on 2016-08-03, 00:00 authored by Gilbert S. Omenn, Lydie Lane, Emma K. Lundberg, Ronald
C. Beavis, Christopher M. Overall, Eric W. DeutschThe HUPO Human Proteome Project (HPP)
has two overall goals: (1)
stepwise completion of the protein parts listthe draft human proteome including confidently identifying and characterizing at least one protein product
from each protein-coding gene, with increasing emphasis on sequence
variants, post-translational modifications (PTMs), and splice isoforms
of those proteins; and (2) making proteomics an integrated counterpart
to genomics throughout the biomedical and life sciences community.
PeptideAtlas and GPMDB reanalyze all major human mass spectrometry data
sets available through ProteomeXchange with standardized protocols
and stringent quality filters; neXtProt curates and integrates mass
spectrometry and other findings to present the most up to date authorative compendium of the human proteome. The HPP Guidelines for Mass Spectrometry
Data Interpretation version 2.1 were applied to manuscripts submitted
for this 2016 C-HPP-led special issue [www.thehpp.org/guidelines]. The Human Proteome presented as neXtProt version 2016-02 has 16,518
confident protein identifications (Protein Existence [PE] Level 1),
up from 13,664 at 2012-12, 15,646 at 2013-09, and 16,491 at 2014-10.
There are 485 proteins that would have been PE1 under the Guidelines
v1.0 from 2012 but now have insufficient evidence due to the agreed-upon
more stringent Guidelines v2.0 to reduce false positives. neXtProt
and PeptideAtlas now both require two non-nested, uniquely mapping
(proteotypic) peptides of at least 9 aa in length. There are 2,949
missing proteins (PE2+3+4) as the baseline for submissions for this
fourth annual C-HPP special issue of Journal of Proteome Research.
PeptideAtlas has 14,629 canonical (plus 1187 uncertain and 1755 redundant)
entries. GPMDB has 16,190 EC4 entries, and the Human Protein Atlas
has 10,475 entries with supportive evidence. neXtProt, PeptideAtlas,
and GPMDB are rich resources of information about post-translational modifications (PTMs), single amino acid variants (SAAVSs), and splice isoforms. Meanwhile, the Biology- and Disease-driven
(B/D)-HPP has created comprehensive SRM resources, generated popular
protein lists to guide targeted proteomics assays for specific diseases,
and launched an Early Career Researchers initiative.
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Guidelines v 1.0date authorative compendiumGuidelines v 2.0PTMHuman ProteomePEpost-translational modificationsECC-HPPlife sciences communityneXtProt version 2016-02SRMHuman Protein Atlassplice isoformsCareer Researchers initiativeproteinmass spectrometry data setsMass Spectrometry Data Interpretation version 2.1GPMDBHUPO Human Proteome ProjectHPPentrySAAVSPeptideAtla
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