Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications

Abstract

The HUPO Human Proteome Project (HPP) has two overall goals: (1) stepwise completion of the protein parts list-the 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.

Keywords: GPMDB; Human Protein Atlas; N-termini; PTMs (post-translational modifications); PeptideAtlas; SAAV (single amino acid variants); guidelines; metrics; neXtProt; splice isoforms.

Figure 1

Overview of the Human Proteome Project Workflow. The primary flow of data from investigators through ProteomeXchange to PeptideAtlas leads to protein existence (PE) classification of sequence entries in neXtProt, denoted by the thick blue arrows. Direct data transfers are denoted by thin blue arrows; the dotted blue line indicates occasional direct submission. Transfers from databases to the HPP metrics are denoted by the thin orange arrows. The larger features represent the main stream of the workflow. The 2015–2016 HPP Mass Spectrometry Data Interpretation Guidelines v2.0 are applied to primary HPP publications as well as the final list of peptides transferred from PeptideAtlas to neXtProt denoted by red arrows. The green arrow shows publication of original studies subject to the HPP Guidelines v2.0 with data submitted to ProteomeXchange. Raw data, not published protein IDs, are required by PeptideAtlas and neXtProt.

Figure 2

Basis for neXtProt protein existence PE1 evidence as well as for missing proteins in the human proteome. The green and yellow wedges have curated protein-level PE1 evidence; the red wedge represents the total of 2,949 missing proteins with PE2–4 evidence (see Table 2 and text).