Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project

Abstract

The Human Proteome Project (HPP) annually reports on progress throughout the field in credibly identifying and characterizing the human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2018-01-17, the baseline for this sixth annual HPP special issue of the Journal of Proteome Research, contains 17 470 PE1 proteins, 89% of all neXtProt predicted PE1-4 proteins, up from 17 008 in release 2017-01-23 and 13 975 in release 2012-02-24. Conversely, the number of neXtProt PE2,3,4 missing proteins has been reduced from 2949 to 2579 to 2186 over the past two years. Of the PE1 proteins, 16 092 are based on mass spectrometry results, and 1378 on other kinds of protein studies, notably protein-protein interaction findings. PeptideAtlas has 15 798 canonical proteins, up 625 over the past year, including 269 from SUMOylation studies. The largest reason for missing proteins is low abundance. Meanwhile, the Human Protein Atlas has released its Cell Atlas, Pathology Atlas, and updated Tissue Atlas, and is applying recommendations from the International Working Group on Antibody Validation. Finally, there is progress using the quantitative multiplex organ-specific popular proteins targeted proteomics approach in various disease categories.

Keywords: Biology and Disease-driven HPP (B/D-HPP); Chromosome-centric HPP (C-HPP); HPP Guidelines; Human Proteome Organization (HUPO); Human Proteome Project (HPP); PeptideAtlas; metrics; missing proteins; neXtProt.

Figure 1.

This flow chart depicts the changes in neXtProt PE1–5 categories from release 2017–01-23 to release 2018–01-17. There are 431 missing proteins promoted to PE1 and 44 new SwissProt proteins added as PE1 proteins, while 3 PE1 proteins were demoted to PE2,3,4 MPs and 10 PE1 proteins were deleted altogether. See text for further discussion.

Figure 2.

Identified and predicted proteins by PE level in neXtProt release 2018–01-17.

Figure 3.

These eight datasets added to PeptideAtlas in 2017 provided the evidence needed to raise the PeptideAtlas protein category to “canonical” for more than 10 proteins each. Canonical status requires two or more uniquely-mapping non-nested peptides with length ≥9 residues with high-quality spectra, not accounted for by sequence variants or isobaric PTMs in other proteins. PXD identifiers refer to ProteomeXchange.

Figure 4.

Progress on identification of members of the six most numerous protein families in neXtProt Missing Protein categories PE2,3,4 from 2013 to 2018 (updated from Baker et al).