Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project

The Human Proteome
Organization (HUPO) Human Proteome Project (HPP)
continues to make progress on its two overall goals: (1) completing
the protein parts list, with an annual update of the HUPO draft human
proteome, and (2) making proteomics an integrated complement to genomics
and transcriptomics throughout biomedical and life sciences research.
neXtProt version 2017-01-23 has 17 008 confident protein identifications
(Protein Existence [PE] level 1) that are compliant with the HPP Guidelines
v2.1 (https://hupo.org/Guidelines), up from 13 664 in 2012-12 and 16 518 in 2016-04.
Remaining to be found by mass spectrometry and other methods are 2579
“missing proteins” (PE2+3+4), down from 2949 in 2016.
PeptideAtlas 2017-01 has 15 173 canonical proteins, accounting
for nearly all of the 15 290 PE1 proteins based on MS data.
These resources have extensive data on PTMs, single amino acid variants,
and splice isoforms. The Human Protein Atlas v16 has 10 492
highly curated protein entries with tissue and subcellular spatial
localization of proteins and transcript expression. Organ-specific
popular protein lists have been generated for broad use in quantitative
targeted proteomics using SRM-MS or DIA-SWATH-MS studies of biology
and disease.