Progress on identifying and characterizing the human proteome: 2018 metrics from the HUPO Human Proteome Project

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 multi-omics studies in medicine and the life sciences. NeXtProt release 2018-01-17, the baseline for this 6th 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 applying the quantitative multiplex organ-specific popular proteins targeted proteomics approach in various disease categories.