Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project

J Proteome Res. 2021 Dec 3;20(12):5227-5240. doi: 10.1021/acs.jproteome.1c00590. Epub 2021 Oct 20.


The 2021 Metrics of the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 357 (92.8%) of the 19 778 predicted proteins coded in the human genome, a gain of 483 since 2020 from reports throughout the world reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 478 to 1421. This represents remarkable progress on the proteome parts list. The utilization of proteomics in a broad array of biological and clinical studies likewise continues to expand with many important findings and effective integration with other omics platforms. We present highlights from the Immunopeptidomics, Glycoproteomics, Infectious Disease, Cardiovascular, Musculo-Skeletal, Liver, and Cancers B/D-HPP teams and from the Knowledgebase, Mass Spectrometry, Antibody Profiling, and Pathology resource pillars, as well as ethical considerations important to the clinical utilization of proteomics and protein biomarkers.

Keywords: Biology and Disease-HPP (B/D-HPP); Chromosome-centric HPP (C-HPP); Human Protein Atlas; Human Proteome Project (HPP); Mass Spectrometry Interactive Virtual Environment (MassIVE); PeptideAtlas; missing proteins (MP); neXtProt protein existence (PE) metrics; non-MS PE1 proteins; uncharacterized protein existence 1 (uPE1).

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Benchmarking*
  • Databases, Protein
  • Humans
  • Mass Spectrometry / methods
  • Proteome* / analysis
  • Proteome* / genetics
  • Proteomics / methods


  • Proteome