Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years

Abstract

We celebrate the 10th anniversary of the launch of the HUPO Human Proteome Project (HPP) and its major milestone of confident detection of at least one protein from each of 90% of the predicted protein-coding genes, based on the output of the entire proteomics community. The Human Genome Project reached a similar decadal milestone 20 years ago. The HPP has engaged proteomics teams around the world, strongly influenced data-sharing, enhanced quality assurance, and issued stringent guidelines for claims of detecting previously "missing proteins." This invited perspective complements papers on "A High-Stringency Blueprint of the Human Proteome" and "The Human Proteome Reaches a Major Milestone" in special issues of Nature Communications and Journal of Proteome Research, respectively, released in conjunction with the October 2020 virtual HUPO Congress and its celebration of the 10th anniversary of the HUPO HPP.

Keywords: Human Proteome Project; Mass Spectrometry Data Interpretation Guidelines; blueprint; functionally unannotated proteins; missing proteins; neXtProt.

Graphical abstract

Fig. 1

Schema showing the matrix structure of the Human Proteome Project (HPP). There are 25 chromosome-centric HPP teams corresponding to chromosomes 1–22, X, and Y plus mitochondria, with lead country shown. There are 19 Biology and Disease-driven HPP teams, and four Resource Pillars, of mass spectrometry, antibody profiling, knowledge base, and pathology. MP-50 and CP-50 refer to the C-HPP challenges to find 50 missing proteins per chromosome and generate functional annotations for 50 uncharacterized PE1 proteins. See text.

Fig. 2

The data flow for the Human Proteome Project, including the connectedness of ProteomeXchange with the major proteomics data set resources PRIDE and PeptideAtlas (founding partners), iProX, jPOST, MassIVE, and Panorama (modified fromwww.proteomeXchange.org).