The Human Proteome Project (HPP) releases the first Human Proteome Organization (HUPO)-endorsed, high-stringency Human Proteome Blueprint in Nature Communications (see https://www.nature.com/articles/s41467-020-19045-9). Like the draft “shotgun” Human Genome Project of the Human Genome Organization (HUGO), the HPP has now reached a significant decadal milestone of >90% completion of the Human Proteome that is referred to as the human proteome “parts-list”. This effort recognizes significant community efforts that enabled data inspection and re-analysis, culminating in a high stringency (i.e., rigorous, exacting standards for post-acquisition data processing and protein inferences made from MS spectral data) HPP knowledge base (KB). Additionally, to illustrate the many parallel historical innovations made by the scientific community that have driven proteomics advances, HUPO has created a publicly available interactive historical timeline to be released coincident with publication of this article (hupo.org/Proteomics-Timeline).
The HPP’s mission is to reanalyze and integrate community proteomics data with high-stringency processes, bringing increased granularity to our molecular understanding of the dynamic nature of the proteome, including all its modifications, and their relation to human biology and disease. This mission aligns closely with HUPO’s motto “translating the code of life”, providing crucial information that genomics per se cannot deliver. Completion of the HPP will enhance our understanding of human molecular and cellular biology, laying better foundations for diagnostic, prognostic, therapeutic and precision medicine applications.
In 2010, the Human Proteome Organization launched the Human Proteome Project (HPP), as an international endeavor to create a framework for global collaboration, data sharing and quality assurance, enhancing accurate annotation of the genome-encoded proteome. Over the last decade, the key resources of the HPP (the Human Protein Atlas, PeptideAtlas, MassIVE and neXtProt knowledge bases) have driven the development and refinement of guidelines and metrics to understand the definitive identification of any protein of the human proteome. Their high-stringency reanalysis of community data led to the current status of >90% identification completion rate of the Human Proteome. This knowledge is essential to discern the proteome’s role in health and disease. Here, on behalf of the proteomics community, we report the inaugural high-stringency human proteome project blueprint, illustrating roles in the diagnosis and treatment of cancers, cardiovascular and infectious disease pathologies.