Summary
This 2024 progress report from the Human Proteome Organization's flagship HPP initiative documents major transitions in proteomics infrastructure, including retirement of neXtProt as the official knowledge base in favour of UniProtKB and GENCODE-Ensembl protein targets. The consortium reports achievement of protein expression evidence for 93% of human protein-coding genes, with introduction of a new FE1-5 functional evidence scoring system to complement existing expression classification schemes, intended to advance functional annotation of the human proteome.
Regional applicability
This is a methods and reference resource report of international scope, with applicability to proteomics research globally. It establishes shared standards and databases used by the United Kingdom and international research community for protein identification and functional annotation.
Key measures
Number of protein-coding genes with detected protein expression (PE1); count of missing proteins (PE1-5 classification); protein evidence scoring (PE1-5 and newly developed FE1-5 functional evidence system)
Outcomes reported
The report documents progress in identifying protein isoforms from human protein-coding genes and updates the reference knowledge bases for proteomics research. It reports that 93% of GENCODE protein-coding genes (18,138 of 19,411) now have detected protein expression (PE1), with 1,273 remaining 'missing proteins'.
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