neXtProt has not been updated since October 2023 and solutions are being sought to revive this major database. In the meantime, the resource remains available for users at both nextprot.org and nextprot.cn with a very large number of visitors each month.
To support the HPP as they move forward, UniProt has taken on the role of running the Proteomics Identification pipeline. This has involved upgrading existing UniProt MS peptide identification pipeline to meet the stringency of the HPP3.0 guidelines, and working with Eric Deutsch (PeptideAtlas) and Nuno Bandeira (MassIVE) to ensure all additional criteria for data evaluation are met.
UniProt release 2024_04 shows that 18,417 proteins now have PE1 level evidence, out of a total of 19,835 candidate entries (93%). The data will be visible in the UniProt Feature Viewer and accessible via an API and a full analysis will be published in the 2024 report on the proteome from the HUPO Human Proteome Project, currently in preparation. UniProt has long supported the data generated using HUPO Proteomics Standards Initiative data standards.
In addition to the peptide pipelines, we are working with Eric Deutsch, Andy Jones (U. Liverpool) and Juan Antonio Vizcaino (EMBL-EBI) to use deposited MS data to identify additional high-confidence PTM sites and these will be added to UniProt human protein records over the next few months. Protein interactions and complexes generated by the IMEx databases are already accessible through our records. The UniProt database is committed to supporting the HUPO HPP with its next Grand Challenge of identifying a function for every human protein and looks forward to a closer working relationship with this group in the future.
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