MassIVE Human Proteome Project (HPP) Resources

The HUPO Human Proteome Project (HPP) quest for the novel detection of translated gene products (missing proteins) is a large scale, multi-year community project to establish the existence of proteins in vivo and in specific types of tissues. MassIVE supports HPP with the following series of resources:

• The MassIVE Knowledge Base (MassIVE-KB) contains spectral libraries derived from community big data. Distilled from 31TB of human proteomics HCD data, MassIVE-KB contains a spectral library of in-vivo peptides, which supports the detection of in-vivo protein expression after strictly enforcing global false discovery rates for spectrum, peptide and protein identifications. MassIVE-KB also contains spectral libraries of synthetic peptides, which supports matching of in-vivo peptide spectra to synthetic peptide spectra.


• Protein Explorer allows for the exploration of the evidence and sequence coverage of nearly every human protein, as defined by MassIVE-KB’s systematic reanalysis of 31 terabytes of public data from >20,000 LC/MS runs and including over 1 million synthetic peptide spectra. Interactive exploration of protein evidence includes coverage maps, HPP criteria (e.g., number of polymorphism-tolerant protein matches per peptide), functional sites, and full provenance and dataset mapping of every identified peptide.


• Detailed list of Universal Spectrum Identifier (USI) entries for all 1,296,916 MassIVE-KB entries in support of HPP Protein Existence (PE) classifications for 16,393 proteins. This includes USIs for the best MassIVE-KB spectrum for every peptide detected in in-vivo experiments, as well as USIs and cosines for their matches to the corresponding synthetic peptide spectra (when available).