ProteinExplorer: A Repository-Scale Resource for Exploration of Protein Detection in Public Mass Spectrometry Data Sets

High-throughput
tandem mass spectrometry has enabled the detection
and identification of over 75% of all proteins predicted to result
in translated gene products in the human genome. In fact, the galloping
rate of data acquisition and sharing of mass spectrometry data has
led to the current availability of many tens of terabytes of public
data in thousands of human data sets. The systematic reanalysis of
these public data sets has been used to build a community-scale spectral
library of 2.1 million precursors for over 1 million unique sequences
from over 19,000 proteins (including spectra of synthetic peptides).
However, it has remained challenging to find and inspect spectra of
peptides covering functional protein regions or matching novel proteins.
ProteinExplorer addresses these challenges with an intuitive interface
mapping tens of millions of identifications to functional sites on
nearly all human proteins while maintaining provenance for every identification
back to the original data set and data file. Additionally, ProteinExplorer
facilitates the selection and inspection of HPP-compliant peptides
whose spectra can be matched to spectra of synthetic peptides and
already includes HPP-compliant evidence for 107 missing (PE2, PE3,
and PE4) and 23 dubious (PE5) proteins. Finally, ProteinExplorer allows
users to rate spectra and to contribute to a community library of
peptides entitled PrEdict (Protein Existance dictionary) mapping to
novel proteins but whose preliminary identities have not yet been
fully established with community-scale false discovery rates and synthetic
peptide spectra. ProteinExplorer can be now be accessed at https://massive.ucsd.edu/ProteoSAFe/protein_explorer_splash.jsp.