Using Annotated Peptide Mass Spectrum Libraries for Protein Identification

A system for creating a library of tandem mass spectra annotated with corresponding peptide sequences
was described. This system was based on the annotated spectra currently available in the Global
Proteome Machine Database (GPMDB). The library spectra were created by averaging together spectra
that were annotated with the same peptide sequence, sequence modifications, and parent ion charge.
The library was constructed so that experimental peptide tandem mass spectra could be compared
with those in the library, resulting in a peptide sequence identification based on scoring the similarity
of the experimental spectrum with the contents of the library. A software implementation that performs
this type of library search was constructed and successfully used to obtain sequence identifications.
The annotated tandem mass spectrum libraries for the Homo sapiens, Mus musculus, and Saccharomyces cerevisiae proteomes and search software were made available for download and use by other
groups.
Keywords: peptide spectrum library • X! Hunter • GPM • GPMDB • protein identification