Using the Global Proteome Machine for Protein Identification

This chapter describes the use of an open-source, freely available informatics system for the identification of proteins using tandem mass spectra of peptides derived from an enzymatic digest of a mixture of mature proteins. The chapter describes the use of features of the Global Proteome Machine (GPM) interface that assist in making comprehensive assignments between spectra and sequences, including the detection of point mutations, posttranslational modifications, and experimental artifacts. The use of this interface to validate results using the GPM Database is also described. This data repository allows analysts to compare their own results to those obtained by other scientists to determine the degree to which their data are consistent with previous measurements.