Algorithms and Software

We have developed novel tools for the analysis of MS-MS data to identify modified peptides and to map adducts to specific sequence positions. The SALSA algorithm and software is a tool for identifying MS-MS spectra that display user-defined characteristics, such as product ions, losses and ion series in any combination. The P-Mod algorithm and software enables rapid, direct discovery of protein modifications through analysis of peptide MS-MS spectra. P-Mod detects even novel and unanticipated modifications, maps them to specific sequence positions and provides estimates of the statistical confidence of the sequence-to-spectrum matches. We also employ the Sequest, Mascot and X!Tandem programs to perform database searches to identify peptides and proteins from MS-MS spectra and we use the Peptide Prophet and Protein Prophet programs to assess the quality of database search results. Finally, with our colleagues in the Proteomics Laboratory and at the University of Arizona, we have developed a database and LIMS system called CHIPS, which houses all data acquired in the laboratory, the results of database searches, and P-Mod and SALSA searches.