Code Developments to Improve the Efficiency of Automated MS/MS Spectra Interpretation

• DOI: 10.1021/pr015514r
• Publication Date: 2002-07-26T06:10:30Z
• Authors: Rovshan G. Sadygov; Jimmy Eng; Eberhard Durr; Anita Saraf; Hayes McDonald; Michael J. MacCoss; John R. Yates
• Keywords: Proteasome Endopeptidase Complex; 0303 health sciences; 03 medical and health sciences; Time Factors; Humans; Saccharomyces cerevisiae; Databases, Protein; Crystallins; Mass Spectrometry; Software; Peptide Hydrolases

We report the results of our work to facilitate protein identification using tandem mass spectra and sequence databases. describe a parallel version SEQUEST (SEQUEST-PVM) that is tolerant toward arithmetic exceptions. The changes we effectively separate search processes on slave nodes from each other. Therefore, if one drops out cluster due an error, rest will carry process end. has been widely used for identifications. modifications made code improve its stability effectiveness in high-throughput production environment. evaluate overhead associated with parallelization SEQUEST. A prior software preprocess LC/MS/MS data attempted differentiate charge states ions. Singly charged ions can be accurately identified, but was unable reliably +2 +3 states. have designed implemented computational approach narrow precursor nominal resolution ion-trap spectra. preprocessing code, 2to3, determines state ion mass-to-charge ratio (m/z) fragment contained spectrum. For possible program calculates expected account m/z vlues. If any numbers less than empirically determined threshold value then spectrum corresponding removed. both are higher copies kept. present comparison experiments without 2to3. It shown by determining eliminating poor quality 2to3 decreases number spectral files searched affecting results. decrease reduces computer requirements researcher efforts analysis Keywords: spectrometry • database determination