Method for screening peptide fragment ion mass spectra prior to database searching

A methodology is described for screening fragment ion spectra of peptides p rior to database searching for protein identification. A software routine w ritten in the Perl programming language was used to analyze data from previ ous Sequest database searches and develop a set of statistical descriptors that could be used to identify spectra not likely to yield useful results i n a database search. A second Perl program used an evolutionary algorithm t o optimize the criteria for each statistical descriptor and generate a form ula for determining spectral quality. This formula was used by a third Perl program to screen data sets from four independent liquid chromatography ta ndem mass spectrometry runs. On the average, use of the screening program r educed the time required for a database search by 1/2 with little loss of u seful information from the database search results. (C) 2000 American Socie ty for Mass Spectrometry.