title: Peptide charge state determination for low-resolution tandem mass spectra.
abstract: Mass spectrometry is a particularly useful technology for the rapid and robust identification of peptides and proteins in complex mixtures. Peptide sequences can be identified by correlating their observed tandem mass spectra (MS/MS) with theoretical spectra of peptides from a sequence database. Unfortunately, to perform this search the charge of the peptide must be known, and current chargestate- determination algorithms only discriminate singlyfrom multiply-charged spectra: distinguishing +2 from +3, for example, is unreliable. Thus, search software is forced to search multiply-charged spectra multiple times. To minimize this inefficiency, we present a support vector machine (SVM) that quickly and reliably classifies multiplycharged spectra as having either a +2 or +3 precursor peptide ion. By classifying multiply-charged spectra, we obtain a 40% reduction in search time while maintaining an average of 99% of peptide and 99% of protein identifications originally obtained from these spectra.
authors.affiliation: Department of Genome Sciences, Seattle, WA 98195-7730, USA. aklammer@u.washington.edu
authors.forename: Aaron A
authors.initials: AA
authors.lastname: Klammer
authors.forename: Christine C
authors.initials: CC
authors.lastname: Wu
authors.forename: Michael J
authors.initials: MJ
authors.lastname: MacCoss
authors.forename: William Stafford
authors.initials: WS
authors.lastname: Noble
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D003198:Computer Simulation; D013058:Mass Spectrometry / Q000379:methods*; D008956:Models, Chemical; D010363:Pattern Recognition, Automated / Q000379:methods*; D010449:Peptide Mapping / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D055672:Static Electricity
chemical_list: D010455:Peptides