Peptide charge state determination for low-resolution tandem mass spectra

A.A. Klammer, C.C. Wu, M.J. MacCoss, W.S. Noble
2005 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05)  
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
more » ... om +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. Availability:
doi:10.1109/csb.2005.44 dblp:conf/csb/KlammerWMN05 fatcat:7jbwx5v2vfhbbb4suj3uamy4ra