Peptide charge state determination for low-resolution tandem mass spectra

Aaron Klammer, Christine C. Wu, Michael J. MacCoss and William Stafford Noble

Proceedings of the Computational Systems Bioinformatics Conference 2005

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 charge-state-determination algorithms only discriminate singly- from 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 multiply-charged 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.

Charge Czar

Charge Czar is a software tool for the classification of multiply-charged low-resolution tandem mass spectra into either a +2 or +3 charge state. It consists of a single program:

charge_czar

Charge Czar is written in Python and ANSI C. Source code for the latest version, as well as some pre-compiled versions for popular platforms (Linux, Cygwin) can be downloaded here. Charge Czar is distributed under an open source Apache license.

Here are some installation instructions and release notes. The data used to train Charge Czar can be found in a directory here and as a zipped tar file here.

Charge Czar was written by Aaron Klammer in the Department of Genome Sciences at the University of Washington. The paper describing the method used by Charge Czar is available here, and should be cited as:
A. A. Klammer, C. C. Wu, M. J. MacCoss and W. S. Noble. Peptide charge state determination for low-resolution tandem mass spectra. Proceedings of the 2005 Computational Systems Bioinformatics Conference. Aug 8-12, 2005: 175-185.