title: Improved peptide charge state assignment.
abstract: We present a new approach capable of assigning charge states to peptides based on both their intact mass spectrum and their fragmentation mass spectrum. More specifically, our approach aims at fully exploiting available information to improve correct charge assignment rate. This is achieved by using information provided by the fragmentation spectrum extensively. For low-resolution spectra, charge assignment based on fragmentation mass spectrum is better than charge assignment based on intact peptide signal only. We introduce two methods that allow to integrate information contributing to successful peptide charge state assignment. We demonstrate the performance of our algorithms on large ion trap data sets. The application of these algorithms to large-scale proteomics projects can save significant computation time and have a positive impact on identification false positive rates.
authors.affiliation: GeneProt Inc., Pré de la Fontaine 2, CH-1217 Meyrin, Switzerland. jacques.colinge@geneprot.com
authors.forename: Jacques
authors.initials: J
authors.lastname: Colinge
authors.forename: Jérôme
authors.initials: J
authors.lastname: Magnin
authors.forename: Thierry
authors.initials: T
authors.lastname: Dessingy
authors.forename: Marc
authors.initials: M
authors.lastname: Giron
authors.forename: Alexandre
authors.initials: A
authors.lastname: Masselot
mesh_terms: D000465:Algorithms; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000737:chemistry*
chemical_list: D010455:Peptides