title: Charge prediction machine: tool for inferring precursor charge states of electron transfer dissociation tandem mass spectra.
abstract: Electron transfer dissociation (ETD) can dissociate highly charged ions. Efficient analysis of ions dissociated with ETD requires accurate determination of charge states for calculation of molecular weight. We created an algorithm to assign the charge state of ions often used for ETD. The program, Charge Prediction Machine (CPM), uses Bayesian decision theory to account for different charge reduction processes encountered in ETD and can also handle multiplex spectra. CPM correctly assigned charge states to 98% of the 13,097 MS2 spectra from a combined data set of four experiments. In a comparison between CPM and a competing program, Charger (ThermoFisher), CPM produced half the mistakes.
authors.affiliation: Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Brazil. paulo@buscario.com.br
authors.forename: Paulo C
authors.initials: PC
authors.lastname: Carvalho
authors.forename: Daniel
authors.initials: D
authors.lastname: Cociorva
authors.forename: Catherine C L
authors.initials: CC
authors.lastname: Wong
authors.forename: Maria da Gloria da C
authors.initials: Mda G
authors.lastname: Carvalho
authors.forename: Valmir C
authors.initials: VC
authors.lastname: Barbosa
authors.forename: John R
authors.initials: JR
authors.lastname: Yates
mesh_terms: D001185:Artificial Intelligence; D004579:Electron Transport / Q000502:physiology*; D007477:Ions / Q000737:chemistry; D013058:Mass Spectrometry / Q000379:methods*; D008956:Models, Chemical; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D010446:Peptide Fragments / Q000737:chemistry*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D055672:Static Electricity; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D007477:Ions; D010446:Peptide Fragments