title: Improving mass and liquid chromatography based identification of proteins using bayesian scoring.
abstract: We present a method for peptide and protein identification based on LC-MS profiling. The method identified peptides at high-throughput without expending the sequencing time necessary for CID spectra based identification. The measurable peptide properties of mass and liquid chromatographic elution conditions are used to characterize and differentiate peptide features, and these peptide features are matched to a reference database from previously acquired and archived LC-MS/MS experiments to generate sequence assignments. The matches are scored according to the probability of an overlap between the peptide feature and the database peptides resulting in a ranked list of possible peptide sequences for each peptide submitted. This method resulted in 6 times more peptide sequence identifications from a single LC-MS analysis of yeast than from shotgun peptide sequencing using LC-MS/MS.
authors.affiliation: University of Washington, Department of Bioengineering, Seattle, Washington 98105, USA.
authors.forename: Sharon S
authors.initials: SS
authors.lastname: Chen
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.forename: Eugene C
authors.initials: EC
authors.lastname: Yi
authors.forename: Xiao-jun
authors.initials: XJ
authors.lastname: Li
authors.forename: David R
authors.initials: DR
authors.lastname: Goodlett
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D002851:Chromatography, High Pressure Liquid; D002853:Chromatography, Liquid / Q000379:methods*; D030562:Databases, Protein; D005656:Fungal Proteins / Q000737:chemistry; D013058:Mass Spectrometry / Q000379:methods*; D015233:Models, Statistical; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization; D015003:Yeasts / Q000378:metabolism
chemical_list: D005656:Fungal Proteins; D010455:Peptides; D011506:Proteins