title: ProteinProcessor: A probabilistic analysis using mass accuracy and the MS spectrum.
abstract: Current approaches to protein identification rely heavily on database matching of fragmentation spectra or precursor peptide ions. We have developed a method for MALDI TOF-TOF instrumentation that uses peptide masses and their measurement errors to confirm protein identifications from a first pass MS/MS database search. The method uses MS1-level spectral data that have heretofore been ignored by most search engines. This approach uses the distribution of mass errors of peptide matches in the MS1 spectrum to develop a probability model that is independent of the MS/MS database search identifications. Peptide mass matches can come from both precursor ions that have been fragmented as well as those that are tentatively identified by accurate mass alone. This additional corroboration enables us to confirm protein identifications to MS/MS-based scores that are otherwise considered to be only of moderate quality. Straightforward and easily applicable to current proteomic analyses, this tool termed "ProteinProcessor" provides a robust and invaluable addition to current protein identification tools.
authors.affiliation: Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Epstein
authors.affiliation: Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
authors.forename: Paul S
authors.initials: PS
authors.lastname: Blank
authors.affiliation: Proteome Software Inc, Portland, OR, USA.
authors.forename: Brian C
authors.initials: BC
authors.lastname: Searle
authors.affiliation: Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
authors.forename: Aaron D
authors.initials: AD
authors.lastname: Catlin
authors.affiliation: Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA.
authors.forename: Stephanie M
authors.initials: SM
authors.lastname: Cologna
authors.affiliation: Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Olson
authors.affiliation: Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
authors.forename: Peter S
authors.initials: PS
authors.lastname: Backlund
authors.affiliation: Faculty of Graduate Studies and the Departments of Health Sciences and Biological Sciences, Brock University, St. Catharines, ON, Canada.
authors.forename: Jens R
authors.initials: JR
authors.lastname: Coorssen
authors.affiliation: Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA. aly@helix.nih.gov.
authors.forename: Alfred L
authors.initials: AL
authors.lastname: Yergey
mesh_terms: D000465:Algorithms; D000818:Animals; D030562:Databases, Protein; D006801:Humans; D051379:Mice; D015233:Models, Statistical; D010449:Peptide Mapping / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D053719:Tandem Mass Spectrometry / Q000379:methods*
keywords: Bayesian analysis; Bioinformatics; MALDI; Protein sequencing; Tandem mass spectrometry