title: Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: II. New developments in Protein Prospector allow for reliable and comprehensive automatic analysis of large datasets.
abstract: A thorough analysis of the protein interaction partners of the yeast GTPase Gsp1p was carried out by a multidimensional chromatography strategy of strong cation exchange fractionation of peptides followed by reverse phase LC-ESI-MSMS using a QSTAR instrument. This dataset was then analyzed using the latest developmental version of Protein Prospector. The Prospector search results were also compared with results from the search engine "Mascot" using a new results comparison program within Prospector named "SearchCompare." The results from this study demonstrate that the high quality data produced on a quadrupole selecting, quadrupole collision cell, time-of-flight (QqTOF) geometry instrument allows for confident assignment of the vast majority of interpretable spectra by current search engines.
authors.affiliation: Mass Spectrometry Facility, University of California, San Francisco, California 94143-0446, USA. robertc@.itsa.ucsf.edu
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Chalkley
authors.forename: Peter R
authors.initials: PR
authors.lastname: Baker
authors.forename: Lan
authors.initials: L
authors.lastname: Huang
authors.forename: Kirk C
authors.initials: KC
authors.lastname: Hansen
authors.forename: Nadia P
authors.initials: NP
authors.lastname: Allen
authors.forename: Michael
authors.initials: M
authors.lastname: Rexach
authors.forename: Alma L
authors.initials: AL
authors.lastname: Burlingame
mesh_terms: D001322:Autoanalysis; D002138:Calibration; D002853:Chromatography, Liquid; D019204:GTP-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D010446:Peptide Fragments / Q000032:analysis*; D010449:Peptide Mapping; D020543:Proteome; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D010446:Peptide Fragments; D020543:Proteome; D019204:GTP-Binding Proteins