title: Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: I. How much of the data is theoretically interpretable by search engines?
abstract: An in-depth analysis of a multidimensional chromatography-mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight (QqTOF) geometry instrument was carried out. A total of 3269 CID spectra were acquired. Through manual verification of database search results and de novo interpretation of spectra 2368 spectra could be confidently determined as predicted tryptic peptides. A detailed analysis of the non-matching spectra was also carried out, highlighting what the non-matching spectra in a database search typically are composed of. The results of this comprehensive dataset study demonstrate that QqTOF instruments produce information-rich data of which a high percentage of the data is readily interpretable.
authors.affiliation: Mass Spectrometry Facility, University of California San Francisco, 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: Kirk C
authors.initials: KC
authors.lastname: Hansen
authors.forename: Katalin F
authors.initials: KF
authors.lastname: Medzihradszky
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: D002853:Chromatography, Liquid; D019204:GTP-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D010446:Peptide Fragments / Q000032:analysis*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D010446:Peptide Fragments; D019204:GTP-Binding Proteins