title: Evaluation of front-end higher energy collision-induced dissociation on a benchtop dual-pressure linear ion trap mass spectrometer for shotgun proteomics.
abstract: We report the implementation of front-end higher energy collision-induced dissociation (fHCD) on a benchtop dual-pressure linear ion trap. Software and hardware modifications were employed, described in detail vide-infra, to allow isolated ions to undergo collisions with ambient gas molecules in an intermediate multipole (q00) of the instrument. Results comparing the performance of fHCD and resonance excitation collision-induced dissociation (RE-CID) in terms of injection time, total number of scans, efficiency, mass measurement accuracy (MMA), unique peptide identifications, and spectral quality of labile modified peptides are presented. fHCD is approximately 23% as efficient as RE-CID, and depending on the search algorithm, it identifies 6.6% more or 15% less peptides (q < 0.01) from a soluble whole-cell lysate ( Caenorhabditis elegans ) than RE-CID using Mascot or Sequest search algorithms, respectively. fHCD offers a clear advantage for the analysis of phosphorylated and glycosylated (O-GlcNAc) peptides as the average cross-correlation score (XCorr) for spectra using fHCD was statistically greater (p < 0.05) than for spectra collected using RE-CID.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Bereman
authors.forename: Jesse D
authors.initials: JD
authors.lastname: Canterbury
authors.forename: Jarrett D
authors.initials: JD
authors.lastname: Egertson
authors.forename: Julie
authors.initials: J
authors.lastname: Horner
authors.forename: Philip M
authors.initials: PM
authors.lastname: Remes
authors.forename: Jae
authors.initials: J
authors.lastname: Schwartz
authors.forename: Vlad
authors.initials: V
authors.lastname: Zabrouskov
authors.forename: Michael J
authors.initials: MJ
authors.lastname: MacCoss
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000378:metabolism; D006020:Glycopeptides / Q000032:analysis; D013058:Mass Spectrometry / Q000295:instrumentation* / Q000379:methods; D010748:Phosphopeptides / Q000032:analysis; D011312:Pressure; D040901:Proteomics / Q000295:instrumentation*; D012984:Software
chemical_list: D006020:Glycopeptides; D010748:Phosphopeptides