title: Infrared multiphoton dissociation for quantitative shotgun proteomics.
abstract: We modified a dual-cell linear ion trap mass spectrometer to perform infrared multiphoton dissociation (IRMPD) in the low-pressure trap of a dual-cell quadrupole linear ion trap (dual-cell QLT) and perform large-scale IRMPD analyses of complex peptide mixtures. Upon optimization of activation parameters (precursor q-value, irradiation time, and photon flux), IRMPD subtly, but significantly, outperforms resonant-excitation collisional-activated dissociation (CAD) for peptides identified at a 1% false-discovery rate (FDR) from a yeast tryptic digest (95% confidence, p = 0.019). We further demonstrate that IRMPD is compatible with the analysis of isobaric-tagged peptides. Using fixed QLT rf amplitude allows for the consistent retention of reporter ions, but necessitates the use of variable IRMPD irradiation times, dependent upon precursor mass to charge (m/z). We show that IRMPD activation parameters can be tuned to allow for effective peptide identification and quantitation simultaneously. We thus conclude that IRMPD performed in a dual-cell ion trap is an effective option for the large-scale analysis of both unmodified and isobaric-tagged peptides.
authors.affiliation: Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States.
authors.forename: Aaron R
authors.initials: AR
authors.lastname: Ledvina
authors.forename: M Violet
authors.initials: MV
authors.lastname: Lee
authors.forename: Graeme C
authors.initials: GC
authors.lastname: McAlister
authors.forename: Michael S
authors.initials: MS
authors.lastname: Westphall
authors.forename: Joshua J
authors.initials: JJ
authors.lastname: Coon
mesh_terms: D000595:Amino Acid Sequence; D002851:Chromatography, High Pressure Liquid; D016208:Databases, Factual; D007259:Infrared Rays; D013058:Mass Spectrometry; D010455:Peptides / Q000032:analysis; D017785:Photons; D040901:Proteomics
chemical_list: D010455:Peptides