title: Comparison of a Salmonella typhimurium proteome defined by shotgun proteomics directly on an LTQ-FT and by proteome pre-fractionation on an LCQ-DUO.
abstract: Shotgun proteomics is rapidly becoming one of the most efficient and popular tools to examine protein expression in cells. Numerous laboratories now have a wide array of low- and high-performance mass spectrometry instrumentation necessary to complete proteome-wide projects. Often these laboratories have time and financial constraints that prohibit all projects from being conducted on high-performance state-of-the-art mass spectrometers. Here, we compare shotgun proteomic results using a direct 'lyse, digest and analyse' approach on a high-performance mass spectrometer (i.e. the LTQ-FT) with the results from a much lower-performance instrument (i.e. the LCQ-DUO) where, for the latter, various traditional protein pre-fractionation steps and gas-phase fractionation were used to increase the proteome coverage. Our results demonstrate that shotgun proteomic analyses conducted on the lower-performance LCQ-DUO mass spectrometer could adequately characterize a PhoP constitutive strain of Salmonella typhimurium if proteome pre-fractionation steps and gas-phase fractionation were included.
authors.affiliation: Goodlett Laboratory.
authors.forename: Brook L
authors.initials: BL
authors.lastname: Nunn
authors.forename: Scott A
authors.initials: SA
authors.lastname: Shaffer
authors.forename: Alexander
authors.initials: A
authors.lastname: Scherl
authors.forename: Byron
authors.initials: B
authors.lastname: Gallis
authors.forename: Manhong
authors.initials: M
authors.lastname: Wu
authors.forename: Samuel I
authors.initials: SI
authors.lastname: Miller
authors.forename: David R
authors.initials: DR
authors.lastname: Goodlett
mesh_terms: D002851:Chromatography, High Pressure Liquid / Q000379:methods*; D005583:Fourier Analysis; D013058:Mass Spectrometry / Q000379:methods*; D009154:Mutation; D020543:Proteome / Q000032:analysis* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012486:Salmonella typhimurium / Q000737:chemistry* / Q000235:genetics; D014357:Trypsin / Q000494:pharmacology
chemical_list: D020543:Proteome; D014357:Trypsin