title: Multidimensional proteomic analysis of the soluble subproteome of the emerging nosocomial pathogen Ochrobactrum anthropi.
abstract: We report the first large-scale gel-free proteomic analysis of the soluble subproteome of the emerging pathogen Ochrobactrum anthropi. Utilizing our robust offline multidimensional protein identification protocol, a total of 57 280 peptides were initially identified utilizing automated MS/MS analysis software. We describe our investigation of the heuristic protein validation tool PROVALT and demonstrate its ability to increase the speed and accuracy of the curation process of large-scale proteomic datasets. PROVALT reduced our peptide list to 8517 identified peptides and further manual curation of these peptides led to a final list of 984 uniquely identified peptides that resulted in the positive identification of 249 proteins. These identified proteins were functionally classified and physiochemically characterized. A variety of typical "housekeeping" functions identified within the proteome included nucleic acid, amino and fatty acid anabolism and catabolism, glycolysis, TCA cycle, and pyruvate and selenoamino acid metabolism. In addition, a number of potential virulence factors of relevance to both plant and human disease were identified.
authors.affiliation: School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry, BT52 1SA, United Kingdom. rl.graham@ulster.ac.uk
authors.forename: Robert Leslie James
authors.initials: RL
authors.lastname: Graham
authors.forename: Catherine E
authors.initials: CE
authors.lastname: Pollock
authors.forename: S Naomi
authors.initials: SN
authors.lastname: O'Loughlin
authors.forename: Nigel G
authors.initials: NG
authors.lastname: Ternan
authors.forename: D Brent
authors.initials: DB
authors.lastname: Weatherly
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Jackson
authors.forename: Rick L
authors.initials: RL
authors.lastname: Tarleton
authors.forename: Geoff
authors.initials: G
authors.lastname: McMullan
mesh_terms: D000595:Amino Acid Sequence; D001331:Automation; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D020621:Ochrobactrum anthropi / Q000737:chemistry* / Q000235:genetics / Q000472:pathogenicity; D010446:Peptide Fragments / Q000737:chemistry / Q000302:isolation & purification; D020543:Proteome; D040901:Proteomics / Q000379:methods
chemical_list: D001426:Bacterial Proteins; D010446:Peptide Fragments; D020543:Proteome