Multidimensional proteomic analysis of the soluble subproteome of the emerging nosocomial pathogen Ochrobactrum anthropi

• Published in: Journal of proteome research 2006-11, Vol.5 (11), p.3145-3153
• Main Authors: Graham, Robert Leslie James, Pollock, Catherine E, O'Loughlin, S Naomi, Ternan, Nigel G, Weatherly, D Brent, Jackson, Philip J, Tarleton, Rick L, McMullan, Geoff
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Automation; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - isolation & purification; Electrophoresis, Gel, Two-Dimensional - methods; Mass Spectrometry; Molecular Sequence Data; Ochrobactrum anthropi - chemistry; Ochrobactrum anthropi - genetics; Ochrobactrum anthropi - pathogenicity; Peptide Fragments - chemistry; Peptide Fragments - isolation & purification; Proteome; Proteomics - methods
• ISSN: 1535-3893
• DOI: 10.1021/pr060293g

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.