Multidimensional Proteomic Analysis of the Soluble Subproteome of the Emerging Nosocomial Pathogen <i>Ochrobactrum </i><i>a</i><i>nthropi</i>

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. Keywords: proteomics • 2D LC−MS/MS • Ochrobactrum anthropi • pathogen本研究首次针对新兴病原体人苍白杆菌（Ochrobactrum anthropi）的可溶性亚蛋白质组开展大规模无凝胶蛋白质组学分析。本团队采用稳定的离线多维蛋白质鉴定流程，通过自动化串联质谱（MS/MS）分析软件，初步共鉴定得到57280条肽段。本研究针对启发式蛋白质验证工具PROVALT开展研究，并证实其可提升大规模蛋白质组数据集整理流程的速度与准确率。经PROVALT处理后，肽段列表缩减至8517条；对这些肽段进行进一步人工整理后，最终得到984条唯一鉴定肽段，据此可明确鉴定得到249种蛋白质。对上述鉴定得到的蛋白质进行了功能分类与理化特征表征。该蛋白质组中鉴定得到多种典型持家功能相关蛋白，涵盖核酸、氨基酸与脂肪酸的合成代谢与分解代谢、糖酵解、三羧酸（TCA）循环，以及丙酮酸与硒代氨基酸代谢通路。此外，本研究还鉴定得到多种与植物及人类疾病相关的潜在毒力因子。 关键词：蛋白质组学 • 二维液相色谱-串联质谱（2D LC−MS/MS） • 人苍白杆菌（Ochrobactrum anthropi） • 病原体