Integrating Mass Spectrometry Based Proteomics and Bioinformatics Technologies for the Molecular Level Characterization of Shewanella oneidensis to Chromate Exposure

The research outlined in this dissertation involves the development and demonstration of a mass spectrometry-based proteomics approach to characterize the global level molecular response of Shewanella oneidensis MR-1 to chromate exposure. The proteomics approach is centered on a high performance technique of multidimensional on-line liquid chromatographic separations with subsequent tandem mass spectrometric detection. Since very complex proteome samples are digested into peptides and then directly measured by MS, this technique is termed shotgun proteomics. This approach affords the identification and quantification of complex mixtures by directly analyzing their proteolytic peptides and then using computational techniques to reassemble the protein information. The research goals for this dissertation project were two-fold: (1) enhancement of the experimental and computational methodologies to permit deeper and more confident proteome characterizations, and (2) demonstration of this optimized approach for the comprehensive investigation of the molecular level response of the bacterium S. oneidensis to chromate insult. To address research needs, we developed a single-tube lysis method for cell lysis-proteome digestion to enable investigations of small amounts of cellular biomass, and identified suitable bioinformatic approaches to mine post-translational modifications from proteome datasets. These advancements were then utilized to examine the molecular level response of S. oneidensis to chromate insult, which was accomplished by varying chromate concentrations, dosages, and time points. These measurements provided the first global proteome-level observation of the dynamic changes of S. oneidensis in response to chromate insult.