Liquid chromatography/quadrupole time of flight mass spectrometry (LC/QTOF MS) utilizing electrospray ionization was employed to monitor protein expression in Escherichia coli and Shigella organisms. Automated charge state deconvolution, spectral subtraction and spectral mirroring were used to reveal subtle differences in the LC/MS data. Reproducible intact protein biomarkers were discovered based on their unique mass, retention time and relative intensity. These markers were implemented to differentiate closely related strain types, (e.g. two distinct isolates of E. coli O157:H7) and to correctly identify unknown pathogens. Notable, was the distinction of multiple serotypes of enterohaemorrhagic E. coli which cannot be distinguished by clinical manifestation alone. Additionally, speciation of Shigella was achieved, a task for which no commercial real-time polymerase chain reaction (PCR) primers exist. This method was subsequently applied to two pathogenic Clostridium species: C. difficile and C. perfringens. Due to the increased difficulty during lysis, two new lysis protocols were developed, and each extracted a distinct set of proteins (by both mass and retention time). Extracts from both lysis procedures were utilized to discover biomarkers useful for identification and characterization at the species and strain levels. These biomarkers were successfully implemented to identify unknowns during a blind study and would enhance serological and genetic approaches by serving as new targets for detection. Two sets of the C. perfringens isolates that were deemed 100% similar by the gold standard for strain differentiation, pulsed-field gel electrophoresis (PFGE), were distinguished using LC/MS, demonstrating the high specificity of this approach. The final part of this work demonstrated the application of ultra performance liquid chromatography (UPLC) to this project to improve the throughput of the method. Given that numerous small molecule applications of UPLC have been published, efforts were made to examine the potential of UPLC to enhance the separation of intact proteins. Beginning with typically employed conditions, column temperature and organic solvent were optimized followed by an HPLC vs. UPLC comparison. When applied to a mixture of ten protein standards, the optimized UPLC method yielded improved chromatographic resolution, enhanced sensitivity, and a three-fold increase in throughput. Application of this method to cell lysate analysis demonstrated no compromise in chromatographic or mass spectral data quality; a reduction in run time from 75 minutes to 25 minutes was achieved.
| Identifer | oai:union.ndltd.org:vcu.edu/oai:scholarscompass.vcu.edu:etd-2106 |
| Date | 01 January 2008 |
| Creators | Everley, Robert A. |
| Publisher | VCU Scholars Compass |
| Source Sets | Virginia Commonwealth University |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | Theses and Dissertations |
| Rights | © The Author |
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