Date of Award


Degree Type


Degree Name

Doctor of Philosophy


Life Sciences

Major Professor

Robert L. Hettich

Committee Members

Dale A. Pelletier, Gregory B. Hurst, Cynthia B. Peterson, Frank W. Larimer


The goals of this dissertation research were to develop an integrated computational and experimental platform for characterizing protein isoforms and post translational modifications (PTMs) in microbial systems by top-down FT-ICR mass spectrometry. To accomplish this goal, we employed methodologies of microbial growth, intact protein and protein complex extractions, followed by sample preparation and then progressed to identification of the instrumentation needed to integrate the top-down and bottom-up proteomics methodologies used in these studies. Emphasis is placed on the development of integrated top-down and bottom-up informatics and the challenges faced in the integration of these two large mass spectrometry data sets and extraction of relevant biological data. We then illustrate how top-down and bottom-up methods can be applied to the analysis of complex protein mixtures, protein complexes, and microbial proteomes. Through the work of this dissertation we have contributed to the advancement of top-down proteomics by providing an experimental platform which will aid in the analysis of intact proteins and their associated PTMs and isoforms, as well as providing a computational method that allows for the integration of top-down and bottom-up data sets.

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Included in

Life Sciences Commons