Mass Spectrometry: Toward Elucidating the Biosignature of Coccidioidomycosis and Insights into Surface Induced Dissociation of Biologically Relevant Carbohydrates

Abstract

Mass spectrometry (MS) has proven itself to be indispensable for the analysis of biomolecules and molecular systems. This research has three goals: (1) expand on prior work toward the discovery of novel diagnostic targets for Valley Fever, (2) evaluate current mass spectrometry based proteomics for the discovery of non-host protein in complex host biological samples, and (3) investigate the potential for two gas phase techniques, surface induced dissociation, and ion mobility for the analysis of carbohydrate based molecules. Mass spectrometry has allowed for great advances in the identification of proteins in biological samples through implementing liquid chromatography tandem mass spectrometry and bioinformatics techniques known as proteomics. Proteomics techniques were used to elucidate a portion of the biosignature of Valley Fever (VF), a disease of great importance in the arid regions of the western United States. Current diagnostics for this fungal lung disease are remarkably unreliable which creates a need for an unfailing diagnostic method. Using a new generation of instrumentation along with directed methods, four previously discovered VF marker proteins were evaluated for their presence in mouse plasma, lung homogenate and bronchoalveolar lavage fluid samples. Due to inconclusive data, discovery proteomics approaches were then used to identify possible diagnostic targets in both human and mouse bronchoalveolar lavage fluid. In human bronchoalveolar lavage fluid, one potential target was discovered in five out of eight VF positive samples, and two further identifications of VF in negative samples. Mouse bronchoalveolar lavage fluid also showed the presence of this protein. Multiple-reaction monitoring based validation, using two-dimensional online separations for the presence of either the newly discovered protein or the four previously discovered proteins, was inconclusive. Emerging from the difficulties observed by the author and colleagues in identifying infectious agent proteins in complex host biological samples, an investigation of the feasibility of undertaking such endeavors was performed. One of the main complications thwarting the discovery of infectious agent proteins is the dynamic range of protein concentration in the host biological sample. This issue was resolved by using commercially available mass spectrometry and a two-dimensional liquid chromatographic separations platform. This enhanced separation combined with cost-effective protein normalization techniques, identified non-host proteins with good sequence coverage and spectral counts. Combining antibody-based depletion of highly abundant plasma proteins in bronchoalveolar lavage fluid, with at least a three fraction sample analysis enabled detection of a low abundant non-host protein (2pmol in 50μg host protein) with high sequence coverage. Glycosylation, an abundant post-translational modification of protein composed of carbohydrate oligomers may hold within its structure more biologically relevant information than the DNA that encoded the protein on which the glycan resides. The analysis of glycosylation plays a critical role in understanding biology. Carbohydrate based moieties pose many distinct challenges to their analysis; two of which are isobaric fundamental units and complex branching chemistry. Mass spectrometry provides a way of overcoming some of these challenges. To examine the complex biomolecules, a gas phase ion separation technique, known as ion mobility, and a non-traditional ion activation technique, surface-induced dissociation, were used. Surface-induced dissociation provides analogous fragmentation patterns to those generated via collision-induced dissociation (CID); however, much more extensive fragmentation can be achieved in a single tandem MS experiment. Using the gas-phase separations power of ion mobility showed that multiple conformations were adopted by relatively simple oligosaccharides. Ion mobility was also successfully used to determine fragment ion lineage of isobaric fragment ions, through inline separation between two differential fragmentation experiments.