Targeted Quantitative Lipidomics of Cold Stress and the Development of Methods to Increase the Sensitivity of Proteomics Analyses Using Mass Spectrometry

This thesis focuses on mass spectrometry-based techniques and uses them to discover new lipidomic profiles of species that adapt to cold temperatures in the northern climates. Additionally, techniques were developed to enhance MS-based proteomics analyses for better protein identification. The focus in the lipidomic work is mainly quantitative in nature while the proteomics work enhances qualitative analyses.A lipid bilayer is of interest and will be examined in the tissues of several animal models. The composition of lipid bilayers is investigated in three different cold stress adaptation mechanisms including hibernation, freeze tolerance and freeze avoidance. Also examined are lipid bilayer differences in cold adaption in vital versus non-vital organs. Research was also conducted on how certain circadian rhythms are preserved even in the absence of environmental cues. The study models that were used were the thirteen-lined ground squirrel for hibernation, the wood frog for freeze tolerance and the goldfish for freeze avoidance traits. Our results elucidate some interesting patterns of lipid bilayers adaptation to cold stress. Increases in the concentration of unsaturated phospholipids in cold temperatures, particularly in the squirrel and frog liver tissues were observed. Also, in some cases increases in phosphatidylethanolamine lipids were observed in the lipid bilayers during winter months in comparison to summer months. These biomolecular dynamics are linked with increases in the fluidity of the lipid bilayer which is necessary for continued physiological function at lower temperatures.Proteomics work was focused further developments of the Trimethylation Enhancement using Diazomethane (TrEnDi) technique. Diazomethane was used to methylate tryptically digested peptides or commercial peptides. TrEnDi derivatization allows for the formation of fixed permanent charges on the peptides making them more sensitive in MS analyses. These results also highlight a novel method to identify the phosphorylation of peptides, which holds great interest in a great deal of clinical and health-based research as dysfunctional phosphorylation pathways are linked to numerous diseases. Although TrEnDi derivatization requires further optimization on peptide samples at this point in time, the developments described herein demonstrate that it is a unique method that can enhance the sensitivity of MS-based peptide analysis in numerous ways.