Predicting Favorable Habitat for Bobcats (Lynx Rufus) in Iowa

Proteins have essential roles in nearly all cellular processes ranging from cell signaling to structure support of the cell. The proteome is the entire complement of proteins expressed by a given cell, tissue, or organism at a given time under defined conditions. A proteome is typically more complex than the corresponding genome. This complexity is due in large part to post-translational modifications (PTMs), such as phosphorylation, methylation, and acetylation. The characterization of PTMs and their biochemical roles is vital to understanding cellular processes and regulation. Mass spectrometry is a powerful analytical tool for the study of protein PTMs because of its sensitivity and the ability to directly identify modification sites. Presented in this dissertation are three projects that demonstrate the utility of high resolution MS with CAD and ETD MS/MS used in a complementary fashion to characterize PTMs.

First, we optimized phosphopeptide enrichment methods for analysis of the phosphorylation profile of non-muscle myosin II regulatory light chain. In the second project, we analyzed the PTMs of histone proteins from nucleosomes enriched for tri-methylation on lysine 4 of histone H3. This modification localizes to actively transcribing regions of chromatin and is present at very low abundance in mammalian cells. For this analysis a variety of protein digestion and peptide derivatization were utilized. Lastly, we began to characterize the PTMs on intact and proteolytically cleaved forms of histone H3 in Tetrahymena thermophilia micronuclei.