| Mass spectrometry is a powerful tool in the identification of peptides and proteins, especially when coupled to liquid chromatography. Mass spectrometry can identify proteins and peptides regardless of peptide modification, protein/DNA mutation, and sample complexity. Mass spectrometry can advance the study of innumerable biological systems because it is so versatile. Different mass spectrometers have rapid peptide fragmentation capabilities, high sensitivity, and high mass accuracy, such that depending on the goals of one's project different instruments can be used.; The different goals of the studies presented in this work span the abilities of mass spectrometry. Chapter 1 describes a proteomics analysis of mRNA binding proteins localized in dendrites. The challenge of this project was to identify as many proteins in a complex mixture as possible, all in the context of an incomplete rat genome. The studies discussed in chapter 2 and 3 involve the identification of immunologically relevant peptides. In chapter 2, the isolation and identification of phosphorylated peptides, either solely presented or overpresented by cancer cells, were optimized such that, as compared to initial analyses of these class I cell surface peptides, over 10 times the number phospho-peptides were found. In Chapter 3, the reactive peptide that allowed a prevalent population of T-cells to destroy insulin-producing beta-cells, which ultimately led to diabetes, was identified. The challenge in both of these studies was to identify a small population of peptides or, as in chapter 3, the one reactive peptide in a mixture of over ten thousand other peptides of similar length and motif.; In the end, mass spectrometry is a critical tool that enables scientists to study important biological phenomenon. In these studies alone, proteins and peptides were identified that were involved to the formation of long-term memory, that allowed the propagation of an auto-immune disease, and that could be used to train the immune system to attack and eliminate cancer cells. Advances in biology are the true success of mass spectrometry. |
