Understanding MS Approaches to Peptide Characterization

Proteomics studies using mass spectrometry have become routine. The overarching goal of proteomics is to understand how the proteome changes within individuals over time, in disease states, and between individuals. Currently the field is limited by the quality of the data that can be obtained for low concentration proteins in complex biological mixtures, and by the lack of chemical knowledge that needs to be incorporated into the automated data analysis protocols that are needed to handle the massive volumes of data generated by proteomics studies. The work in this dissertation addresses both limitations. IRMPD was found to increase in efficiency with the size of a peptide, unlike CID. Attempts to quantify the increase in internal energy responsible for the increase in IRMPD efficiency with size were precluded by non-Boltzmann internal energy distributions in the population of trapped ions. FMOC derivatized peptides were found to promote sodium binding, and thereby facilitate C-terminal dissociation patterns that are easily interpreted. Infrared spectroscopy was used to measure the structure of b3 and a4 peptide fragments to gain insight into sequence and size dependent dissociation patterns. Comparison of the structures found by spectroscopy with dissociation patterns seen in CID and IRMPD gave further information about the dissociation kinetics of b3 and a4 peptide fragments.Doctor of Philosoph