Gas-phase ion/ion and dissociation reactions of polypeptides and their noncovalent complexes

Methodological aspects of synthesizing protein-protein complexes using ion/ion chemistry have been demonstrated. It has been noted that complex formation often competes with proton transfer. Different strategies to build complexes while minimizing unwanted proton transfer side reactions are discussed. A preliminary study has identified model systems that undergo dissociation as a result of proton transfer reactions. While most of these systems are small noncovalent complexes, a majority of proton transfer ion/ion reactions explored to date have shown lack of dissociation of covalent bonds. The experimental systems have been subjected to modeling strategies to explain dissociation or lack-there-of as a result of proton transfer. Various aspects of the newly developed electron transfer dissociation technique are presented throughout this dissertation. Among the many variables involved in electron transfer dissociation, the nature of the reagent anion, and the functionality of the peptides charge bearing groups have been shown to significantly affect the partitioning of the product ion distribution. A predictive model based on the Landau-Zener theory for electron transfer has been developed to evaluate a range of reagent anions for their ability to induce electron transfer dissociation. The role of the reagent and more importantly the role of charge bearing sites has been carefully evaluated against a couple of reagents to study the partitioning of the different product ion channels. The importance of labile protons in the electron transfer dissociation of disulfide bonds has also been presented by comparing the partitioning of the various ion/ion products of a protonated species against their fixed charge derivatized analogs. The charge state dependent fragmentation behavior of insulin cations shows that the charge state of insulin plays a role in determining dissociation phenomena. An application involving of phosphopeptide mixtures is presented where phosphopeptide anions are converted to positively charged ions via proton transfer followed by structural interrogation using electron transfer dissociation. The application of cation switching ion/ion chemistry to perform selective disulfide bond cleavage is also introduced. Both these types of reactions exemplify the importance of gas-phase ion/ion methods as a processing technique for further structural characterization or mapping of important post translational modifications