Gas -phase dissociation and ion /ion reactions of biomolecules in a quadrupole ion trap mass spectrometer
Quadrupole ion trap mass spectrometers can be used as reaction vessels for ion/ion reactions between positively and negatively charged ions. These reactions are useful in the gas-phase analysis of peptide and protein ions. Gas-phase fragmentation is another informative tool, which can be used in conjunction with ion/ion reactions for bioanalytical applications. In order to use gas-phase dissociation and ion/ion reactions to their full potential, it is necessary to gain an understanding of the underlying ion chemistry of these processes. This dissertation discusses several studies involving the use of ion/ion reactions and gas-phase dissociation of both model peptides and proteins for protein characterization.
Lysine guanidination was explored as a modification to affect the dissociation behavior of peptide and protein ions. The collision-induced dissociation (CID) spectra of guanidinated peptides and proteins are similar to the CID spectra, of higher charges states, of the unmodified forms. This fragmentation is consistent with the concept that proton mobility is a major factor in determining favored fragmentation channels. Electron transfer ion/ion reactions have also been shown to give rise to informative fragmentation. Several aspects of these reactions are described, including comparing the electron transfer dissociation behavior (ETD) of triply versus doubly protonated peptides, the effect of bath gas temperature on the ETD of peptides, and electron transfer ion/ion reactions with disulfide linked polypeptides. Parallel ion parking techniques, applied during ion/ion reactions to optimize the conversion of parent ions to first-generation products during ETD, and parallel ion parking for the analysis of protein mixtures, will also be discussed. Finally, the charge-state dependent fragmentation behavior of a model non-covalent protein-protein complex will be investigated using ion/ion proton transfer reactions.