| The fundamental properties of proteins in the gas phase are investigated in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) employing ion/molecule reactions of protonated ions generated by fast atom bombardment (FAB) and electrospray ionization (ESI). Theoretical studies including semi-empirical calculations and molecular dynamics are used to garner further information on protonation sites, reactivity trends and peptide conformation.; The gas-phase basicities (GBs) of the imino acid, proline, and its di- and tripeptides with glycine are assigned by monitoring the deprotonation reaction of the protonated molecular ion, [M+H]+ generated by FAB, with reference bases. The importance of intrinsic basicity and intramolecular hydrogen bonding is demonstrated by the enhanced basicity of the dipeptide, prolylproline (ProPro). AM1 calculations show two H-bonding interactions that stabilize the protonation site and contribute to the observed reactivity of the dipeptide.; Deprotonation reactions and molecular dynamics studies of ESI-generated [M+2H]2+ for bradykinin and its analogues, des-Arg1 -bradykinin and des-Arg9-bradykinin, were also performed. The assigned apparent gas-phase basicities (GBapp) of [M+H] + for the peptides are compared to literature values. This study addresses the use of 0.1 as a reasonable deprotonation reaction efficiency to signal the transition from an endoergic to exoergic reaction for multiply-charged ions. The GBapp for des-Arg1-bradykinin and des-Arg 9-bradykinin agree with the literature values. However, the value obtained for bradykinin differs by 10 kcal/mol. This difference might be attributed to two different conformers of bradykinin [M+2H]2+ being investigated in the two studies.; Deprotonation studies and hydrogen/deuterium exchange on [M+4H] 4+ generated by electrospray for insulin chain B (oxidized), which contains cysteic acid groups, revealed two reacting populations. The reactivity and dissociation patterns differed from insulin chain B (reduced), which contains no cysteic acid residues. These experimental results coupled to molecular modeling results strongly suggest that the cysteic acid groups affect the reactivity of multiply-charged ions by forming stable zwitterionic interactions with protonation sites.; The first survey study on the negative ion dissociation of multiply charged ions of three commercially available proteins in a FT-ICR is presented. The results suggest that negative ion dissociation is a complementary technique to positive ion dissociation and traditional sequencing techniques for providing primary structural elucidation. |
