Characterizing biomolecules via mass spectrometry

Mass spectrometry is an incredibly versatile and powerful tool that is poised to greatly influence the routine analysis of biological molecules. The work presented in this dissertation endeavors to elucidate unique gas phase chemistry and develop analytical techniques that will aid routine biomolecular analysis with a quadrupole ion trap. Two main types of molecules are studied, oligosaccharides and peptides. The oligosaccharide dissociation mechanisms described by others that are indicative of glycosidic linkage sequence are shown to occur in the quadrupole ion trap with the ion trap allowing enhanced pathway elucidation. Oligosaccharides also provide an excellent system to demonstrate and evaluate Collision-induced Signal Enhancement (CISE). CISE is a technique using either a form of resonant excitation or boundary activation to dissociate product ions to increase the population of a product ion desired for tandem mass spectral analysis. CISE is shown to be capable of enhancing the signal for oligosaccharide product ions up to 1600%. Peptides are studied to gain insight into the optimal transition state ring size of a particular gas phase rearrangement reaction that was elucidated previously. Peptides with non-naturally occurring amino acids are used to alter the number of atoms in the peptide backbone thus altering the number of atoms comprising the transition state structure. The optimal transition state ring size is shown to be twelve atoms for the set of peptides examined in the gas phase which is very different from the most stable six atom rings found in solution. Molecular modeling indicates the driving force of this rearrangement is related to intramolecular interactions that orient the N-terminus close to the charge site. Also, while enthalpy considerations appear to favor three and five residue reactions, a favorable entropy change in the four residue peptide may overcome the enthalpy barrier. One of the peptides with a non-naturally occurring amino acid exhibits an interesting dissociation behavior. A transient intermediate exists in this case and kinetic analysis of the dissociation reactions allows the prediction of the reactive time frame for the transient intermediate. A highly modified scan function allows the observation of the transient intermediate.