Gaining insight into electron capture dissociation mass spectrometry of peptides and proteins

The study of protein structure is crucial to the understanding of protein function as the two are inter-dependent. Protein structure analysis is especially important as misfolded proteins often result in fatal diseases. Gas-phase protein structure analysis provides a way to study the forces the effects of solvent and involved in the determination of protein structure. Mass spectrometry (MS) is a rapid and sensitive technique that can be used for the analysis of gas-phase protein structure.;Electron capture dissociation (ECD) tandem mass spectrometry (MS/MS) has been used in the analysis of primary, secondary, and tertiary gas-phase protein structure. ECD-MS/MS has proved to be exceptionally applicable in the study of protein structure due to the ability to cleave protein backbone bonds with the retention of noncovalent interactions and small-molecule post-translational modifications. The work described in this dissertation expands the use ECD and other electron capture techniques for protein structure analysis.;All of the experiments were performed using a unique and versatile hybrid linear ion trap/time-of-flight (LIT/TOF) mass spectrometer capable of multiple ion activation techniques, such as collision induced dissociation (CID), infrared multiphoton dissociation (IRMPD), ECD, hot ECD (HECD), and activated-ion ECD (AI-ECD). IR activation in conjunction with ECD (AI-ECD) to disrupt noncovalent interactions was used to enhance primary structure analysis and monitor changes in tertiary structure via gas-phase protein unfolding. The structure of the z·-type product ions was probed using ion-molecule reactions, and the formation different structures was found to depend on the electron capture technique used to dissociate the parent ion.;The work described in this dissertation demonstrates the use of AI-ECD for analysis of gas-phase protein structure. Also, the first analysis of z ·-ion structure from various electron capture techniques is presented. This work highlights the versatility and utility of the LIT-TOF for ECD-MS/MS as an alternative to the commercial Fourier transform ion cyclotron resonance (FTICR) mass spectrometers.