Glycan sequencing and isoaspartate characterization by electron activated dissociation tandem mass spectrometry

Thesis (Ph.D.)--Boston UniversityIn this study, we carefully examined several types of electron activated dissociation (ExD) processes and developed new ExD techniques that should facilitate biological research, placing particular emphasis on glycan and protein characterization. The first part of this study focused on determination of ExD fragmentation mechanisms and application of ExD to glycan de novo sequencing. Through variation of the electron energy and metal charge carriers, the behaviors of model glycans were systematically studied and a new ExD fragmentation process, designated as electronic excitation dissociation (EED), was found to be the most informative. By identifying and controlling the key parameters, we improved the EED efficiency, to a level that now allows EED to be performed on a time scale that is compatible with the peak widths in high performance liquid chromatography. Theoretical modeling was employed to gain insights into the charge remote fragmentation behavior inherent in the EED process. The experimental results demonstrated that EED has the potential to provide the experimental basis for highthroughput, de novo glycan sequencing. The second part of this study focused on the determination of deamidation of asparagine residues and isomerization of aspartate residues within proteins. In order to avoid the generation of artifacts during trypsin digestion, a comprehensive top-down ExD method was developed to identify both asparagine deamidation and isoaspartate formation at the level of the intact protein With the consideration that the top-down strategy will eventually fail for high molecular weight proteins, a middle-down ExD method was next developed, for the analysis of peptides generated by proteolysis with Staphylococcal serine protease Protease V8 (GluC), carried out at slightly acidic conditions. In addition, the potential for use of in-source decay in isoaspartate analyses was evaluated and its fragmentation mechanisms were investigated. This research established new tools for structural determinations of glycans and significant improvements in methods for the isomer- and site-specific analysis of proteins that contain Asp or Asn residues that can undergo conversion to isoAsp, and provides insight toward understanding and controlling the fundamental processes that lead to the types of fragment ions observed in electron activated dissociation mass spectra