| Mass spectrometry is an efficient and sensitive technique for protein sequence determination and structure elucidation. The research in this dissertation relates to both of these areas. The first part investigates the application of S-methyl thioacetamidate (SMTA) as a chemical label to study protein structure, protein-ligand/protein interaction and a large RNA-protein complex. The protein regions buried in 3D structure or involved in non-covalent interaction with other biomolecules can be distinguished successfully using SMTA and mass spectrometry. The second part of the dissertation elucidates photodissociation selection rules through a study of synthetic peptide libraries. A de novo sequencing algorithm has been developed to derive peptide sequences using photodissociation and post-source decay (PSD) data. However, this algorithm often fails to sequence peptide N-terminal regions. In order to improve de novo sequencing results, the photodissociation propensities were generalized by investigating synthetic peptide libraries. Therefore, more complete and confident peptide sequences can be derived from an improved de novo algorithm by applying the additional strategies. |
