This dissertation, "Formation, Isomerization and Dissociation of Radical Cationic Peptides" by Chun-ming, Dominic, Ng, 伍俊明, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: A fundamental understanding of the isomerization and fragmentation of peptide ions forms the scientific basis underlying peptide sequencing in the gas phase-an important emerging analytical technique routinely used in proteomics applications. Gas phase dissociation of odd-electron radical peptide cations (M?+) provides an alternative and complementary analytical method for identifying peptide sequences; this fragmentation behavior is distinct from that of even-electron protonated peptides ([M]H]+). Despite recent experimental and theoretical advances in studies of radical cationic peptides, their gas phase chemistry remains poorly understood. The first part of this Thesis documents three mechanistic studies on the formation, isomerization, and dissociation of prototypical tripeptide radical cations in the gas phase using biological mass spectrometry. A combination of low-energy collision-induced dissociation (CID) experiments and density functional theory calculations at the B3LYP 6-31++G(d, p) level of theory was used to investigate the influence of the position of the radical site and the basicity of the amino acid residues in the radical cationic tripeptide analogs on their dissociation pathways. The CID spectra of two isomeric glycylglycyltryptophan radical cations-[GGW]?+ and [G?GW]+, with well-defined initial radical sites at the 3-methylindole ring and the N-terminal α-carbon atom, respectively-are significantly different. The former leads to the formation of [a3 ] H]?+, [c2 ] 2H]?+, and [z1 - H]?+ product ions through C-Cα and N-Cα peptide bond cleavages, while the latter leads to the predominant fragment ions of y1+, [b2 - H]?+, and [b3 - H]?+ via amide bond cleavages. After substitution of the central glycine residue of GGW with an arginine residue, however, the two isomers [G?RW]+ and [GRW]?+ produced almost identical CID spectra. The calculated energy barriers and microcanonical rate constants for isomerizations and competitive dissociations are in accordance with the perception that isomerizations between the GGW isomers could not compete with their fragmentations. For the radical cationic isomers, the presence of the highly basic arginine residue decreases the isomerization barriers (ca. 7-11 kcal/mol) and mediates facile hydrogen atom transfers-both along the peptide backbone and within the side chain residues-prior to subsequent dissociations. The effect of a basic amino acid residue on the isomerizations and dissociations of α-carbon-centered radical peptides also extends to distinctive Cβ-Cγ bond cleavages of isobaric leucine and isoleucine (Xle) residues. The CID spectra of [G?RXle]+ radical cations lead to the formation of characteristic product ions resulting from losses of ?CH(CH3)2 in [G?RL]+ and ?CH2CH3 in [G?RI]+ through Cβ-Cγ side-chain cleavages of (iso)leucine residues, allowing the two peptides to be distinguished. Finally, the first implementation of laser-induced dissociation (LID) on a hybrid quadrupole linear ion trap mass spectrometer is presented. After laser irradiation of mass-selected and -trapped ions in the quadrupole linear ion trap, LID spectra of [M]H]+ undergo both facile backbone and side-chain cleavages. These products are strikingly different from those formed in the CID spectra of [M]H]+, but are similar to those in the corresponding CID spectra of M?+. This approach provides an alternati