Novel fragmentation pathways of various model peptides were generated by collision-induced dissociation (CID) mass spectrometry. For the series AXAG where X=ßA, γAbu, εCap, or 4AMBz, the CID of the [b₃-1+Cat]⁺ where the residue to the C-terminal side of X is changed and labeled with 15N and 13C leads us to believe that the dissociation pathway most likely leads to a metal-cationized nitrile that is most prominent relative to the [a₃-1+Cat] ⁺ species in the order ßA < γAbu < εCap < 4AMBz. The product ion is also most prominent with Li+ and Na+ metal-cationized peptides and to a small extent for Ag⁺. Extensive isotope labeling was also used to investigate using CID and multiple-stage tandem mass spectrometry the elimination of H₂O from lithium-cationized model tripeptide methyl esters. The loss of H₂O is initiated by a nucleophilic attack from the N-terminal side upon an amide carbonyl carbon atom forming a five-membered ring intermediate and successive 1,2-elimination of H₂O. The same isotope-type experiments were used to investigate the b₃⁺ to a₃* dissociation reaction for the model peptide tetraglycine (GGGG). Isotope labeling indicated the reaction pathway involves the elimination of CO and NH₃, most notably the NH₃ is composed of two amide hydrogen atoms with the third coming from an a-carbon position. The loss of NH₃ also involves the loss of the nitrogen atom of the b₃⁺ oxazolinone ring. Density functional studies were performed to account for the unexpected scrambling of a-carbon hydrogens as well as the loss of CO and NH₃ through what is indicated to be a multistep reaction cascade involving various ion-molecule complexes. Placement of the alternative amino acids ßA, γAbu, εCap, or 4AMBz in varied positions of model peptides, most notably AAXG, AXAG and XAAG, we were able to directly affect the propensity to form specific bn⁺- and yn⁺-type product ions for protonated peptides. Substitution of the aforementioned residues at the varied positions within the model peptides confirmed our hypothesis that by forcing the formation of larger ring intermediates, certain ion formations would no longer be favorable. The proton transfer and intramolecular nucleophilic attack required to form the respective b∞n⁺- and yn⁺-type product ions was hindered as indicated by decreased ion intensity or lack of any presence of the desired ions. For the series AXAG and XAAG, the abundance of b-type ions indicates that either the protonated molecular ions are initially protonated at amide oxygen atoms or involve larger, whole peptide cyclic intermediates as was studied with the model peptide sequence FGGFL. 15NF labeling within FGGFL in the final study was used to validate the mechanism proposed in the previous a₃* study of tetraglycine for the formation of the a₄* ion from a₄⁺. A new rearrangement pathway is also presented for the a₄*-CO which transfers the C-terminal residue to the N-terminus.