In this study, we investigated the fragmentation spectra of dipeptides containing lysine or ornithine and pentapeptides containing lysine, ornithine, Daba, or Dapa. Lysine is one of the 20 protein amino acids whereas ornithine, Daba, and Dapa are non-protein amino acids that resemble lysine. Each of these homologs has an amine side chain that is consecutively shorter than lysine\u27s, making their differing effects on fragmentation interesting to observe. By looking at the fragments created by each peptide upon collision-induced dissociation (CID) in an ESI ion trap mass spectrometer, we could compare the fragments between the peptides and interpret those differences as a result of structural differences. Performing CID on lysine containing peptides, produced many more significant fragments than ornithine, and to similar extent, Daba, and Dapa containing peptides. Ornithine-containing pentapeptides consistently gave a dominant b fragment in which ornithine was the C-terminal of that fragment. Dapa and Daba-containing pentapeptides seemed to favor the loss of water from the parent in fragmentation, yet they also produced peaks that were in good agreements with the lysine containing pentapeptides. The amount of peaks for each amino acid did not follow a set pattern from lysine to Dapa, as the Daba-containing did at times contain more significant peaks than the ornithine. These comparisons are only a preliminary investigation into better understanding the mechanism with which amine side chains can affect fragmentation of the peptide backbone during CID
