Date Thesis Awarded


Access Type

Honors Thesis -- Access Restricted On-Campus Only

Degree Name

Bachelors of Science (BS)




John C. Poutsma

Committee Members

Randolph A. Coleman

Douglas D. Young

Joel S. Levine


The fragmentation patterns of lysine and lysine-analog containing tetrapeptides were analyzed in this study using collision induced dissociation (CID) in an ESI-ion trap mass spectrometer. Understanding the fragmentation mechanisms of lysine-containing peptides is integral to improving bottom-up proteomics techniques and peptide sequencing and searching algorithms. Lysine and its non-protein amino acid (NPAA) analogs ornithine, DABA, and DAPA have been shown to affect fragmentation patterns based on their basicities in dipeptides and tripeptides. Studies have shown the occurrence of sequence scrambling due to macrocyclization of pentapeptides during fragmentation, which can result in inaccurate database matching. This study of the twenty tetrapeptides AAAX, AAXA, AXAA, XAAA, and YAGX (X = Lys, Orn, DABA, or DAPA) looked for macrocyclization leading to sequence scrambling and analyzed the effects of positional variance and of differing basicities between lysine and its analogs on tetrapeptide fragmentation patterns.

Fragmentation studies confirmed the occurrence of the ornithine effect, where there is selective cleavage C-terminal to an ornithine residue within the tetrapeptides. Macrocyclic sequence scrambling was found to not occur in significant amounts for these tetrapeptides. The formation of bn + H2O ions was found to be most prevalent when the basic amino acid residues were at the C-terminus of the tetrapeptides. Positional variance and basicities of the lysine and its NPAA analogs affected the stabilities of the tetrapeptides, and influenced fragmentation patterns. Further investigations of lysine-containing peptides are necessary to better understand the fragmentation mechanisms at work and improve the robustness of proteomics experiments using mass spectrometry.

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