Date Thesis Awarded


Access Type

Honors Thesis -- Open Access

Degree Name

Bachelors of Science (BS)




John C. Poutsma

Committee Members

Nathanael Kidwell

Stephen Trefethen


Peptide fragmentation plays a crucial role in the analysis of proteins through mass spectrometry-based proteomics. Most proteomics experiments take place in the low-energy regime and are governed by the mobile proton model which predicts random cleavages along the peptide backbone; however, there sometimes arise circumstances where the mobile proton model fails causing sequencing algorithms to misidentify peptides. One such example is noted in the “proline effect” wherein proline-containing peptides preferentially fragment N-terminal. While it has been established that the “proline effect” is due to the rigidity and basicity of the proline N-terminus, a further understanding of the factors influencing the “proline effect” is desired. This paper aims to work towards an understanding of how adjacent amino acid residues aid in enhancing or hindering the “proline effect”.

To this effect, tandem mass spectrometry was used with the extended kinetic method to evaluate the proton affinities of the ProXxx dipeptides. ProArg and ProLys were unable to be quantified, but the remaining dipeptides ranged in proton affinity from 969.2 ± 13 kJ/mol to 1010.8 ± 17 kJ/mol for ProGly and ProGlu respectively. Additional computational work was performed using DFT with the B3LYP basis set to identify proton affinities for each dipeptide, as well as provide structurally resolved information. There is general agreement between the computational and experimental results. Further work is still required to form a more complete understanding of the “proline effect”.