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Mass Spectrometry-based Proteomics Experiments and Peptide Fragmentation Studies of Lysine and its Homologues
Platner, Charlotte B.
Platner, Charlotte B.
Abstract
This thesis presents mass spectrometry-based proteomics experiments and peptide fragmentation studies of lysine and its homologues. Proof of concept experiments were performed with a tryptic digest of bovine serum albumin (BSA) to optimize the proteomics protocols. Solvent gradients from the high performance liquid chromatography (HPLC) instrument were optimized first using a mixture of methanol and water and subsequently with acetonitrile and water. Data-dependent scans were run to isolate and fragment peptides to gain sequence information. Proteins were identified using the proteomics sequencing software SEQUEST. Peptide fragmentation studies of lysine and its homologues were performed by placing a lysine homologue in each of the three positions on a tripeptide with alanine in the other two positions to give tripeptides in the forms AXA, XAA, and AAX. Our results found a pattern of sequence scrambling in the AAX and AXA peptides to give fragments that appear to be from the XAA peptide. Sequence scrambling was not seen in the XAA peptides. This result suggests that the lysine homologues are most stable at the N-terminus which could be a result of their high gas phase proton affinities. Correlations between side chain length and fragmentation pattern were also seen.
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Thesis is part of Honors ETD pilot project, 2008-2013. Migrated from Dspace in 2016.
Date
2013-01-01
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Keywords
Mass Spectrometry, Proteomics, Peptide, Peptide Fragmentation, Lysine
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Department
Chemistry