Gas-Phase Hydrogen-Deuterium Exchange and Fragmentation Studies of Tetrapeptides Containing Lysine and Its Homologs

Mass spectrometry- based proteomics is becoming a common method in proteomics. Peptides can be identified by automated database searches, and relative protein abundances can be obtained from the mass spectra. Understanding the fragmentation mechanisms may refine and provide additional rules that will increase the confidence in automated primary sequencing of peptides and eventually relate the information on gas-phase fragmentation patterns and energetics of dissociation to the gas-phase conformations of intact and fragment peptides and proteins; this will improve protein identification and profiling. Improvements are necessary for continual use of these quantitative approaches and bottom-up proteomics. Lysine and its homologs, ornithine, DABA, and DAPA have been shown to affect fragmentation patterns based on their basicities. Lysine-analog containing tetrapeptides and their fragments were analyzed using hydrogen deuterium exchange (HDX) in a modified ESI-ion trap mass spectrometer. Fragments in this study were obtained using collision induced dissociation (CID). This study involved systematically varying the position of lysine and its homologs in the tetrapeptides, XAAA, AXAA, AAXA, and AAAX, where X is lysine or its homolog and A is alanine. Positional variance and systematic difference in side chain length affects the hydrogen deuterium exchange reaction. Results suggest that tetrapeptides containg short, basic side chains like Dapa, possess weak intramolecular bonds. Longer side residues have stronger intramolecular boning schemes in tetrapepetides. Results suggest that bn+ ions are either diketopiperazine or lactam structures. In addition, HDX was used to indirectlyprobe the structures of XA+, AX+, AAX+ bn+ ions. Further investigations using IRMPD spectroscopy is necessary to identify b ion structures