GCRIS

Now showing 1 - 2 of 2

Gas-Phase Fragmentation Mechanisms of Protonated Peptides Via Tandem Mass Spectrometry
(Izmir Institute of Technology, 2013) Taşoğlu, Çağdaş; Yalçın, Talat
Protein identification based on enzymatic digestion of proteins and tandem mass spectrometric (MS/MS) analysis of peptide fragments has become a more popular method than classical approaches like Edman degradation. However, today’s protein sequencing tools have been constructed on a limited basis of peptide fragmentation chemistry such that some peptides can fragment in unusual ways that may not be predicted by the current bioinformatics software. Thus, erroneous assignments can be done in protein identification, which can lead to vital problems. Herein, it was aimed to reveal the rich chemistry lying behind the gas-phase fragmentation of peptides containing specific residues using MS/MS and collision induced dissociation (CID) analysis. As a result, the implementation of more detailed peptide fragmentation mechanisms into bioinformatics algorithms will no doubt help to improve database search tools. Results clearly indicate that b6 and b7 ions have higher tendency towards macrocyclization when compared to b5 ions. Besides it was observed that neighboring amino acid influences the selective opening of the macrocyclic structure and no preferential cleavage order can be specified depending on the amino acid residue. Next study showed that proline-containing peptides have high tendency to place the proline residue in the N-terminal position during the ring opening of macrocyclic structure. This is then followed by dipeptide elimination of proline with its adjacent C-terminal residue. Moreover, we demonstrated that sequence-scrambling exists for all histidine-containing peptides whatever the residue position and neighbor residue is. Additionally, we suggest that α-amino-ε-caprolactam formation at the side chain of lysine prevents macrocyclization reaction of b7 when K is positioned at the C-terminus. Finally, it was observed that macrocyclization reaction proceeds for peptides containing arginine when arginine gets closer to the C-terminus. Besides arginine was found to behave like lysine and forms ornithine when located at the C-terminus.
Studies of Gas-Phase Fragmentation Mechanisms of Peptide B Ions by Mass Spectrometry
(Izmir Institute of Technology, 2013) Atik, Ahmet Emin; Yalçın, Talat
This dissertation presents detailed studies of gas-phase fragmentation mechanism of peptide b ions under low-energy collision-induced dissociation (CID). Understanding the gas-phase structures and fragmentation mechanisms of the b ions is especially important for interpretation of peptide mass spectra. Recently, larger bn (n = 5, 6, 7...) ions are shown to form macrocyclic structures which can lead to erroneous in sequencing of unknown peptides. Therefore, in the first part of thesis, the effect of acidic amino acid residues (glutamic or aspartic acid) on the formation of macrocyclic structure is probed using various model hepta- and octapeptides. The results indicate that neither the presence nor the positions of acidic residues in peptides prevents macrocyclization of b ions. In addition, the dependence of preferential cleavage of acidic residues on applied collision energy is investigated for macrocyclic b ions. In the second part, the effect of ε-amine group of lysine residue is examined for the macrocyclization of b ions even if the N-terminal of the peptide is acetylated. The obtained results reveal that the macrocyclization is accomplished between ε-amine group of lysine and the oxazolone structure in the N-terminal acetylated peptide. Moreover, the lysine position is important parameter for the macrocyclization of b ions for N-terminal acetylated peptide. In the third and fourth parts of the thesis, the novel rearranged fragment ions are detected in the CID mass spectra of b ion series of acetylated lysine and side chain hydroxyl group containing model peptides, respectively. The gas-phase structures and fragmentation mechanisms of these novel fragment ions are investigated via multi-stage tandem mass spectrometry (MS4) experiments. In conclusions, the results presented in this dissertation can be used to elucidate the correct and reliable peptide sequences, and this improve protein identification strategies which is required for high-throughput proteomic studies.

Phd Degree / Doktora

Browse

Filters

Settings

Sort By

Results per page

Search Results