Phd Degree / Doktora

Permanent URI for this collectionhttps://hdl.handle.net/11147/2869

Browse

Filters

2013 - 20184

Settings

Author: search.filters.author.Yalçın, Talat

Search Results

Now showing 1 - 4 of 4
  • Doctoral Thesis
    Proteomic Analyses of Biological Samples by Using Different Mass Spectrometric Strategies
    (Izmir Institute of Technology, 2018) Dinç, Melilke; Yalçın, Talat
    The advent of soft ionization techniques MALDI and ESI have opened the doors of mass spectrometry to biological samples. Particularly protein research exploited this opportunity to the utmost that qualitative, quantitative, structural and distributional analyses of proteins have become achievable. Comparison of all expressed proteins belonging to two or more states is defined as differential proteomics and commonly performed either separating the proteins on a gel or separating the peptides in the mixture within a column. In this study, both of these methods were applied to a parasite that causes to the infectious disease, Leishmaniasis. Consequences of the disease become severe when parasite is multiplied in viscera rather than skin. Occurrence of different clinical manifestations is attributed to the variety in species however some species can cause to both such as L.infantum and L.tropica. The purpose of this study was to investigate this duality in L.infantum. Despite originating from two different species, cutaneous leishmaniasis isolates obtained from ten different patients exhibited considerably similar protein profiling on the gels however isolates belonging to five visceral leishmaniasis patients were discriminated from them with regards to protein abundances. Additionally, several differential proteins between cutaneous leishmaniasis and visceral leishmaniasis samples were determined by gel-free approach. Apart from that, another mass spectrometric strategy for the abovementioned distributional analysis namely mass spectrometry imaging was included in the last section. Herein, a method incorporating the application of enzyme with matrix was developed for easy sample preparation to on-tissue digestion and promising results were obtained for a start.
  • Doctoral Thesis
    Proteomic Studies and Its Application To Biological Samples Using Mass Spectrometry
    (Izmir Institute of Technology, 2017) Güray, Melda Zeynep; Yalçın, Talat; Karakaya, Hüseyin Çağlar
    Mass spectrometry (MS) is a powerful analytical tool with its application in the field of biological sciences for identification of proteins, defining post-translational modifications, studying protein expression and protein interactions. This thesis presents MS analyses of proteins for defining modifications observed during sample preparation and identification of proteins isolated from clinical samples and microorganisms. The first part of the thesis includes proteomic analysis of antimony resistant L. tropica. The results clearly indicated that the generation of antimony resistance by parasites, either in host organism or in vitro, causes alteration of protein expression levels, and the mechanism of antimony resistance in host organism and in vitro conditions follow different strategies. In the second part of the study, proteomic analysis of Bence Jones proteins isolated from urine of multiple myeloma patients was performed. Gel electrophoresis and MS analysis revealed that the proteins from different patients with different nephrotoxicity have different tendencies to form multimeric structures and contained different type of light chain. In the third part, it was shown that precipitation of proteins in acetone causes +98 u mass artifacts on proteins when analyzed by MS. The parameters affecting the formation of modification was studied and it was revealed that this modification is dependent on solution pH, incubation time and temperature. In the last part, aspartic acid and glutamic acid containing synthetic peptides were shown to be methylated upon incubation in acidified methanol solution. MS analysis revealed that the reaction is dependent on temperature and time and is affected by the type of acid included in methanol solution. All in all, this thesis provides a comprehensive study of proteins by mass spectrometry for identification of proteins from different sources, as well as defining protein modifications observed as artifacts during sample handling in proteomic workflows.
  • Doctoral Thesis
    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.
  • Doctoral Thesis
    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.