Phd Degree / Doktora

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

Browse

Filters

2013 - 20184

Settings

Subject: search.filters.subject.Mass spectrometry

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
    A Computational Study on the Structures of Protonated Peptides
    (Izmir Institute of Technology, 2014) Karaca, Sıla; Elmaci Irmak, Nuran
    The reliable protein identification can be achieved by the knowledge of the structures and fragmentation mechanisms of gas-phase peptide fragment ions. Depending on the size and variety of amino acids in the peptide sequence, the probable structures of b-type fragments have been proposed as an acylium, a diketopiperazine, and an oxazolone structures. Recently, a macrocyclic structure has also been reported in the literature for larger b ions (b4 and greater). The macrocyclic structure is one of the problems for determining the correct sequence of peptides because original primary peptide structure is lost. Another problem is the unclear structure of the fragment ions depending on the peptide size and type. In such cases, the databases which are used with the MS/MS results will be insufficient to identify peptide/protein. In this thesis, the structures of peptide bn + ions having different size and type with a sequence of XAAAA, AAXAA and AAAAX (where A is Ala and X is Asn, Asp, Leu, Phe, Tyr or Cys) have been analyzed by using computational methods. The results showed that, the macrocyclic structure is more favorable than linear oxazolone structure for all b5 + ions studied in this work. The proton prefers to be on the oxygen atoms in the macrocycle while it likes to be on the nitrogen atom for the corresponding linear isomer. However, histidine containing b5 + ions do not obey this observation, for those, proton always is found on the nitrogen on the side chain of histidine. There is no significant position effect of amino acid residue for those b5 + ions, the energies of the most of the linear isomers with different position are very similar. Additionally, the proton affinity calculations have also been carried out to explain intensities of PX (where P is Pro and X is Ala, Phe, Asp, Trp or His) and AAAA fragment ions in the mass spectra. The results demonstrated that the mass spectrum consist of both PX and AAAA fragments were in competition with each other, this is explained by the proton affinity calculations.
  • Doctoral Thesis
    Investigation of Carotenoid Contents of Various Microalgae by Chromatographis/Spectroscopic Methods
    (Izmir Institute of Technology, 2013) Erdoğan, Ayşegül; Eroğlu, Ahmet Emin
    Microalgae are the most important energy sources among microorganisms. Carotenoids, as important pigments and antioxidants, are produced by microalgae and are used both for health purposes and as natural colorants. There has been considerable research for the development, identification and determination of new strains of organisms to produce a variety of carotenoids. New methods for the isolation of carotenoids should be developed also for analytical purposes. This study aimed the biosynthesis of carotenoids from microalgae, (Prochlorococcus sp., Scenedesmus protuberans and Nitzschia sp.) their identification and quantification. It is known that some types of microalgae can produce high amount of carotenoids under different stress conditions while some others can produce carotenoids only under stress. For this purpose, cultivation conditions were optimized for the production of new or high value of carotenoids in the selected microalgal strains. Freeze-dried microalgae were extracted using different organic solvents and their carotenoid contents were investigated by high performance liquid chromatography (HPLC) and other chromatographic techniques such as liquid chromatography-mass spectrometry (LC-MS); in addition to (UV-VIS) spectroscopy. In green microalgae lutein (2.54 mg/g for Prochlorococcus sp. and 2.45 mg/g for Scenedesmus protuberans) is the most abundant carotenoid. On the other hand, in brown microalga fucoxanthin (6.58 mg/g for Nitzschia sp.) is the highly accumulated carotenoid. Under stress conditions, many microalgae alter their biosynthetic pathways for the formation and accumulation of carotenoids. Therefore, the effect of different nitrogen sources, oxidative stress conditions and different light sources on lutein content in green microalgae and on fucoxanthin content in brown microalga were investigated.