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RISS 인기검색어
- 검색키워드
- 저자 : ( Ozan Kaplan ) (검색결과 4 건)
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Evaluation of Recent Data Processing Strategies on Q-TOF LC/MS Based Untargeted Metabolomics
( Ozan Kaplan ),( Mustafa Çelebier ) 한국질량분석학회 2020 Mass spectrometry letters Vol.11 No.1
In this study, some of the recently reported data processing strategies were evaluated and modified based on their capabilities and a brief workflow for data mining was redefined for Q-TOF LC-MS based untargeted metabolomics. Commercial pooled human plasma samples were used for this purpose. An ultrafiltration procedure was applied on sample preparation. Sample set was analyzed through Q-TOF LC/MS. A C18 column (Agilent Zorbax 1.8 μM, 50 × 2.1 mm) was used for chromatographic separation. Raw chromatograms were processed using XCMS - R programming language edition and Isotopologue Parameter Optimization (IPO) was used to optimize XCMS parameters. The raw XCMS table was processed using MS Excel to find reliable and reproducible peaks. Totally 1650 reliable and reproducible potential metabolite peaks were found based on the data processing procedures given in this paper. The redefined dataset was upload into MetaboAnalyst platform and the identified metabolites were matched with 86 metabolic pathways. Thus, two list were obtained and presented in this study as supplement files. The first list is to present the retention times and m/z values of detected metabolite peaks. The second list is the metabolic pathways related with the identified metabolites. The briefly described data processing strategies and dataset presented in this study could be beneficial for the researchers working on untargeted metabolomics for processing their data and validating their results.
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Comparison of Cell Lysis Techniques via Q-TOF LC/MS
Kaplan, Ozan,Oncul, Selin,Ercan, Ayse,Celebier, Mustafa Korean Society for Mass Spectrometry 2020 Mass spectrometry letters Vol.11 No.2
Untargeted metabolomics is a useful tool for drug development focusing on novel chemotherapeutic and chemopreventative agents against cancer cells. In recent years, quadrupole time of flight liquid chromatography-mass spectrometry (Q-TOF LC/MS)-based untargeted metabolomic approaches have gained importance to evaluate the effect of these agents at the molecular level. The researchers working on cell culture studies still do not apply standardized methodologies on sample preparation for untargeted metabolomics approaches. In this study, the rough and wet lysis techniques performed on MCF-7 breast cancer cells were compared with each other via the Q-TOF LC/MS-based metabolomic approach. The C18 and hydrophilic interaction liquid chromatography (HILIC) columns were used for the separation of the metabolites in MCF-7 cell lysates. 505 peaks were detected through the HILIC column and 551 peaks were found through the C18 column for the wet lysis technique. This situation supported by the base peak chromatograms showed that the wet lysis technique allowed us to extract higher number of non-polar metabolites. Almost equal number of metabolites was found for the C18 and HILIC columns (697 peaks for the HILIC column and 695 peaks for the C18 column) when the rough lysis technique was used. However, the intensities of polar metabolites were higher for the rough lysis technique on base peak chromatograms for both the HILIC and C18 columns. Although cell lysis technique, which is the first step in the sample preparation for cell culture studies, does not cause dramatic differences in the number of the detected metabolite peaks, it affects the polar and non-polar metabolite ratio significantly. Therefore, it must be considered carefully especially for in vitro drug development studies.
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Ozan Kaplan,Nagehan Saltan,Arzu Köse,Yavuz Bülent Köse,Mustafa Çelebier 사단법인 한국질량분석학회 2023 Mass spectrometry letters Vol.14 No.2
Carthamus tinctorius L. (known as safflower) is a valuable oil plant whose importance is increasing rapidly in the world due to its high adaptation to arid regions. The seeds of this unique plant are especially used in edible oil, soap, paint, varnish and lacquer production. Its flowers are used in vegetable dye production and medicinal purposes beside its features as a coloring and flavoring in food. After the oil is removed, the remaining pulp and plant parts are used as animal feed, and dry straw residues are used as fuel. Beside all these features, its usage as a herbal medicinal plants for various diseases has gained importance on recent years. In this study, it was designed a plant metabolomic approach which transfers all the recent data processing strategies of untargeted metabolomics in clinical applications to the present study. Q-TOF LC/MS-based analysis of the extracts (70% ethanol, hexane, and chloroform) for both seed and flowers was performed using a C18 column (Agilent Zorbax 1.8 µM, 100 × 2.1 mm). Differences were observed in seed and fruit extracts and these differences were visualized using principal component analysis (PCA) plots. The total number and intersections of the peaks in the extracts were visualized using peak count comparison graph. Based on the experimental results, the number of the detected peaks for seeds was higher than the ones for the flowers for all solvent systems to extract the samples.
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Berk, Veli,Kaplan, Mehmet Ali,Tonyali, Onder,Buyukberber, Suleyman,Balakan, Ozan,Ozkan, Metin,Demirci, Umut,Ozturk, Turkan,Bilici, Ahmet,Tastekin, Didem,Ozdemir, Nuriye,Unal, Olcun Umit,Oflazoglu, Utk Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.12
Background: Inoperable and metastatic hepatocellular carcinoma (HCC) is associated with a poor prognosis and low chemotherapeutic efficiency. Sorafenib is an oral multi-kinase inhibitor exerting its effects via the RAF/MEK/ERK pathway, vascular endothelial growth factor receptor (VEGFR) and platelet derived growth factor receptor beta (PDGFR-${\beta}$) tyrosine kinases. Randomized studies have shown a significant contribution of sorafenib to life expectancy and quality of life of cancer patients. The aim of the present study is to evaluate the efficacy and side effects of sorafenib therapy in Turkey. Materials and Methods: Data for 103 patients (82 males, 21 females) receiving sorafenib therapy in 13 centers from February 2008 to December 2012 were evaluated. Median age was 61 years and median ECOG performance status was 1 (range: 0-2). 60 patients (58%) had hepatitis B, 15 patients (15%) had hepatitis C infection and 12 patients (12%) had a history of alcohol consumption. All of the patients had Child scores meeting the utilization permit of the drug in our country (Child A). Results: A total of 571 cycles of sorafenib therapy were administered with a median of four per patient. Among the evaluable cases, there was partial response in 15 (15%), stable disease in 52 (50%), and progressive disease in 36 (35%). Median progression-free survival was 18 weeks and median overall survival was 48 weeks. The dose was reduced only in 6 patients and discontinued in 2 patients due to grade 3-4 toxicity, 18 patients (17%) suffering hand-foot syndrome, 7 (7%) diarrhea, and 2 (2%) vomiting. Conclusions: This retrospective study demonstrated better efficacy of sorafenib therapy in patients with advanced HCC compared to the literature while progression-free survival and overall survival findings were comparable. The side effect rates indicate that the drug was tolerated well. In conclusion, among the available treatment options, sorafenib is an efficient and tolerable agent in patients with inoperable or metastatic HCC.
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