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Scoring Processing System for Protein Identification in Tandem Mass Spectrometry
Valla, Martin ; Svobodová-Vařeková, Radka (referee) ; Provazník, Ivo (advisor)
The goal of my diploma thesis was finding a suitable method for unifying score values from various protein identification search tools in MS/MS mass spectrometry into one single score value. Data coming from the output of mass spectrometer are processed in two independent search tools Mascot and X!Tandem. These were selected especially for their wide usage in proteomic labs. Both results are evaluated through newly designed function and unified by single valued score clearly identifying found proteins. Newly designed scoring value is called Matascore and function producing this score was implemented in MATLAB. Function and its results were successfully tested by real data available in public databases on the Internet.
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The Usage of Separation Methods for Research of Biologically Active Substances in Waters
Vydrová, Lucie ; Friedl, Zdeněk (referee) ; Opatřilová, Radka (referee) ; Chýlková,, Jaromíra (referee) ; Vávrová, Milada (advisor)
Pharmaceuticals are biological active compounds with different functional groups, physico-chemical and biological properties. These chemical compounds are called as “new contaminants” which cumulate in various environmental components. These contaminants input to environment from industrial processes, hospitals and health care institutions or household sources and these pollutants can to negatively interact with environmental components. Pharmaceuticals are separated according to structure and their effects to live organisms. On the basis of drug consumption in Czech Republic the non-steroidal anti-inflammatory drugs are the most using pharmaceuticals, because these drugs can be obtain without prescriptions. The choosing analgesics for study were monitored in waste water from waste waters treatment plant (WWTP Brno – Modřice) and in surface water from two sampling sites of river Kretinka. Pharmaceuticals were monitored in surface waters in Czech Republic, in Scotland (river Thurso) and in Taiwan (river Erren, Agongdian, Yanshuei and canal of Tainan) Solid phase extraction (SPE) is used for extraction of study pharmaceutical from water system. The high performance liquid chromatography (HPLC) with diode array detection or mass spectrometry was used for determination of drugs in surface waters from Czech Republic. The water samples from Scotland and Taiwan were analysed and the high performance liquid chromatography with mass spectrometry (HPLC/MS) was used for determination of pharmaceuticals. The method of HPLC/MS enables the determination of study compounds in the very low range of concentrations (ng ? l-1). All monitored pharmaceuticals were identified and quantified in water samples from river Kretinka in Czech Republic, river Thurso (Scotland) and rivers Erren, Agongdian, Yanshuei and canal of Tainan in Taiwan and the obtained data were compared.
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The Usage of Separation Methods for Research of Biologically Active Substances in Waters
Vydrová, Lucie ; Friedl, Zdeněk (referee) ; Opatřilová, Radka (referee) ; Chýlková,, Jaromíra (referee) ; Vávrová, Milada (advisor)
Pharmaceuticals are biological active compounds with different functional groups, physico-chemical and biological properties. These chemical compounds are called as “new contaminants” which cumulate in various environmental components. These contaminants input to environment from industrial processes, hospitals and health care institutions or household sources and these pollutants can to negatively interact with environmental components. Pharmaceuticals are separated according to structure and their effects to live organisms. On the basis of drug consumption in Czech Republic the non-steroidal anti-inflammatory drugs are the most using pharmaceuticals, because these drugs can be obtain without prescriptions. The choosing analgesics for study were monitored in waste water from waste waters treatment plant (WWTP Brno – Modřice) and in surface water from two sampling sites of river Kretinka. Pharmaceuticals were monitored in surface waters in Czech Republic, in Scotland (river Thurso) and in Taiwan (river Erren, Agongdian, Yanshuei and canal of Tainan) Solid phase extraction (SPE) is used for extraction of study pharmaceutical from water system. The high performance liquid chromatography (HPLC) with diode array detection or mass spectrometry was used for determination of drugs in surface waters from Czech Republic. The water samples from Scotland and Taiwan were analysed and the high performance liquid chromatography with mass spectrometry (HPLC/MS) was used for determination of pharmaceuticals. The method of HPLC/MS enables the determination of study compounds in the very low range of concentrations (ng ? l-1). All monitored pharmaceuticals were identified and quantified in water samples from river Kretinka in Czech Republic, river Thurso (Scotland) and rivers Erren, Agongdian, Yanshuei and canal of Tainan in Taiwan and the obtained data were compared.
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Scoring Processing System for Protein Identification in Tandem Mass Spectrometry
Valla, Martin ; Svobodová-Vařeková, Radka (referee) ; Provazník, Ivo (advisor)
The goal of my diploma thesis was finding a suitable method for unifying score values from various protein identification search tools in MS/MS mass spectrometry into one single score value. Data coming from the output of mass spectrometer are processed in two independent search tools Mascot and X!Tandem. These were selected especially for their wide usage in proteomic labs. Both results are evaluated through newly designed function and unified by single valued score clearly identifying found proteins. Newly designed scoring value is called Matascore and function producing this score was implemented in MATLAB. Function and its results were successfully tested by real data available in public databases on the Internet.
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