The aim of presented diploma thesis was to characterize recent knowledge in the field of beer proteomics. The main part of this work was focused on modern instrumental methods of protein analysis, especially on protein identification by mass spectrometry. In experimental part proteins from selected beer samples were isolated, purified and separated by 2-D electrophoresis. The identification was performed by MALDI MS/MS and LC-MS/MS. Identified proteins were divided into 6 groups - serpines and protein Z, trypsine/-amylase inhibitors, yeast proteins, LTP protein, hordeins and other proteins. Proteomic analysis provided identification of proteins important for final analytical and sensory characteristics of the beer - for final beer quality and taste

<p>Clopidogrel is an antiplatelet substance that prevents blood coagulation in the arteries. It is an inactive pro drug that becomes activated after first-pass metabolism by the liver. The active metabolite of clopidogrel is 2-oxoclopidogrel, which is unstable therefore pharmacokinetic data is obtained by measuring the inactive metabolite clopidogrel acid in plasma. Clopidogrel is taken orally in tablet form. The aim of this project was to develop a LC-MS/MS method for quantification of clopidogrel and its metabolite in plasma.</p><p> </p><p>The method has been developed by optimizing the sample preparation. Different extraction procedures and extraction columns were tested, for example, by changing the extraction column from a C8 silica sorbent to Oasis HLB (a polymer sorbent). Different internal standards were evaluated as a result of discovering the signal suppression of the previous internal standard clopidogrel acid.  Flupentixol was found to be the best candidate.</p>

The main research of this thesis includes three sections. The purpose of first part is to develop a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for simultaneous determination of 8 macrolide antibiotics and lincosamides inside fish tissue, including erythromycin (ERM), oleandomycin (OLD), kitasamycin (KIT), tylosin (TYL), josamycin (JOS), spiramycin (SPM), tilmicosin (TIL), and lincomycin (LIN). Homogenized samples are first extracted with acetonitrile, dehydrated with sodium sulphate anhydrous, and then condensed. After the residue was redissolved in methanol and the extracts were partitioned with n-hexane to remove lipids, the sample is filterced and detected by LC/MS-MS using chromatography columns of Agilent HC-C18 (5£gm, 150 mm ¡Ñ4.6 mm). The mobile phase A was 5mM ammonium acetate containing 0.1% formic acid, while the mobile phase B was acetonitrile. The analysis of 8 macrolide antibiotics and lincosamides can be achieved within 10 minutes with electrospray ionization-tandem mass spectrometry in positive mode using multiple reaction monitoring (MRM) for simultaneous detection. The second part is to verify the method by regulation of European Union (EU) resolution scheme (2002/657/EC). In the case where the drug is set as allowed drug, the recovery rate under gradient addition according to MRL is between 93.64% to 106.67%, and the CV is between 0.27% to 7.17%. In the case where the drug is set as prohibited drug, the recovery rate under gradient addition according to MRPL is between 96.35%~104.88%, and the CV is between 6.77%~13.91%. As a result, the decision limit (CC£\) and the Detection capability (CC£]) of the 8 macrolide antibiotics and lincosamides is between 0.24 to 0.40£gg kg-1 and 0.33 to 0.49£gg kg-1. The last section is to evaluate the stability of drugs in fish body under domestic preservation and process methods on fish, including refrigeration at -20¢J and cold storage at 4 ¢J. The test is implemented by adding the drug into fish tissue according to MRL and detecting the antibiotics residue after regulated 40 days. Besides, the effect on activity of drug residue in fish body after boiling at 100 ¢J is compared. The results show that the residual amount of spiramycin, josamycin, tilmicosin, and lincomycin is below 35% while that of erythromycin, oleandomycin, kitasamycin, and tylosin will be below 20%. Therefore, the drugs including erythromycin, josamycin, tylosin, and lincomycin will stay stably in fish tissue if they are stored under -20 ¢J. However, it may affect human health if the fish contains such antibiotic residues is not boiled.

Hou-Chin stream, Love river, and Chien-Chen river, the three main rivers in Kaohsiung city, flow through the populous residential and industrial areas. A large portion of sewage from domestic and industrial sources are discharged into these rivers, then the Love river and Chien-Chen river pour into the harbor area. In order to understand the pollution of alkylphenol polyethoxylates in these areas, water and sediment samples in Hou-Chin stream, Love river, Chien-Chen river and harbor area in Kaohsiung city were collected and the contents of alkylphenol and corresponding polyethoxylates were analyzed in this study. LC/MS/MS was used as the analytical instrument which is relatively time-saving in comparison with other instruments. It is also more convenient due to the facts that no derivation or colorization are needed in sample pretreatment. The detection limit can reach to 0.03 ng/ml and recovery can be around 83.6~91.6%. It can analyze alkylphenols combinded with long ethoxylate chain with improved sensitivity and selectivity. In the four sampling areas, the concentration of NPs in water were between 7.4~241.8ng/ml, and OPs were between 0.66~64.2ng/ml. The most contaminated water samples were found at Chih-Ping Bridge on the mainstream of Love river and Pau-Chu-Kou Dam Station and Min-Tsu Bridge on the tributary of Love river where the concentrations of NPs were greater than 200ng/ml, OPs were greater than 30ng/ml. We found that the main pollution sources were from Lung-Hsin Bridge, Tzu-Yu Bridge, Lung -Hua Bridge, and Pau-Chu-Kou Dam Station. The pollution sources of the Chien-Chen river were mainly from Chung-An Bridge and Chen-Chuan Bridge. Concentration of NPs in upper sediments were between 633.1~2113.8ng/g, OPs were between 50.3~287.9ng/g. The highest concentration of NPs was at Ho-Ti Bridge on the mainstream of Love river, and the lowest concentration of NPs was at Chung-An Bridge on Chien-Chen river. The highest concentration of OPs was at Chen-Chuan Bridge in Chien-Chen river, and the lowest concentration of OPs was Min-Tsu Bridge on the tributary of Love river. The concentration of NPs in deeper sediments were between 523.9~1919.5ng/g, OPs were between 39.9~322.0ng/g. The highest concentration of NPs was at Chung-Hua Bridge on the tributary of Lover river, and the lowest concentration of NPs was at Chung-An Bridge on Chien-Chen river. The highest concentration of OPs was at Chi-Chin Fishing Port, and the lowest concentration of OPs was at Min-Tsu Bridge on the tributary of Love river. The salinity of water samples and the total organic carbon in sediment sample will influence the distribution coefficient of alkylphenol polyethoxylates with different length of ethoxylate chains, their distribution coefficients were between 0.48~2.67. In comparison with foreign studies, the concentrations of alkylphenol polyethoxylates of water and sediments amples in this study were between the highest and lowest values reported. However, the observed concentrations of alkylphenols in these study areas were higher then other rivers in Taiwan. These values were higher than the Probable No Effect Concentrations ( PNEC) of NP risk assessed by European Union. It can be concluded that the pollution of alkylphenol polyethoxylates of water and sediment is getting more serious in Hou-Chin stream, Love river, Chien-Chen river and harbor area in Kaohsiung city.

The plant peroxidases (EC1.11.17) exit as a large family of isozymes. These isozymes have more than 50% amino acid sequence differences. The function of Wasaba japonica peroxides plays the role as IAA oxidases. The kinetics result shows Wasabia japonica peroxidases displayed affinity (Km = 17.1 £gM) for IAA. The kinetics results in Wasabia japonica peroxidases display affinity (Km = 80.6 £gM) for syringaldazine. LC/MS/MS technique described the data that has proven to be a method for identification and characterization of proteins. The soluble proteins extracted form Wasabia japonica was purified by gel filtration chromatography and two-dimensional gel electrophoresis (2-DE). LC-MS/MS analyses of 2-DE gel spots and identify proteins structure based on the protein fragmentation characteristics. The Mascot Search Results showed that Wasabia japonica peroxidase has a significant similarity (10%) with Arabidopsis thaliana peroxidase.

Nitrofurans have been widely used either in waterbath or feed additives for the prevention and treatment of aquatic products. The European Union was able to assign a maximum residue limit and prohibited nitrofurans used to animals in 1995, because of the potential carcinogenic effects of their residues on human health. This study is focusing on the analytical method of four kinds of commonly used nitrofurans and corresponding residual metabolites by LC-MS/MS. The detection limits of furazolidone, furaltadone, nitrofurazone and nitrofurntoin were 6.11, 3.63, 4.52 and 6.20 £gg kg-1,respectively. The detection limits of AOZ, AMOZ, SC and AH were 0.23, 0.30, 0.36, 0.53 £gg kg-1, respectively. The lightness is the main factor to cause the decomposition of nitrofurans. It is not significant for temperature to depredate nitrofurans. The adsorbtion of metabolites by the plastic tube was in the extraction procedure. Equipments in glass are suggested to be used for the sample pretreatment and plastic meterials are averted to be exercised. About the comparation of determination of AOZ by ELISA and LC-MS/MS. The result demonstrated that the ELISA method might overestimate the residual AOZ content at low concentrations. The detection limit and recovery of the known addition were 0.05 £gg kg-1 and 108% for the LC-MS/MS method and 0.31 £gg kg-1 and 305% for the ELISA method, respectively. The amounts of residual nitrofurans and metabolites in muscle, liver, gill and skin tissue of tilapia which were treated in different conditions were compared. The depletion data of bathing treatment group obtained showed similar be haviors of furazolidone, furaltadone, nitrofurazone, nitrofurantoin in tilapia which the residual time was less than 24 hr. The amounts of residual nitrofurans appeared the highest concentration in gill and the lowest concentration in muscle. Bonded residues of metabolites can be detected for at least 4 weeks after administration in muscle, skin, liver and gill. The concentrations of residual bonded metabolites were higher than non-bonded metabolites in gill and muscle besides liver during depletion periods. After bathing medication, there were more residual nitrofurans and corresponding metabolites in sea water tilapia than fresh water group, because sea water fish survives in high osmotic condition to reduce their urination. Nitrofurans and metabolites were deconstructed by enzyme in gills, livers, intestines and muscles. Then tissues of fish accumulated nitrofurans and metabolites soon after medication. The maturity of fish is one of facters to effect different residual concentration during depletion periods. Liver is the main tissue to deconstruct nitrofurans and metabolites for the bathing medication and intestine is the major tissue to decompose antibiotics for the feeding medicaton. In this research, we built a completed way to determine nitrofurans and corresponding metatbolites. Comparation of fish in different conditions and different medicative ways were in this investigation. These results could be helpful for aquacultures and government institutions.

De novo peptide sequencing from MS/MS spectra has become of primary importance in proteomics. It provides essential information for studies of protein structure and function. With the availability of various MS/MS spectra, a lot of computational methods have been developed to infer peptide sequences from them. However, current de novo peptide sequencing methods still have limitations. Some major ones include a lack of suitable models reflecting MS/MS spectra, limited information extracted from MS/MS spectra, and the inefficient use of multiple spectra. This thesis addresses some of the limitations with a series of novel computational methods designed for various MS/MS spectra and their combinations. The main content of the thesis starts with a comprehensive review of recent developments in de novo peptide sequencing methods, followed by two novel methods for single spectrum sequencing problems, and then presents two paired spectra sequencing methods. The first chapter introduces relevant background information, objectives of the study, and the structure of the thesis. After that, a comprehensive review of de novo peptide sequencing methods is given. It summarizes recent developments of computational methods for various experimental spectra, compares and analyzes their advantages and disadvantages, and points out some future research directions. Having these potential research directions, the thesis next presents two novel methods designed for higher-energy collisional dissociation (HCD) spectra and electron capture dissociation (ECD) (or electron transfer dissociation (ETD)) spectra, respectively. These methods apply new spectrum graph models with multiple types of edges, integrate amino acid combination (AAC) information and peptide tags, and consider spectrum-specific information to suit different spectra. After that, multiple spectra sequencing problem is studied. A framework for de novo peptide sequencing of multiple spectra is given with applications to two different spectra pairs. One pair is spectrally complementary to each other, and the other is similar spectra with property differences. These methods include effective spectra merging criteria and parent mass correction steps, and modify the previously proposed graph models to fit the merged spectra. Experiments on several experimental MS/MS spectra datasets and datasets pairs show the advantages of the proposed methods in terms of peptide sequencing accuracy. Finally, conclusions and future work directions are given at the end of the thesis. To summarize the work in the thesis, a series of novel computational methods for de novo peptide sequencing are proposed. These methods target different types of MS/MS spectra and their combinations. Experiential results show the proposed methods are either better than competing methods that already exist, or fill gaps in the suite of currently available methods.

Stress conditions such as heat shock, UV, alkylating agents, and H2O2 have been shown to result in the modification of a variety of protein targets via the production of reactive electrophiles. These modifications can directly impact protein function or can alter posttranslational modifications, thus leading to a disruption of cellular regulatory processes. Recent studies have shown that stress-induced protein modifications can modulate posttranslational modification by the small ubiquitin related modifier (SUMO) family of proteins. Unlike ubiquitination, which primarily targets proteins for proteasomal degradation, sumoylation exerts a variety of effects including protein stabilization, subcellular localization, and the alteration of protein-protein interactions and transcriptional activity. To investigate the effects of alkylation and oxidative stress on sumoylation, HEK293 cells were treated with iodoacetamide, hydroquinone, benzoquinone, Texas Red C5 bromoacetamide, hydrogen peroxide, and 4-hydroxynonenal (HNE), a highly reactive product of lipid peroxidation associated with oxidative stress. Western blot analysis revealed that the agents tested resulted in concentration-dependent changes in the patterns of SUMO-1 and SUMO-2/3 protein conjugation. Localization studies using western blot analysis and confocal immunofluorescence microscopy demonstrated that SUMO-1 protein conjugates were located primarily in the nucleus, whereas SUMO-2/3 protein conjugates were more equally distributed between the nucleus and the cytoplasm. SUMO-associated proteins were harvested from vehicle- and HNE-treated non-transfected HEK293 cells using agarose conjugated anti-SUMO-1 antibodies or from HA-SUMO-1- and HA-SUMO-3-expressing HEK293 cells using immunoaffinity chromatography. Multidimensional liquid chromatography-tandem mass spectrometry analyses resulted in the identification of 54 HA-SUMO-1-associated proteins and 37 HA-SUMO-3-associated proteins in vehicle-treated cells and 21 HA-SUMO-1- and HA-SUMO-3-associated proteins in HNE treated cells. Additionally, 27 SUMO-1-associated proteins were identified in the HNE-treated non-transfected cells. The functional classes of proteins targeted included RNA binding and processing proteins, metabolic enzymes, cytoskeletal regulators, and chaperone proteins. HNE treatment resulted in a near complete redistribution of both SUMO-1 and SUMO-3 to different targets. There was a 15% overlap in SUMO-1 and SUMO-3 associated proteins in vehicle-treated cells and a 10% overlap in HNE-treated cells indicating that SUMO proteins target distinct protein groups. These results indicate that protein modifying reactive electrophiles can regulate protein functions through the indirect alteration of endogenous posttranslational modifications.

Conselho Nacional de Desenvolvimento Científico e Tecnológico / The use of pesticides always has been associated with the effective control of pests or invasive weeds to ensure an increase in the food production. However, the indiscriminate use of these substances has caused the degradation of water resources. In Brazil, the Ministry of Health through Ordinance 2914 defines several parameters of potability, among them, the maximum limits allowed for same pesticides. In this work it was developed and validated a method for the determination of residues of 70 pesticides in drinking water using (SPE) for sample preparation and determination by Gas and Liquid Chromatography coupled to tandem mass spectrometry, triple quadrupole analyzer (GC-(TQ)MS/MS and LC- (TQ)MS/MS). It was evaluated different sample volume, sorbents and solvent of elution. The best results were obtained using 100 mL sample acidified at pH 2.5, Oasis® SPE cartridge HLB 60 mg/3 mL and dichloromethane/methanol as eluent. Analytical curves were linear between 10 and 250 Sg L-1, with r2 values greater than 0.99 for all compounds. The values of method LOQ were 0.02 Sg L-1 for aldrin, dieldrin and chlordane and 0.5 Sg L-1 for the other compounds. To evaluate accuracy the blank samples ware fortified at 0.5, 1.5 and 4.0 Sg L- 1 and an extra level at 0.02 Sg L-1 for aldrin, dieldrin and chlordane. The method showed good precision, with RSD values below to 20% and good accuracy, with recoveries between 70 and 120%. Only the compounds methamidophos, aldicarb, benfuracarb, terbufos, benomyl and thiophanate methyl were not recovered adequately. The matrix effect was evaluated, showing upper 10% for the most compounds. In order to compensate this effect, analytical curves were obtained with standarts prepared in blank extracts of the matrix. The validated method was applied to 12 samples of drinking water of different characteristics (river, shed, well and treated water), and just one of the river samples presented residues of lambda-cyhalothrin. The results indicate that the proposed method is suitable for analysis of pesticides residues in drinking water, since all the validation parameters met the suggested limits and parameters for validation of chromatographic methods. / O uso de agrotóxicos sempre esteve associado à efetividade no controle de pragas ou plantas invasoras para aumentar a produção de alimentos. No entanto, o uso indiscriminado dessas substâncias vem causando a degradação dos recursos hídricos. No Brasil, o Ministério da Saúde através da Portaria 2914 define diversos parâmetros de potabilidade, entre eles, os limites máximos permitidos para alguns agrotóxicos. No presente trabalho foi desenvolvido e validado um método para a determinação de resíduos de 70 agrotóxicos em água potável, utilizando Extração em Fase Sólida (SPE) para o preparo de amostra e determinação por Cromatografia Gasosa e Líquida, acopladas à Espectrometria de Massas sequencial, com analisador triplo quadrupolo (GC-(TQ)MS/MS e LC- (TQ)MS/MS). Foram avaliados diferentes volumes de amostra, sorventes e solventes de eluição. Os melhores resultados foram obtidos com 100 mL de amostra acidificada em pH 2,5, cartucho SPE Oasis® HLB 60 mg/3 mL e diclorometano/metanol como eluente. As curvas analíticas apresentaram linearidade entre 10 e 250 Sg L-1, com valores de r2 maiores que 0,99 para todos os compostos. Os valores de LOQ do método foram 0,02 Sg L-1 para aldrin, dieldrin e clordano e de 0,5 Sg L-1 para os demais compostos. Para avaliação da exatidão as amostras branco foram fortificadas em 0,5, 1,5 e 4,0 Sg L-1 e um nível extra em 0,02 Sg L-1 para os compostos aldrin, dieldrin e clordano. O método apresentou boa precisão, com valores de RSD inferiores a 20% e boa exatidão, com recuperações entre 70 e 120%. Apenas os compostos metamidofós, aldicarbe, benfuracarbe, terbufós, benomil e tiofanato metílico não foram recuperados de forma adequada. O efeito matriz foi avaliado, mostrando-se superior a 10% para a maioria dos compostos. A fim de compensar este efeito, utilizou-se curvas analíticas preparadas no extrato branco da matriz. O método validado foi aplicado em 12 amostras de água potável de diferentes características (rio, vertente, poço e água tratada), sendo que apenas uma das amostras de água de rio apresentou resíduos de lambda-cialotrina. Os resultados indicam que o método proposto é adequado à análise de resíduos de agrotóxicos em água potável, visto que todos os parâmetros de validação atenderam os limites e parâmetros sugeridos para validação de métodos cromatográficos.

A highly sensitive and rapid method for the analysis of isradipine in human plasma using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) was developed. The procedure involves a simple liquid-liquid extraction of isradipine and amlodipine (IS, internal standard) with methyl-t-butyl ether after alkaline treatment and separation by RP-HPLC. Detection was performed by positive ion electrospray ionization (ESI) in multiple reaction monitoring (MRM) mode, monitoring the transitions m/z 372.1 → m/z 312.2 and m/z 408.8 → m/z 237.9, for quantification of isradipine and IS, respectively. The standard calibration curves showed good linearity within the range of 10 to 5000 pg/mL (r2 ≥ 0.9998). The lower limit of quantitation (LLOQ) was 10 pg/mL. The retention times of isradipine (0.81 min) and IS (0.65 min) suggested the potential for high throughput of the proposed method. In addition, no significant metabolic compounds were found to interfere with the analysis. This method offered good precision and accuracy and was successfully applied for the pharmacokinetic and bioequivalence studies of 5 mg of sustained-release isradipine in 24 healthy Korean volunteers.