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<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>

La découverte, la caractérisation et le dosage de biomarqueurs ont permis douvrir de nouveaux horizons tant en thérapeutique que dans létablissement dune médecine personnalisée. Dans un contexte danalyse en milieu complexe, lapplication de techniques fiables, sensibles, exactes et de haute résolution est de rigueur. Dans ce but, le couplage de la spectrométrie de masse à une technique séparative telle que la chromatographie liquide (LC-MS) ou lélectrophorèse capillaire (CE-MS) offre des potentialités intéressantes. Une méthode de dosage de la cysdopa, un marqueur du mélanome, dans le plasma par LC-MS a été mise au point. Une étape préliminaire dextraction en phase solide sur un support hybride alliant des interactions de type hydrophobe, hydrophile et échangeurs de cations a conduit à lobtention dexcellents taux de récupération. Les conditions chromatographiques assurant la séparation de la cysdopa des composés endogènes susceptibles dinterférer et les paramètres de la détection par spectrométrie de masse en tandem ont été optimisés. La présence déventuels effets de la matrice a été investiguée en détails. Une étude de la stabilité de la cysdopa dans les différentes conditions opératoires a été réalisée répondant ainsi aux normes préscrites par la FDA. Ensuite, une validation complète de la méthode en milieu plasmatique selon lapproche faisant appel aux profils dexactitude sur une gamme de concentration allant de 1,6 à 200 ng/ml a été menée avec succès démontrant ladéquation de la méthode. Enfin, une étude pilote ainsi quune validation en cours détude ont permis de tester cette méthode de dosage. La seconde technique mise en oeuvre consiste en lapplication du couplage CE-MS à lanalyse de lhepcidine, un petit peptide régulant le métabolisme du fer. Les conditions électrophorétiques assurant la séparation de ce peptide des constituants dun mélange type ont été déterminées. Le traitement de la paroi interne du capillaire et laddition dune cyclodextrine nont pas permis dans la présente application daméliorer la sélectivité et lefficacité des pics. Lutilisation dun électrolyte de haute force ionique associé à laddition dun modificateur organique a par contre offert les meilleures performances. Une approche multivariée en deux temps (criblage puis modélisation) a été appliquée pour loptimisation des paramètres CE-MS. Les effets principaux du voltage du capillaire et de la pression du gaz nébulisant se sont révélés être significatifs tout comme leffet quadratique de ce dernier ainsi que les interactions entre la concentration en électrolyte et le voltage du capillaire dune part et la pression du gaz nébulisant dautre part. Finalement, la sensibilité en terme de rapport signal/bruit a été comparée en CE-UV et CE-MS établissant les potentialités du couplage CE-MS pour lanalyse de peptides. Discovery, caracterization and determination of biomarkers provide new perspectives in therapeutics and establishment of personnal medecine. Analysis in complex matrix requires reliable, sensitive, accurate and high resolution techniques. To achieve this, coupling of mass spectrometry with separative techniques such as liquid chromatography (LC-MS) or capillary electrophoresis (CE-MS) offer interesting potentialities. A method for the determination of cysdopa, a melanoma biomarker, in human plasma was developed using LC-MS. Solid phase extraction in mixed mode, combining hydrophobic, hydrophilic and cation exchange interactions led to excellent recovery. The chromatographic conditions ensuring separation of cysdopa from potential by interfering endogenous compounds and tandem mass spectrometry detection parameters were optimised. The presence of matrix effect was investigated in detail. A full stability study was then performed according to FDA requirements. Finally, a complete validation of the method in plasma following the approach of accuracy profiles over a concentration range from 1,6 to 200 ng/ml was successfully performed, demonstrating adequacy of the developed method. A pilot study and an in-study validation were finally perfomed to test this assay method. The second implemented technique consists in the application of CE-MS coupling to hepcidin analysis, a small peptide regulating iron metabolism. Electrophoretic conditions ensuring separation of hepcidin from model peptides have been determined. Resolution and/or efficiency were not improved by using coated capillaries or by adding a cyclodextrin. A high ionic strength electrolyte associated to the addition of an organic modifier provided the best performance. A multivariate approach (screening and modeling) was applied to the optimisation of CE-MS parameters. The principal effet of capillary voltage and nebulizing gas pressure were significant as well as the quadratic effet of the last parameter and the interactions of electrolyte concentration and, for one part, capillary voltage and, for another part, nebulizing gas pressure. Finally, sensitivity with respect to signal/noise ratio was compared between CE-UV and CE-MS, assessing potentialities of CE-MS for peptide analysis.

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.

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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.