BACKGROUND:The widespread utilization of organic compounds in modern society and their dispersion through wastewater have resulted in extensive contamination of source and drinking waters. The vast majority of these compounds are not regulated in wastewater outfalls or in drinking water while trace amounts of certain compounds can impact aquatic wildlife. Hence it is prudent to monitor these contaminants in water sources until sufficient toxicological data relevant to humans becomes available. A method was developed for the analysis of 36 trace organic contaminants (TOrCs) including pharmaceuticals, pesticides, steroid hormones (androgens, progestins, and glucocorticoids), personal care products and polyfluorinated compounds (PFCs) using a single solid phase extraction (SPE) technique with ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS). The method was applied to a variety of water matrices to demonstrate method performance and reliability.RESULTS:UHPLC-MS/MS in both positive and negative electrospray ionization (ESI) modes was employed to achieve optimum sensitivity while reducing sample analysis time (<20min) compared with previously published methods. The detection limits for most compounds was lower than 1.0 picogram on the column while reporting limits in water ranged from 0.1 to 15ng/L based on the extraction of a 1L sample and concentration to 1mL. Recoveries in ultrapure water for most compounds were between 90-110%, while recoveries in surface water and wastewater were in the range of 39-121% and 38-141% respectively. The analytical method was successfully applied to analyze samples across several different water matrices including wastewater, groundwater, surface water and drinking water at different stages of the treatment. Among several compounds detected in wastewater, sucralose and TCPP showed the highest concentrations.CONCLUSION:The proposed method is sensitive, rapid and robust / hence it can be used to analyze a large variety of trace organic compounds in different water matrixes.

Formamide is a solvent of great interest to prebiotic chemists because it is liquid over a wide range, it is less volatile than either water or HCN, and it possesses a versatile reactivity. When formamide is heated in the presence of minerals or inorganic catalysts, a variety of products including purine nucleobases are generated. Irradiation of formamide reaction solutions with ultraviolet light increases the yield and diversity of products, and eliminates the need for a mineral catalyst. We have also performed formamide reactions in the presence of pyrite, a mineral which is likely to have been available on the primordial Earth, under a variety of atmospheric conditions. Our results indicate the greatest yield and diversity of products result from the combination of a pyrite mineral catalyst, heat, UV irradiation, and a carbon dioxide atmosphere. Purine nucleobases are simple to synthesize in model reactions and they stack well in aqueous solution; it has been hypothesized that the first nucleic acids were composed of only purine bases, and that water-soluble, cationic, aromatic molecules with large stacking surfaces (“”molecular midwives””) may have aided the assembly of the earliest nucleic acid analogs. We have characterized the interactions of various intercalators with a standard DNA duplex as well as with an antiparallel homopurine DNA duplex and have determined that molecules which possess four or more rings and a curved shape interact selectively with all-purine DNA; such molecules can serve as models for putative prebiotic midwives.

<p>Disease-specific compounds (biomarkers) are analyzed in clinical laboratories to assist with diagnosing diseases. This thesis describes development and validation of liquid chromatography tandem mass spectrometry (LC-MS/MS) based tests for diagnosing a diverse group of endocrine and metabolic diseases. The analytical methods used on-line and off-line sample extraction and analytical derivatization as means of enhancing the analytical sensitivity, specificity and clinical utility. All developed methods were extensively validated and reference intervals for the biomarker concentrations were established in blood samples of healthy adults and children. Advantages of the LC-MS/MS as an analytical technique include possibility of simultaneous measurement of multiple analytes and ability of confirming their identity. In this thesis we proposed and evaluated approaches for the assessment of the specificity of analysis in the methods that use tandem mass spectrometry detection. To enhance throughput of the LC-MS/MS tests for the biomarkers that have endogenous or exogenous isomers an approach was developed for quantitation of isomers from unresolved chromatographic peaks. Using methods developed in this thesis we performed a study of the steroidogenesis in ovarian follicles of healthy women and women with polycystic ovary syndrome (PCOS). Obtained data on the steroid concentrations and associations between the steroid metabolites in the pathway would be helpful for better understanding of the ovarian pathophysiology. Potential biomarkers of PCOS were identified in the thesis; further studies will be necessary to confirm their clinical utility.</p>

Enzymes and biochemical mechanisms essential to survival are under extreme selective pressure and are highly conserved through evolutionary time. We applied this evolutionary concept to barnacle cement polymerization, a process critical to barnacle fitness that involves aggregation and cross-linking of proteins. The biochemical mechanisms of cement polymerization remain largely unknown. We hypothesized that this process is biochemically similar to blood clotting, a critical physiological response that is also based on aggregation and cross-linking of proteins. Like key elements of vertebrate and invertebrate blood clotting, barnacle cement polymerization was shown to involve proteolytic activation of enzymes and structural precursors, transglutaminase cross-linking and assembly of fibrous proteins. Proteolytic activation of structural proteins maximizes the potential for bonding interactions with other proteins and with the surface. Transglutaminase cross-linking reinforces cement integrity. Remarkably, epitopes and sequences homologous to bovine trypsin and human transglutaminase were identified in barnacle cement with tandem mass spectrometry and/or western blotting. Akin to blood clotting, the peptides generated during proteolytic activation functioned as signal molecules, linking a molecular level event (protein aggregation) to a behavioral response (barnacle larval settlement). Our results draw attention to a highly conserved protein polymerization mechanism and shed light on a long-standing biochemical puzzle. We suggest that barnacle cement polymerization is a specialized form of wound healing. The polymerization mechanism common between barnacle cement and blood may be a theme for many marine animal glues. / Dissertation

La protéogénomique consiste à affiner l'annotation du génome d'organismes modèles pour lesquels des données protéomiques sont générées à haut-débit. Des erreurs d'annotation structurale ou fonctionnelle sont encore fréquentes. Innover dans les méthodologies permettant de lever ces ambiguïtés est essentiel. L'étude spécifique du N-terminome permet de vérifier expérimentalement l'identification du codon d'initiation de la traduction et de certifier les données obtenues. Pour cela, deux stratégies innovantes ont été développées basées sur : i) le marquage sélectif du N-terminal des protéines, ii) une digestion multienzymatique en parallèle, et ii) l'enrichissement spécifique des peptides N-terminaux marqués par chromatographies liquides successives ou immunocapture dirigée contre le groupement N-terminal ajouté. L'efficacité de ces méthodologies a été démontrée à partir du modèle bactérien Roseobacter denitrificans. Après enrichissement par chromatographie, 480 protéines ont été validées et 46 ré-annotées. Plusieurs sites d'initiation de la traduction ont été décelés et l'annotation par similarité a été remise en cause dans certains cas. Après immunocapture, 269 protéines ont été caractérisées dont 40% ont été identifiées spécifiquement après enrichissement. Trois gènes ont également été annotés pour la première fois. Les résultats complémentaires obtenus après analyse par spectrométrie de masse en tandem facilitent l'interprétation des données pour révéler les sites d'initiation réels de la synthèse des protéines et identifier de nouveaux produits d'expression des gènes. La ré-annotation peut devenir automatique et systématique pour améliorer les bases de données protéiques. / Proteogenomics is a recent field at the junction of genomics and proteomics which consists of refining the annotation of the genome of model organisms with the help of high-throughput proteomic data. Structural and functional errors are still frequent and have been reported on several occasions. Innovative methodologies to prevent such errors are essential. N-terminomics enables experimental validation of initiation codons and certification of the annotation data. With this objective in mind, two innovative strategies have been developed combining: i) selective N-terminal labeling of proteins, ii) multienzymatic digestion in parallel, and iii) specific enrichment of most N-terminal labeled peptides using either successive liquid chromatography steps or immunocapture directed towards the N-terminal label. Efficiency of these methodologies has been demonstrated using Roseobacter denitrificans as bacterial model organism. After enrichment with chromatography, 480 proteins were validated and 46 re-annotated. Several start sites for translation initiation were detected and homology driven annotation was challenged in some cases. After immunocapture, 269 proteins were characterized of which 40% were identified specifically after enrichment. Three novel genes were also annotated for the first time. Complementary results obtained after tandem mass spectrometry analysis allows easier data interpretation to reveal real start sites of translation initiation of proteins and to identify novel expressed products. In this way, the re-annotation process may become automatic and systematic to improve protein databases.

This dissertation thesis is focused on development and optimization of high- performance liquid chromatography (HPLC) and tandem mass spectrometry (LC-MS/MS) methods, and its utility for diagnosis of inherited metabolic diseases. The first thematic part describes a comprehensive laboratory approach to diagnostics of patients with hereditary xanthinuria by determination of specific markers and enzyme activity. For this purpose HPLC method with diode array detection for measurement of hypoxanthine, xanthine, allopurinol and oxypurinol in urine and plasma and HPLC method with fluorimetric detection for analysis of pterin and isoxanthopterin in plasma were employed. These methods were successfully applied in clinical practice to ascertain two patients with hereditary xanthinuria type I. The second thematic part aims at developing and clinical application of new LC-MS/MS method for simultaneous determination of total homocysteine (tHcy), methionine (Met) and cystathionine (Cysta) in dried blood spots (DBS) and plasma. The results demonstrated the clinical utility of this method for detection of patients with homocystinuria and possibility to distinguish between defects in the remethylation and transsulfuration pathways of homocysteine metabolism. Due to ease of DBS collection and sample transportation...

Recentemente, foi descrito um grupo de alterações no metabolismo da creatina denominado Síndromes de Deficiência de Creatina. Há três formas da doença geneticamente determinadas que cursam com deficiência de creatina, seja por comprometimento de sua síntese ou por defeito na proteína transportadora. O espectro de apresentação clínica dessa condição é inespecífico e inclui atraso ou estagnação do desenvolvimento neuromotor, hipotonia muscular, movimentos involuntários do tipo coreoatetose, retardo ou ausência do desenvolvimento da fala, retardo mental de grau variável, comportamento autista e epilepsia. Neste trabalho, foi desenvolvida e validada uma alternativa metodológica àquelas disponíveis na literatura, com a utilização de extração por troca catiônica forte e separação e detecção por cromatografia líquida de interação hidrofílica acoplada a espectrometria de massas em tandem em que foram exploradas as características químicas das moléculas de creatina e guanidinoacetato, metabólito intermediário da síntese de creatina. Os valores de referência para o método foram definidos pela sua aplicação a 150 amostras de urina e 197 amostras de soro de indivíduos de ambos os sexos e idades entre 0 e 16 anos. Foram também analisadas amostras de urina, soro e plasma de 54 pacientes com clínica compatível com a síndrome de deficiência de creatina sendo que 3 deles apresentaram perfil bioquímico característico de uma das formas dessa condição / Recently, a new group of inborn errors of metabolism, collectively named as creatine deficiency syndrome, was identified. Three genetically determined presentations are currently known, affecting both creatine synthesis and transport. Clinical presentation spectrum is non-specific and includes developmental delay, hypotonia, involuntary movements as choreoathetosis, delay or lack of speech acquisition, mental retardation of variable severity, autistic behavior, and epilepsy. Herein, we developed and validated an innovative method for determination of creatine and of its metabolic intermediate, guanidinoacetate, based on cation-exchange solid-phase extraction and hydrophilic interaction liquid chromatography coupled to tandem mass spectrometry. Reference values for the method were defined testing 150 urine and 197 serum samples in males and females with age ranging from 0 to 16 years. Urine and serum samples from 54 patients with some clinical features that might be attributable to creatine deficiency were also evaluated, and in three, biochemical profile characteristic of one of the disorders was detected

Ces travaux de thèse sont consacrés au développement de nouvelles méthodologies pour l’analyse structurale et quantitative de composés isomères ou isobares en mélange par spectrométrie de masse en tandem (MS/MS) ainsi que par la technique des ions survivants (SY). À l’aide de cette technique, nous avons développé une méthode de « purification collisionnelle en phase gaz » consistant à purifier un composé par fragmentation sélective du contaminant isomère ou isobare afin de permettre l’analyse structurale et quantitative du composé d’intérêt. Nous avons montré que cette approche peut être utilisée avec succès à la fois lors de l’étape d’excitation collisionnelle (CID) d’une expérience MS/MS, mais également lors du processus d’ionisation (in-source CID). Utilisant cette approche MS/MS sur une fenêtre de 15 m/z, nous avons ainsi pu quantifier, par la méthode de l’étalon interne, un peptide trypsique malgré la présence d’un contaminant isobare. L’optimisation des performances de quantification pour la technique SY a ensuite été étudiée sur des peptides isomères topologiques en mélange et comparée à l’analyse par microscopie infrarouge. Parmi les alcalins, alcalino-terreux et métaux de transition testés, nous avons obtenu les meilleurs résultats avec les adduits au césium. Des résultats comparables à la technique infrarouge ont confirmé la pertinence de notre approche avec de surcroît de meilleures performances analytiques, en particulier en terme de rapidité d’exécution, de sensibilité, d’erreur de prédiction et de limite de quantification. / This PhD work focused to the development of new methodologies for the structural and quantitative analysis of isomers or isobars compounds in mixture using tandem mass spectrometry (MS/MS) and the Survival Yield technique (SY).Using this technique, we have developed a method of « gas phase collisional purification » of purifying a compound by selective fragmentation of the isomeric or isobaric contaminant to allow the structural and quantitative analysis of the compound of interest. We have shown that this approach can be used successfully both during the collisional excitation step (CID) of a MS/MS experiment, but also during the ionization process (in-source CID). Using this MS/MS approach on an isolation window of 15 m/z, we were able to quantify, by the internal standard method, a tryptic peptide despite the presence of an isobaric contaminant.Optimization of quantification performances for the SY technique was then studied on topological isomeric peptides in mixture and compared with infrared microscopy analysis. Among the alkali, alkaline earth and transition metals tested, we obtained the best results with cesium adducts.Results comparable to the infrared technique confirmed the relevance of our approach with, moreover, better analytical performances, in particular in terms of speed of execution, sensitivity, prediction error and limit of quantification.

Le développement de nouveaux donneurs d’oxyde nitrique (NO) dans le traitement chronique des maladies cardiovasculaires nécessite l’étude de leur biodisponibilité après administration par voie orale. Les S-nitrosothiols (RSNOs) apparaissent d’intéressants candidats médicaments pour ce faire, et l’étude de leur perméabilité intestinale est une première étape indispensable. Il est nécessaire de disposer d’une méthodologie analytique suffisamment sensible et sélective, en particulier permettant de différencier entre la production endogène de NO, l’apport alimentaire en ions nitrites et nitrate et le médicament lui-même. Nos travaux de thèse ont consisté à utiliser le S-nitrosoglutathion (GSNO) comme modèle après son marquage par l’isotope stable 15 de l’azote (15N). La dérivation du 15NO libéré par deux méthodes conventionnelles (méthode de Griess conduisant à la formation d’un adduit azoïque ; réaction avec le 2,3-diaminonaphtalène (DAN) formant l’adduit 2,3-naphtotriazole (NAT)) et l’étude de la fragmentation en spectrométrie de masse tandem (MS/MS) des deux adduits correspondants ont mené à sélectionner la dérivation par le DAN comme étant la plus sensible. Une transition originale résultant de la fragmentation du NAT en mode Higher-energy Collisional Dissociation (HCD) au lieu du mode conventionnel Collisionally Induced Dissociation (CID) a été mise en évidence ; elle permet d’atteindre une limite de quantification de 5 nM (soit 20 fois plus basse que celle offerte par la fluorescence). La méthode LC-MS/MS a été validée et appliquée à l’étude de la perméabilité intestinale du GS15NO par deux modèles : l’un in vitro (monocouche de cellules épithéliales type Caco-2), l’autre ex vivo (intestin de rat isolé (ileum) dans une chambre de Ussing). Les valeurs de perméabilité apparente calculées à partir des concentrations des métabolites du GS15NO (ions nitrites, nitrates et RSNOs) le classent comme un médicament de perméabilité intermédiaire. En outre, des études sur les mécanismes de dénitrosation du GSNO ont été menées sur intestin isolé, démontrant en particulier le rôle d’enzymes telles que la γ-glutamyltransférase et la protein disulfide isomerase / The development of innovative nitric oxide (NO) donors for the chronic treatment of cardiovascular diseases implies their bioavailability studies after oral administration. S-nitrosothiols (RSNOs) look interesting drug candidates for this purpose and evaluating their intestinal permeability appears the first step to be realized. Thus, an analytical method offering high sensitivity is needed; moreover this method should be selective by differentiating between the endogenous production of NO, the intake of nitrite and nitrate ions via the diet, and the drug itself. Our work consisted in using S-nitrosoglutathione (GSNO) labeled with the stable nitrogen isotope 15 (15N) as a model. Released 15NO species were derivatized by two conventional methods: Griess method leading to the formation of an azo adduct; reaction with 2,3-diaminonaphthalene (DAN) producing 2,3-naphtotriazole (NAT); fragmentation studies of the two adducts by tandem mass spectrometry (MS/MS) allow the selection of DAN method because it provides the highest sensitivity. An original transition resulting from the NAT fragmentation in Higher-energy Collisional Dissociation (HCD) mode instead of the conventional Collisionally Induced Dissociation (CID) mode was pointed out and permitted to reach a limit of quantification of 5 nM (20 fold less than when using fluorescence). The LC-MS/MS method was validated and applied to the GS15NO intestinal permeability studies with two models: in vitro (a monolayer of Caco-2 epithelial cells), and ex vivo (isolated intestine of rat (ileum) in an Ussing chamber). The apparent permeability values calculated with concentrations of GS15NO metabolites (nitrite, nitrate ions and RSNOs) classify it as a middle permeable drug. Studies on GSNO denitrosating processes using isolated rat intestine demonstrate that the enzymes γ-glutamyltransferase and protein disulfide isomerase play a pivotal role

<p>Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) has been established as a powerful tool for qualitative and quantitative analysis of biomolecules. However, mass spectrometric analysis of biomolecules is often limited by poor ionization efficiency of analyte for sensitive detection and limited fragmentation for structural characterization. Over the years, various solution phase as well as gas-phase derivatization techniques, have been coupled with MS to increase the ionization efficiency and facilitate the formation of structural informative fragment ions. The research presented in this dissertation falls into two major parts; focusing on method development and application of radical chemistry for enhanced biomolecule analysis on an ESI-MS/MS platform. In the first part, a method of rapid charge tagging of neutral lipids (e.g. sterols, glycerides) with a thiol radical-based charge tag is developed, followed by comprehensive analysis via ESI-MS/MS without the use of a chromatographic separation (shotgun lipidomics). This charge tagging is performed in an easily constructible fused silica capillary-based microflow photo-reactor which is relatively low in cost and requires no instrument modifications. This method significantly enhances the ionization efficiency of the neutral lipids for sensitive MS detection (pM range). This method can be applied to the small volume of biological complex samples (e.g. 1 µL plasma) and doesn’t require extensive sample pretreatment procedure (analysis time of 2 min vs. traditional >60 min on GC-MS and HPLC-MS systems). Furthermore, the derivatized neutral lipids can also be fragmented via soft collision-induced dissociation to obtain fatty acyl chain composition of the neutral lipids (sterol esters, diacylglycerols, triacylglycerols, etc.) for structural characterization. This can especially be useful for determination for fatty acyl compositional isomers in neutral lipids for analysis related to biomarker detection. The characteristic fragmentation pattern of tagged neutral lipids has also been utilized for quantitation of lipids from biological mixture samples. Initial application of this method has shown alteration in the concentration of diacylglycerol lipid species in clinical samples of Type 2 Diabetes Mellitus patients, suggesting the potential of understanding the biological roles of such lipids in insulin resistance. </p> <p>In the second part, a unique approach of radical-induced disulfide bond cleavage in peptides and proteins is demonstrated. Using 254 nm UV emission, acetone was used as a photoinitiator to initiate secondary radical formation i.e. hydroxyalkyl radical, from alcohol co-solvents used for electrospray. These radicals can then be used to efficiently cleave the disulfide bonds (R-S-S-R) in peptide/proteins to give reduced reaction products (RSH) at the cleavage site. Upon soft collision-induced dissociation, the reduced product gave abundant <i>b-</i> and <i>y-</i> type fragment ions for complete or enhanced sequence coverage as compared to intact disulfide-linked peptides and proteins. With the use of a simple microflow photo-reactor, this radical based approach can also be coupled with infusion ESI-MS/MS for a rapid online-based peptide and protein analysis. The yield for disulfide bond reduction was almost 100% within less than 5 s of UV irradiation. Furthermore, by adjusting the UV irradiance time, different degrees of partial reduction could be achieved, which greatly facilitated the disulfide linkage mapping in peptides and proteins with multiple disulfide bonds. This method has been incorporated with both bottom-up and top-down approach for protein analysis for unraveling the molecular complexity, quantifying and deep sequencing of disulfide-linked proteins.</p>