Motion of ions under the influence of electric field has been a subject of scientific interest for many decades. Capillary electrophoresis in particular benefited greatly from this research and mathematical models of electromigration applicable to capillary electrophoresis have been developed. As the sophistication of the models grew, so did the computational demands to evaluate them. In order to fully exploit the possibilities of advanced mathematical models a computer implementation capable of solving non-trivial problems at sufficient speed is necessary. This dissertation thesis explores applications of computer implementations of mathematical models re- lated to electromigration in two different areas. The main focus of this thesis is on the topic of linear theory of electromigration. We discuss the extension of the linear theory of electromigration beyond of just acid-base equilibria and computer implementation of this extented theory which is specialized to include complex-forming equilibria in order to be able to deal with affinity capillary electrophoresis prob- lems. Some technical aspects of the computer implementation are also discussed. This is followed upon by investigating certain selected affinity capillary electrophoresis systems. The purpose of this investi- gation is to re-derive...

Capillary electrophoresis mass spectrometry (CE-MS) is a versatile instrumental method for metabolomics, which allows for comprehensive metabolite profiling of volume-limited biological specimens in order to better understand the molecular mechanisms associated with chronic diseases, including an alarming epidemic of obesity worldwide. Multiplexed CE separations enable high-throughput metabolite screening with quality assurance to prevent false discoveries when combined with rigorous method validation, robust experimental designs, complementary statistical methods, and high-resolution tandem mass spectrometry (MS/MS) for unknown metabolite identification. In this thesis, multiplexed CE-MS technology is applied for both targeted and untargeted metabolite profiling of various biological fluids, including covalently bound thiol-protein conjugates, as well as free circulating metabolites in serum and plasma, and excreted/bio-transformed compounds in urine due to complex host-gut microflora co-metabolism. This work was applied to characterize aberrant metabolic responses of obese subjects in response to dietary challenges, and measure the benefits of dietary interventions that reduce adiposity without deleterious muscle loss. Chapter 2 presents, a simple, sensitive yet robust analytical protocol to expand metabolome coverage in CE-MS for the discovery of labile protein thiols in human plasma using a rapid chemical derivatization method based on N-tert-butylmaleimide (NTBM). Chapter 3 describes targeted metabolite profiling of serum and plasma to investigate the differential metabolic responses between healthy and unhealthy obese individuals before and after consumption of a standardized high-caloric meal, respectively. Chapter 4 of this thesis describes an untargeted metabolite profiling strategy for urine using multisegment-injection (MSI)-CE-MS for elucidating the effects of protein supplementation following a short-term dietary weight-loss intervention study. This work revealed six urinary metabolites that were classified as top-ranking treatment response biomarkers useful for discriminating between subjects consuming carbohydrate (control), soy, and whey supplemented diets. In summary, this thesis demonstrated the successful implementation of multiplexed CE-MS technology for biomarker discovery in nutritional-based metabolomic studies as required for more effective treatment and prevention of obesity for innovations in public health. / Thesis / Doctor of Philosophy (PhD)

Exposomics applies metabolomics methods and technologies to the comprehensive analysis of all low molecular weight molecules (< 1.5 kDa) in complex biological samples to characterize the interaction between cellular metabolism and exogenous lifestyle exposures that determine health and quality of life. To fully access the diverse classes of biological molecules related to an individual’s metabolic profile, metabolomics frequently requires the use of complementary analytical platforms, and employs targeted and untargeted molecular profiling strategies to identify biomarkers that are clinically relevant to an individual’s health status. Chapter 2 describes a quinoline-based boronic acid biosensor for N-acetylneuraminic acid that undergoes a striking binding enhancement under strongly acidic conditions. For the first time, this work allows for direct analysis of acidic sugars with high selectivity when using UV absorbance or fluorescence detection based on formation of a highly stable boronate ester complex with metabolites containing an α-hydroxycarboxylate moiety. Chapter 3 describes a targeted analysis of 24 different organic contaminants using GC-MS that can serve as biomarkers of recent smoke exposure following search-and-rescue training exercises by firefighters located at three different sites across the province of Ontario. Importantly, skin and possible respiratory uptake of various polycyclic aromatic hydrocarbons, methoxyphenols, and resin acids was confirmed by peak excretion of several wood smoke biomarkers in urine within 6 h following acute exposure. Chapter 4 applied a cross-platform metabolomics strategy based on CE-MS and GC-MS in order to identify and validate dietary biomarkers in matching plasma and urine samples collected from healthy participants in the pilot Diet and Gene Interaction Study (DIGEST). For the first time, we demonstrate that a panel of metabolites can serve as reliable biomarkers following contrasting Prudent and Western diets over 2 weeks of food provisions, which correlated well with self-reported diet records. This work paves the way for the development of objective biomarkers for accurate assessment of wood smoke exposures, as well as complex dietary patterns as required for new advances in occupational health and nutritional epidemiology. / Dissertation / Doctor of Philosophy (PhD) / Exposomics is an emerging multidisciplinary science aimed at deciphering the complex interactions that impact human health and gene expression, such as lifestyle choices (i.e., habitual diet) and lifelong environmental exposures. There is growing interest in identifying biomarkers that can be readily measured for chronic disease prevention given an alarming global prevalence of obesity and cardiometabolic disorders, including heart disease, type 2 diabetes and cancer. The research in this thesis focuses on developing new analytical methods for identifying and quantifying metabolites that may allow for better assessments of human health, and has contributed to the development of novel biosensors for the targeted analysis of N-acetylneuraminic (sialic) acid and related acidic sugars, as well as high resolution methods for broad spectrum analysis of biotransformed organic contaminants from smoke exposure by GC-MS, and plasma and urinary metabolites that differentiate contrasting Prudent and Western diets and correlate well with self-reported diet records.

Os limites de exposição ocupacional ao benzeno, um agente carcinogênico, vêm diminuindo drasticamente nos últimos anos. Por outro lado, a concentração de benzeno em ambientes não ocupacionais tem aumentado devido à emissão biogênica e antropogênica, como exaustão de motores a gasolina e fumaça de cigarro. Indicadores Biológicos de Exposição (IBE) são utilizados como ferramentas importantes na avaliação da exposição humana ao benzeno. Com a diminuição dos limites de exposição, se faz necessário o desenvolvimento de metodologias analíticas com sensibilidade adequada para a determinação de IBE em fluidos biológicos que se correlacionem com baixas concentrações de benzeno absorvido pelo organismo. A utilização do fenol urinário como IBE ao benzeno, embora reconhecida mundialmente, tem a desvantagem de não apresentar boa correlação com a concentração de benzeno ambiental quando esta é menor do que 10 ppm (32 mg/m3). Os ácidos trans,trans-mucônico e S-fenilmercaptúrico, metabólitos do benzeno encontrados na urina, estão entre os compostos mais estudados como IBE ao benzeno. Neste trabalho, o ácido trans,trans-mucônico foi determinado na urina de indivíduos expostos ao benzeno utilizando as técnicas de Eletroforese Capilar (CE) e HPLC, ambas com detecção no UV. Na determinação por HPLC foi adaptada uma metodologia da literatura utilizando coluna analítica com fase reversa. Na determinação por CE foi proposta uma metodologia empregando duas condições analíticas alternativas: uma que utiliza um capilar especial com cela ótica de alta sensibilidade e a outra que utiliza um capilar comum, mas com adição de um modificador orgânico ao eletrólito. As duas condições apresentaram grandes vantagens, como análise rápida (15 minutos) e baixo limite de detecção (25 &#181;g/L). Foram analisadas amostras de urina de indivíduos fumantes e não fumantes onde a sensibilidade da metodologia proposta foi suficiente para diferenciar estatisticamente os dois grupos avaliados. / The occupational exposure limits for benzene, a well-known carcinogenic agent, showed a drastic and continuous decrease in the last few years. In the other hand, benzene concentrations in non-occupational environments are increasing due to biogenic and anthropogenic emissions, like motor fuelled exhaustion and cigarette smoke. Biological markers of exposure are used like a powerful aid to evaluate human exposure for benzene. With the decrease of the exposure limits, the development of analytical methodologies is needed to accomplish adequate sensitivity for the exposure markers determination founded in biological fluids, in order to establish a correlation between the marker and the benzene concentration absorbed by organism. One of the biological marker of exposure for benzene recognized worldwide is urinary phenol, but the exposure for benzene at concentrations smaller than 10 ppm (32 mg/m3) usually is not correlated with urinary phenol concentration. The benzene metabolites trans,trans-Muconic and S-phenylmercapturic acids found in urine have been largely evaluated as biological markers of exposure. At the present work, trans,trans-muconic acid in urine from exposed individuals was determined by Capillary Electrophoresis (CE) and HPLC using UV detection. For HPLC, a pre-established method from literature using reversed phase column was utilized. A new analytical method was proposed using CE in two different conditions: one utilized a special capillary with high sensitivity optical cell and the other utilized a common capillary and an organic modifier added to the electrolyte. Both conditions showed interesting advantages, such as short-time analysis (15 min) and lower limit of detection (L.O.D = 25 &#181;g/L). Urine samples from smokers and non-smokers individuals were analyzed and the proposed method allowed statistical differentiation between these groups.

La phosphorylation des protéines constitue l’une des plus importantes modifications post-traductionnelles (PTMs) et intervient dans de multiples processus physiologiques tels, la croissance, la différenciation cellulaire, l’apoptose, etc. En dépit de son importance, l’analyse des phosphoprotéines demeure une tâche difficile en raison de leur nature dynamique (car la phosphorylation des protéines est un processus réversible) et de leur faible abondance relative. En effet, la détermination des sites de phosphorylation est souvent difficile car les phosphopeptides sont souvent difficiles à détecter par des méthodes d’analyse chromatographique classique et par spectrométrie de masse (MS). De récentes études ont démontré que les nombreuses méthodes d’enrichissement de phosphopeptides existantes ne sont pas complètes, et que le nombre total de phosphopeptides détectés ne chevauchent pas complètement ces méthodes. C’est pour cela qu’il existe une nécessité de combler les lacunes des méthodes d’enrichissement existantes afin d’avoir des analyses phosphoprotéomiques plus complètes. Dans cette étude, nous avons utilisé les liquides ioniques (LI), plus particulièrement les sels d’imidazolium, comme une technique d’enrichissement alternative, dans le but de favoriser une extraction sélective de phosphopeptides présents en solution. Les sels d’imidazolium ont donc été utilisés en raison de leurs propriétés physico-chimiques "facilement" ajustables selon la nature des substituants sur le noyau imidazolium et la nature de l’anion. Les sels de monoimidazolium et de bis-imidazolium possédant respectivement des chaînes linéaires à 4, 12 et 16 atomes de carbone et ayant différents anions ont été synthétisés et utilisés pour effectuer des extractions liquide-liquide et solide-liquide des phosphopeptides en solution. Dans un premier temps, des extractions liquide-liquide ont été réalisées en utilisant un liquide ionique (LI) ayant une chaine linéaire de 4 atomes de carbone. Ces extractions réalisées avec le bis(trifluoromethanesulfonyl) amide de 3-butyl-1-methylimidazolium (BMIM-NTf2) et l’hexafluorophosphate de 3-butyl-1-methylimidazolium (BMIM-PF6) n’ont pas montré une extraction notable du PPS comparativement au PN. Dans un deuxième temps, des extractions solide-liquide ont été réalisées en fonctionnalisant des particules solides avec des sels d’imidazolium possédant des chaines linéaires de 12 ou 16 atomes de carbone. Ces extractions ont été faites en utilisant un phosphopentapeptide Ac-Ile-pTyr-Gly-Glu-Phe-NH2 (PPS) en présence de 2 analogues acides non-phosphorylés. Il a été démontré que les sels d’imidazolium à chaine C12 étaient meilleurs pour extraire le PPS que les deux autres peptides PN (Ac-Ile-Tyr-Gly-Glu-Phe-NH2) et PE (Ac-Glu-Tyr-Gly-Glu-Phe-NH2) L’électrophorèse capillaire (CE) et la chromatographie liquide à haute performance couplée à la spectrométrie de masse (LC-MS) ont été utilisées pour quantifier le mélange des trois peptides avant et après extraction ; dans le but de mesurer la sélectivité et l’efficacité d’extraction de ces peptides par rapport à la composition chimique du liquide ionique utilisé. / Protein phosphorylation is one of the most important post-translational modifications because it is involved in multiple physiological processes such as growth, differentiation, apoptosis, etc. Despite its importance, the analysis of phosphoproteins remains a difficult task due to their dynamic nature (phosphorylation of proteins is a reversible process) and their low abundance. Indeed, the determination of phosphorylation sites is difficult because phosphopeptides are often difficult to detect by conventional chromatographic analysis and by mass spectrometric (MS) methods. Recent studies have shown that the existing methods of enrichment of phosphopeptides are not complete, and the total number of phosphopeptides detected does not overlap completely with those detected by these methods. The gaps in existing enrichment methods need to be filled in order to have more complete phosphoproteomic analyses. In the current study, ionic liquids (IL), specifically imidazolium salts, have been used in an alternative enrichment technique with potential for selective extraction of phosphopeptides from solution. Imidazolium salts were chosen because their physicochemical properties are readily adjustable depending on the nature of the substituent attached to the imidazolium core and the counter-anion. Monoimidazolium and bis-imidazolium salts with linear chains having respectively 4, 12, and 16 carbon atoms and with different anions were synthesized and used to carry out liquid-liquid and solid-liquid extractions of a phosphorylated peptide from a solution. At first, liquid-liquid extractions were carried out using an ionic liquid (IL) with a linear chain of 4 carbon atoms. These extractions performed with bis (trifluoromethanesulfonyl) amide 3-butyl-1-methylimidazolium (BMIM-NTf2) and hexafluorophosphate 3-butyl-1-methylimidazolium (BMIM-PF6) did not show a considerable extraction of PPS comparatively to the PN. Secondly, solid-liquid extractions were done by first functionalizing solid-phase particles with the imidazolium salts. The extractions were carried out using the phosphopentapeptide Ac-pTyr-Ile-Gly-Glu-Phe-NH2 (PPS) and its acidic non-phosphorylated analogues. It has been shown that the C12 chain imidazolium salts were better to extract PPS than the other two peptides PN (Ac-Ile-Tyr-Gly-Glu-Phe-NH2) and PE (Ac-Glu-Tyr-Gly-Glu-Phe-NH2). The extraction efficiency of these peptides was estimated by capillary electrophoresis (CE) and high performance liquid chromatography coupled with mass spectrometry (LC-MS).

La cellulose et ses dérivés sont utilisés dans un vaste nombre d’applications incluant le domaine pharmaceutique pour la fabrication de médicaments en tant qu’excipient. Différents dérivés cellulosiques tels que le carboxyméthylcellulose (CMC) et l’hydroxyéthylcellulose (HEC) sont disponibles sur le commerce. Le degré de polymérisation et de modification diffèrent énormément d’un fournisseur à l’autre tout dépendamment de l’origine de la cellulose et de leur procédé de dérivation, leur conférant ainsi différentes propriétés physico-chimiques qui leurs sont propres, telles que la viscosité et la solubilité. Notre intérêt est de développer une méthode analytique permettant de distinguer la différence entre deux sources d’un produit CMC ou HEC. L’objectif spécifique de cette étude de maitrise était l’obtention d’un profil cartographique de ces biopolymères complexes et ce, par le développement d’une méthode de digestion enzymatique donnant les oligosaccharides de plus petites tailles et par la séparation de ces oligosaccharides par les méthodes chromatographiques simples. La digestion fut étudiée avec différents paramètres, tel que le milieu de l’hydrolyse, le pH, la température, le temps de digestion et le ratio substrat/enzyme. Une cellulase de Trichoderma reesei ATCC 26921 fut utilisée pour la digestion partielle de nos échantillons de cellulose. Les oligosaccharides ne possédant pas de groupements chromophores ou fluorophores, ils ne peuvent donc être détectés ni par absorbance UV-Vis, ni par fluorescence. Il a donc été question d’élaborer une méthode de marquage des oligosaccharides avec différents agents, tels que l’acide 8-aminopyrène-1,3,6-trisulfonique (APTS), le 3-acétylamino-6-aminoacridine (AA-Ac) et la phénylhydrazine (PHN). Enfin, l’utilisation de l’électrophorèse capillaire et la chromatographie liquide à haute performance a permis la séparation des produits de digestion enzymatique des dérivés de cellulose. Pour chacune de ces méthodes analytiques, plusieurs paramètres de séparation ont été étudiés. / Cellulose and its derivatives are used in a wide range of applications, including the pharmaceutical industry for the manufacturing of medicines as inactive additives. Various cellulosic derivatives such as carboxymethylcellulose (CMC) and hydroxyethylcellulose (HEC) are readily available for such use. The degree of polymerization and modification differs from one supplier to the other, according to the origin of the cellulose and its process of chemical modification, conferring on them different physico-chemical properties, such as viscosity and solubility. Our interest is to develop an analytical method that can distinguish between different sources of a given CMC or HEC product. The specific objective of this master’s study was to obtain a fingerprint of these complex biopolymers by developing an enzymatic digestion method to produce smaller oligosaccharides that could be separated by simple chromatographic methods. The digestion was studied as a function of various parameters, such as the composition of the hydrolysis solution, the pH, the temperature, the duration of digestion and the substrate/enzyme ratio. A cellulase enzyme from Trichoderma reesei ATCC 26921 was used for the partial digestion of our samples of cellulose. Since these oligosaccharides do not possess a chromophore or fluorophore, they can’t be detected either by absorbance or fluorescence. It was thus necessary to work out the labeling method for oligosaccharides using various agents, such as 8-aminopyrene-1,3,6-trisulfonic acid (APTS), 3-acetylamino-6-aminoacridine (AA-Ac) and phenylhydrazine (PHN). Finally, the use of capillary electrophoresis and high performance liquid chromatography allowed the separation of the enzymatic digestion products of the cellulose derivatives (CMC and HEC). For each of these analytical separation techniques, several parameters of the separation were studied.

In current days, examination of circulating tumor DNA (ctDNA) finds new use across different cancers. It is directed at tumor-derived short fragments of DNA present in peripheral blood of patiens (mainly in advanced stages). Due to its minimal invasivity, almost 100 % specificity and relatively high sensitivity in stage IV patients, this approch found its main potential clinical utility especially in early detection of disease relapse or progression after tumor resection (i.e. post-operative follow-up), prediction and monitoring of therapy response and estimation of prognosis. As a result of minute levels of ctDNA on a high background of other non-tumor DNA fragments present in plasma, a suitable method exhibiting highest sensitivity is the key for proper detection of this marker. The approach is predominantly based on initial identification of a mutation in tumor tissue and its subsequent detection in plasma. The present work is aimed at optimization of ctDNA isolation and method of its detection based on PCR amplification followed by heteroduplex analysis by denaturing capillary electrophoresis (DCE) to achieve highest sensitivity for detection of mutated fraction in plasma sample. I have applied the optimized protocol to examine ctDNA in three types of cancers, namely colorectal cancer (122...

Mass spectrometry has in recent years been established as the standard method for protein identification and characterization in proteomics with excellent intrinsic sensitivity and specificity. Fourier transform ion cyclotron resonance is the mass spectrometric technique that provides the highest resolving power and mass accuracy, increasing the amount of information that can be obtained from complex samples. This thesis concerns how useful information on proteins of interest can be extracted from mass spectrometric data on different levels of protein structure and how to obtain this data experimentally. It was shown that it is possible to analyze complex mixtures of protein tryptic digests by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and identify abundant proteins by peptide mass fingerprinting. Coupling on-line methods such as liquid chromatography and capillary electrophoresis increased the number of proteins that could be identified in human body fluids. Protein identification was also improved by novel statistical methods utilizing prediction of chromatographic behavior and the non-randomness of enzymatic digestion. To identify proteins by short sequence tags, electron capture dissociation was implemented, improved and finally coupled on-line to liquid chromatography for the first time. The combined techniques can be used to sequence large proteins de novo or to localize and characterize any labile post-translational modification. New computer algorithms for the automated analysis of isotope exchange mass spectra were developed to facilitate the study of protein structural dynamics. The non-covalent interaction between HIV-inhibitory peptides and the oligomerization of amyloid β-peptides were investigated, reporting several new findings with possible relevance for development of anti-HIV drug therapies and understanding of fundamental mechanisms in Alzheimer’s disease.

In this thesis, improved techniques for biomolecule analysis using capillary electrophoresis (CE) and matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) and hyphenations between those have been presented.A pre-concentration method which is possible to apply in both techniques, has also been investigated. In this work the off-line MS mode has been used either in the form of fractionation (Paper I) or by incorporating the MALDI target in the CE separation system (Paper II).In Paper I, a protocol for CE-MALDI analysis of cyanogen bromide digested bacteriorhodopsin (BR) peptides as model integral membrane protein peptides were established. Also, an improved protocol for partially automated manufacturing of a concentration MALDI-target plate is presented. The design of the targets was suitable for the fractions from the CE. A novel technique for the integration of CE to MALDI-MS using a closed-open-closed system is presented in Paper II, where the open part is a micro canal functioning as a MALDI target window. A protein separation was obtained and detected with MALDI-MS analysis in the micro canal. A method has been developed for detection of monosaccharides originating from hydrolysis of a single wood fiber performed in a micro channel, with an incorporated electromigration pre-concentration step preceding CE analysis in Paper III. The pre-concentration showed to be highly complex due to the fact that several parameters are included that affecting each other. In Paper IV a protocol using enzymatic digestion, MALDI-TOF-MS and CE with laser induced fluorescence (LIF) detection for the investigation of the degree of substitution of fluorescein isothiocyanate (FITC) to bovine serum albumin (BSA), as a contact allergen model system for protein-hapten binding in the skin, is presented. The intention of a further CE-MALDI hyphenation has been considered during the work. In Paper V 2,6-dihydroxyacetophenone (DHAP) was investigated, showing promising MALDI-MS matrix properties for hydrophobic proteins and peptides. 2,5-dihydroxybenzoic acid (DHB) was undoubtedly the better matrix for the hydrophilic proteins, but its performance for the larger and hydrophobic peptides was not optimal. Consequently, DHAP can be used as a compliment matrix for improved analysis of hydrophobic analytes. / QC 20101214

Se desarrolló cinco sistemas automatizados utilizando análisis por inyección secuencial (SIA) y análisis por inyección en flujo multijeringa (MSFIA). Se desarrolló un SI-analizador para la determinación de formaldehído utilizando la reacción de Hantzsch. El analizador fue aplicado a la monitorización en un cultivo de P. pastoris. Se desarrolló un SI-analizador para la determinación de glicerol y sorbitol. Se utilizó periodato para la reacción de Malaprade. El formaldehído generado fue cuantificado con la reacción de Hantzsch. El sistema incluyó la dilución de la muestra y procedimientos seleccionado por decisión inteligente del programa o por el usuario. Se lo aplicó a la monitorización en cultivos de P. pastoris.Se desarrolló un sistema de electroforesis capilar (CE) acoplado a un SIA aplicado a la separación de nitrofenoles. Se acopló por primera vez MSFIA con CE para pre-concentración en fase sólida y separación de nitrofenoles. Ambos sistemas mostraban recuperaciones satisfactorias para aguas ambientales. / Five analytical systems using Sequential Injection Analysis (SIA) and Multisyringe Flow Injection Analysis (MSFIA) were developed and applied with satisfactory analytical performance. A SI-analyzer for formaldehyde was developed automating Hantzsch reaction. It was successfully applied to formaldehyde monitoring in continuous medium filtrate of P. pastoris cultivation. A second SI-analyzer was developed for the determination of glycerol and sorbitol. Periodate was used as additional reagent to carry out Malaprade reaction and formaldehyde generated by polyalcohol oxidation was quantified. The system included automated sample dilution and procedures for two working ranges, selected by smart software decision or user-input. It was applied to monitoring of P. pastoris cultivations.A capillary electrophoresis (CE) system was developed and coupled to SIA. It was applied to the determination of nitrophenols. MSFIA and CE were coupled for the first time. Solid phase concentration and separation of nitrophenols were automated. The systems were applied to environmental water samples.