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Inborn errors of metabolism (IEM) cause significant morbidity and mortality when left untreated. Urine organic acid (UOA) analysis is often a first-line investigation when an IEM is suspected. UOAs are usually qualitatively analyzed via the current gold standard, GC-EI-MS (Gas Chromatography-Electron Impact-Mass Spectroscopy). The Agilent 7890 GC in tandem with the Waters’ Xevo TQ-S MS contains an easily interchangeable LC-ESI (liquid chromatography-electrospray Ionization) and GC-APCI (Atmospheric Pressure Chemical Ionization) instrument set-up, while maintaining accuracy and sensitivity in both LC and GC applications. Utilizing this novel GC-APCI instrument, this project aims to develop and validate a new UOA method for clinical use. Furthermore, utilizing the machine’s MRM mode would increase sensitivities thus allowing for hopefully quantitative analysis. Chemical standards and patient urine samples were extracted via a liquid-liquid ether extraction and derivatized with BSTFA for proper GC elution. Results were compared on the current gold standard GC-EI-MS instrument and the new GC-APCI-MS instrument. Initial instrument suitability and method setup was then optimized. Source moisture levels were modified to explore the wet proton transfer and the dry charge transfer mechanism using [M+H]+ and [M+*]+ ion peak ratios, respectively. Elution times and APCI ion mass spectra profiles of UOA metabolites of interest were identified from full scan mode in preparation for MRM mode analysis. Exploration into the wet and dry mode settings of the APCI source determined that the former induced via methanol had greater peak areas and signal-to-noise ratios. Suitable MRMs were determined for clinically relevant organic acids from which a quantitative assay was developed for methyl malonic acid and several other compounds. The Waters’ Xevo TQ-S micro with Agilent 7890 GC demonstrated promising GC-APCI-MS detection of urine organic acids. With clear avenues for future work, the APCI technique hints at great benefits for biochemical genetic laboratories. / Thesis / Master of Science (MSc) / Inborn errors of metabolism (IEM) are a class of genetic diseases that when left untreated, cause reduced quality of life and sometimes death in newborns. Urine organic acid (UOA) analysis is used for detection using an instrument called GC-EI-MS (Gas Chromatography Electron Impact Mass Spectroscopy). This project explores how a new instrument, the Agilent 7890 GC and the Waters’ Xevo TQ-S MS, can detect these genetic diseases using a technique called APCI (Atmospheric Pressure Chemical Ionization) while still being accurate and sensitive. UOAs are isolated from urine and run through the new machine. When compared to the currently used technique, results were promising but further optimization is needed. Using the new machine, various UOA compounds that were elevated and/or decreased in newborns with genetics diseases were identified and quantified. With clear avenues for future work, the APCI technique can greatly improve newborn diagnosis of IEMs.

The objective of this research was to develop new sample preparation procedures for the isolation of sulfonamides, as well as, to determine the applicability of employing on-line nitrogen selective and mass spectrometric detection methods. The first phase of this research investigated the effect of temperature and pressure on the supercritical fluid extraction (SFE) of sulfonamides from a spiked sand matrix. Temperature effects were either positive or negative with respect to extraction rate and total recovery, depending on the pressure and extraction fluid employed. The second portion of this research compared trifluoromethane (CHF3) and carbon dioxide (CO2) as fluids for the extraction of sulfonamides from spiked non-fat dry milk, beef liver, and egg yolk were found to be more selective using CHF3 than CO2. The polar trifluoromethane improved the extraction efficiency of the polar sulfonamides from the biological matrices and also reduced the amount of co-extractives. The next phase of this research considered the effect of organic modifier and CO2 in the SFE of sulfonamides from chicken liver, beef liver and egg yolk. Methanol, ethanol, acetone, acetonitrile were compared to determine optimum conditions. A SFE method employing 20% acetonitrile modified CO2 yielded quantitative recovery of sulfonamides from chicken liver, but 20% acetone modified CO2 was required to obtain quantitative recovery from beef liver. Either 20% acetone or 20% acetonitrile yielded quantitative recovery from egg yolk. The last phase of this research focused on the evaluation of selective detection methods for sulfonamide analysis. Chemiluminescence nitrogen detection (CLND) parameters were optimized for use with packed column supercritical fluid chromatography (SFC) yielding a minimum detectable quantity (MDQ) of 5 ng of sulfamethazine, on column. Improvements in the detector design decreased the MDQ to 0.5 ng, while, decreasing the column diameter further reduced the MDQ to 125 pg. The second part of this phase evaluated PLC/Atmospheric pressure chemical ionization (APCI) mass spectrometry for the detection of sulfonamides. Sensitivity in selective ion mode was found to be as low as 50 pg on column for sulfamethazine. Supercritical fluid extracts of sulfonamides spiked at 100μg/kg in chicken liver were found to be readily detected by this method. / Ph. D.

<p dir="ltr">Tandem mass spectrometry (MSⁿ) has become the most widely used analytical technique for the chemical characterization of unknown organic compounds in complex mixtures. It has led to the development of a large number of mass spectrometers with different mass analyzers as well as a wide array of ionization methods. This technique can be coupled with a diverse range of chromatography methods, such as gas chromatography (GC) and high-performance liquid chromatography (HPLC). Some of the primary strengths of MS include its great sensitivity, its versatility to seamlessly integrate with various chromatography techniques and its flexibility in the sense of access to different mass analyzers and different ionization methods. During MS experiments, analytes are evaporated and ionized and the resulting ions are separated based on their mass-to-charge (<i>m/z</i>) ratios and then detected. On the other hand, MSⁿ experiments involve isolating a specific ion of interest from all other ions and subjecting them to reactions such as collision-activated dissociation (CAD) or ion-molecule reactions. These reactions generate product ions that can be used to obtain structural information for the analyte. In addition, MSⁿ experiments can be used to generate and study the chemical properties of reaction intermediates, such as oxenium cations. </p><p dir="ltr">The mass spectrometer and the ionization source used to perform the research discussed in this thesis are described in Chapter 2. After this, the development of experiments involving ion-molecule reactions accompanied by collision-activated dissociation in a linear quadrupole ion trap is discussed, with the goals of differentiating the aziridine functionality from structurally related functional groups, such as the amino group and identifying aromatic aldehyde functionalities in protonated oxygen-containing monofunctional analytes. The integration of machine learning with mass spectral data has become an increasingly prevalent and valuable way to interpret data faster and more accurately without human bias than conventional manual approaches. Chapter 5 discusses combining machine learning-guided automated HPLC analysis coupled with MSⁿ experiments based on diagnostic ion-molecule reactions for the structural elucidation of unknown compounds. Finally, experimental and computational studies on the gas-phase reactivity of quinoline-based ground-state singlet oxenium cations are discussed.</p>

Pregnenolona (PREG) e 17-alfa-hidroxipregnenolona (17OHPREG) são dois esteroides produzidos pela glândula adrenal e precursores de vários hormônios esteroidais. A dosagem desses compostos tem aplicações clínicas, como o diagnóstico de doenças relacionadas aos corticoesteroides e mineralocorticóides e especialmente na avaliação da atividade da enzima 3-&#946;-hidroxidesidrogenase que é decisiva no diagnóstico de um dos tipos de hiperplasia da glândula adrenal que causa defeitos severos na síntese de esteroides. Métodos cromatográficos associados à espectrometria de massas superaram a especificidade reduzida dos imunoensaios e tem sido crescentemente utilizados na quantificação de esteroides. Os últimos anos tem sido marcados pela hegemonia da cromatografia líquida acoplada à espectrometria de massas em tandem (LC-MS/MS) em grande parte devido à velocidade e possibilidade da análise direta de vários analitos. Porém, no caso específico dos esteroides de tipo 3-hidroxi-5-eno, que apresentam baixa afinidade protônica e, portanto, baixa eficiência de ionização, são necessárias muitas etapas para a conversão em derivados mais detectáveis. Embora desfavorecida em relação ao LC-MS/MS nos últimos anos, a cromatografia gasosa acoplada à espectrometria de massas (CG-MS) apresenta várias características favoráveis para a análise de esteroides como a eficiência cromatográfica ainda insuperável. Adicionalmente, a incorporação da espectrometria de massas em tandem ao CG (CG-MS/MS) torna a técnica tão seletiva quanto LC-MS/MS. No presente trabalho, foi desenvolvido um novo método que permite a extração e derivatização simultâneas da PREG e 17OHPREG de amostras de soro tornando o método de preparo da amostra tão simples quanto os descritos para LC-MS/MS. O método de detecção desenvolvido baseado em ionização química no modo negativo obteve a sensibilidade necessária para o diagnóstico da deficiência da enzima 3-beta-hidroxidesidrogenase utilizando apenas 250 &#181:L de amostra. / Pregnenolone (PREG) and 17&#945;-hydroxypregnenolone (17OHPREG) are two steroid precursors produced by the adrenal gland. The quantification of these compounds is essential for the evaluation of 3-&#946;-hidroxidesidrogenase enzyme activity, which promotes the conversion of PREG in 17OHPREG. The 3-&#946:-hidroxidesidrogenase deficiency is a rare but severe type of adrenal hyperplasia that causes serious defects in steroid synthesis. Chromatographic methods coupled to mass spectrometry overcame immunoassays limitations such as reduced specificity, and have been widely used for steroids quantification. Recent years have been marked by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) hegemony due to the speed and possibility to analyze directly several analytes. However, in the case of type 3-hydroxy-5-ene steroids, which have low affinity for protons and, therefore, low ionization efficiency, many steps are required for conversion to detectable products. Notwithstanding, gas chromatography coupled to mass spectrometry (GC-MS) has some favorable features for steroid analysis such as unbeatable chromatographic efficiency. In addition, the incorporation of tandem mass spectrometry (GC-MS/MS) makes it as selective as LC-MS/MS. In this study, a new method for simultaneous extraction and derivatization of PREG and 17OHPREG from serum was developed. This procedure makes sample preparation for GC-MS/MS as simples as those described for LC-MS/MS. The detection method based on negative mode chemical ionization achieved the sensitivity required for the diagnosis of 3-&#946;-hidroxidesidrogenase defficiency using only 250 &#181;L of sample.

Les matériaux polymères sont aujourd'hui très présents dans notre environnement et deviennent irremplaçables pour de nombreuses applications : emballage, textile, mobilier,... La connaissance du cycle de vie de ces matériaux, de la production à leur destruction, devient importante pour nos sociétés. Par exemple ces matériaux peuvent émettre des Composés Organiques Volatils qui sont souvent toxiques et leur impact sur le milieu doit être évalué. L’objectif de ce travail de thèse a été de développer une méthode au laboratoire pour identifier et quantifier ces émissions. La difficulté provient de la grande diversité des composés qui peuvent être émis. Par ailleurs la méthode nécessite une fréquence de mesure élevée (temps réel) souvent incompatible avec les techniques actuelles. Une solution analytique couplant un four et un spectromètre de masse haute résolution associé à une méthode d’ionisation chimique contrôlée a été développée. Celle-ci est basée sur un spectromètre FT-ICR compact à bas champ magnétique : BTrap. Les points forts de cette technique sont la très haute résolution en masse qui permet de mesurer la masse exacte des composés et la détection multi composés, simultanée sur toute la gamme de masse. L’ionisation chimique contrôlée permet l'ionisation douce et quantitative des molécules d’intérêt. Le transfert de proton à partir de l’ion H₃O⁺ (PTRMS) a montré son potentiel pour la détection des COV dans de nombreux domaines. Après une présentation du contexte et du besoin, le dispositif expérimental développé est détaillé. La validation de celui-ci pour l'analyse de gaz traces a été effectuée au LPGP, sur un système de dépollution par plasma froid. Les résultats de dégradation de l'acétaldéhyde en fonction des conditions de fonctionnement du réacteur sont présentés.L’ionisation par PTR conduit habituellement à la molécule protonée ce qui simplifie l’identification. Cependant des fragmentations peuvent être observées. L’utilisation d’un précurseur d’ionisation chimique plus lourd et moins réactif que H₃O⁺ pourrait minimiser ces phénomènes. L’utilisation du diflurobenzène protoné a été testée et comparée à celle de l’ion H₃O⁺. Pour cela, des études cinétiques ont été menées sur une série d’alcools connus pour fragmenter avec H₃O⁺, et confirment l'intérêt du nouveau précurseur.Le poly(méthacrylate de méthyle) (PMMA) est un matériau très répandu : plexiglass. Sa dégradation est a priori relativement simple puisqu’il s’agit très majoritairement d’une dépolymérisation, accompagnée de la formation de produits minoritaires. En conséquence, son étude nous a paru intéressante pour la mise au point et la validation de la méthode. La dégradation du PMMA a été étudiée sous atmosphère inerte, puis oxydante. Les résultats obtenus sont présentés : produits émis, bilan en masse, et apport du suivi en temps réel de la dégradation, montrant en particulier que les produits minoritaires sont émis après le monomère.Enfin une dernière partie de conclusion présente les perspectives pour cette nouvelle méthode. / Polymeric materials are now ubiquitous in our environment and become irreplaceable for many applications such as packaging, textile or furniture. Knowledge of the life cycle of these materials from production to destruction becomes important for our societies. For instance, plastics may release Volatile Organic Compounds: VOCs are often toxic and their impact on the environment must be evaluated. The aim of this thesis work is the development of a laboratory method for identification and quantification of these emissions. The difficulty arises from the wide variety of compounds being potentially emitted. Moreover the desired method requires a high measurement rate ("real time") often incompatible with existing techniques. An analytical device coupling a furnace and a high-resolution mass spectrometer associated with a controlled chemical ionization method has been developed. This device is based on a low magnetic field FT-ICR compact mass spectrometer. The strengths of this technique are (i) high mass resolution allowing exact mass measurements, (ii) recording of the whole mass range simultaneously, allowing detection of a large variety of compounds. Controlled chemical ionization allows soft and quantitative ionization of molecules of interest. Proton transfer from H₃O⁺ ion (PTRMS) has shown its potentialities for VOC detection in many areas. After presenting the background and need, the developed experimental device is described in detail.The validation of this instrument for trace gas analysis has been performed at LPGP, using a nonthermal plasma depollution device. The results of acetaldehyde degradation according to operating conditions in the discharge reactor are presented.PTR ionization usually leads to the protonated molecule, so that identification is simplified. However fragmentations are sometimes observed. Use of a chemical ionization precursor ion heavier and less reactive than H₃O⁺ may minimize these drawbacks. Protonated difluorobenzene was selected as a precursor and its reactivity was tested and compared with H3O+ reactivity. In this purpose, kinetic studies were performed on a series of alcohols known for their fragmentation behavior with H₃O⁺. The results confirm the interest of the new precursor.Polymethyl methacrylate (PMMA) is a widespread material: plexiglass. Its degradation process is relatively simple since it consists in predominant depolymerization, along with formation of minor products. Consequently, PMMA study appeared interesting for method development and validation. Thermal degradation of PMMA has been studied under inert, then oxidative atmosphere conditions. The presented results include identification of minor products and mass balance under different temperature conditions. Real-time monitoring of VOC emission showed time differences in emission peaks of MMA monomer and minor products, each of them being emitted slightly later than MMA. Finally, a conclusive part presents the perspectives opened for this new method.

Pregnenolona (PREG) e 17-alfa-hidroxipregnenolona (17OHPREG) são dois esteroides produzidos pela glândula adrenal e precursores de vários hormônios esteroidais. A dosagem desses compostos tem aplicações clínicas, como o diagnóstico de doenças relacionadas aos corticoesteroides e mineralocorticóides e especialmente na avaliação da atividade da enzima 3-&#946;-hidroxidesidrogenase que é decisiva no diagnóstico de um dos tipos de hiperplasia da glândula adrenal que causa defeitos severos na síntese de esteroides. Métodos cromatográficos associados à espectrometria de massas superaram a especificidade reduzida dos imunoensaios e tem sido crescentemente utilizados na quantificação de esteroides. Os últimos anos tem sido marcados pela hegemonia da cromatografia líquida acoplada à espectrometria de massas em tandem (LC-MS/MS) em grande parte devido à velocidade e possibilidade da análise direta de vários analitos. Porém, no caso específico dos esteroides de tipo 3-hidroxi-5-eno, que apresentam baixa afinidade protônica e, portanto, baixa eficiência de ionização, são necessárias muitas etapas para a conversão em derivados mais detectáveis. Embora desfavorecida em relação ao LC-MS/MS nos últimos anos, a cromatografia gasosa acoplada à espectrometria de massas (CG-MS) apresenta várias características favoráveis para a análise de esteroides como a eficiência cromatográfica ainda insuperável. Adicionalmente, a incorporação da espectrometria de massas em tandem ao CG (CG-MS/MS) torna a técnica tão seletiva quanto LC-MS/MS. No presente trabalho, foi desenvolvido um novo método que permite a extração e derivatização simultâneas da PREG e 17OHPREG de amostras de soro tornando o método de preparo da amostra tão simples quanto os descritos para LC-MS/MS. O método de detecção desenvolvido baseado em ionização química no modo negativo obteve a sensibilidade necessária para o diagnóstico da deficiência da enzima 3-beta-hidroxidesidrogenase utilizando apenas 250 &#181:L de amostra. / Pregnenolone (PREG) and 17&#945;-hydroxypregnenolone (17OHPREG) are two steroid precursors produced by the adrenal gland. The quantification of these compounds is essential for the evaluation of 3-&#946;-hidroxidesidrogenase enzyme activity, which promotes the conversion of PREG in 17OHPREG. The 3-&#946:-hidroxidesidrogenase deficiency is a rare but severe type of adrenal hyperplasia that causes serious defects in steroid synthesis. Chromatographic methods coupled to mass spectrometry overcame immunoassays limitations such as reduced specificity, and have been widely used for steroids quantification. Recent years have been marked by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) hegemony due to the speed and possibility to analyze directly several analytes. However, in the case of type 3-hydroxy-5-ene steroids, which have low affinity for protons and, therefore, low ionization efficiency, many steps are required for conversion to detectable products. Notwithstanding, gas chromatography coupled to mass spectrometry (GC-MS) has some favorable features for steroid analysis such as unbeatable chromatographic efficiency. In addition, the incorporation of tandem mass spectrometry (GC-MS/MS) makes it as selective as LC-MS/MS. In this study, a new method for simultaneous extraction and derivatization of PREG and 17OHPREG from serum was developed. This procedure makes sample preparation for GC-MS/MS as simples as those described for LC-MS/MS. The detection method based on negative mode chemical ionization achieved the sensitivity required for the diagnosis of 3-&#946;-hidroxidesidrogenase defficiency using only 250 &#181;L of sample.

Condensed phase membrane introduction mass spectrometry (CP-MIMS) is a direct, in situ analysis technique that is well suited to persistent organic pollutants, pesticides, and other small molecules. In CP-MIMS, neutral analytes permeate a hollow fibre membrane, typically polydimethylsiloxane (PDMS), driven by a concentration gradient. Analytes are subsequently dissolved by a liquid (condensed) solvent acceptor phase that is continuously flowed through the membrane lumen, which finally entrains the analytes to a mass spectrometer for detection. The membrane rejects charged and particulate matrix components, therefore eliminating sample cleanup that is otherwise necessary for conventional (i.e., chromatographic) techniques. However, larger analytes may suffer from relatively lengthy response times and lower sensitivity. A heptane cosolvent was therefore doped into the PDMS membrane, resulting in a polymer inclusion membrane (PIM). Through a system coupling CP-MIMS to electrospray ionization (ESI), the use of a PIM for model compounds resulted in faster response (~3×) and improved sensitivity (~3.5×, parts per trillion level detection limits). While effective for the demonstration of the PIM, pairing ESI with CP-MIMS represents an inherent incongruity: ESI is effective for polar, hydrophilic analytes, whereas CP-MIMS (i.e., PDMS membranes) is effective for hydrophobic analytes. CP-MIMS was therefore coupled with liquid electron ionization (LEI) as a more suitable ionization strategy. In LEI, the post-membrane solvent flow is entrained at nanolitre per minute flowrates to a LEI source, where the liquid is sequentially nebulized, vaporized, and ionized. The CP-MIMS-LEI coupling was optimized for the measurements of polycyclic aromatic hydrocarbon (PAH) isomer classes from aqueous samples, demonstrating low ng/L detection limits and response times (≤1.6 min). CP-MIMS-LEI was also applied to PAH isomer classes from soil samples, demonstrating rapid sample throughput (15 samples/hr) and low μg/kg detection limits, and additionally was quantitatively comparable to conventional techniques. A similar CP-MIMS-LEI system was applied to online monitoring of catalytic oxidation and alkylation reactions, demonstrating quantitative, real-time results for harsh, complex organic reaction mixtures. A significant analytical improvement was conducted by intentionally exploiting the already present liquid acceptor phase as an in situ means of providing liquid chemical ionization (CI) reagents for improved analyte sensitivity and selectivity (i.e., CP-MIMS-LEI/CI). Acetonitrile and diethyl ether were used as a combination acceptor phase/CI reagent system (i.e., proton transfer reagents) for the direct analysis of bis(2-ethylhexyl)phthalate from house dust (6 mg/kg detection limit). CP-MIMS-LEI/CI was then applied to PAHs from soils. Using methanol and dichloromethane combination acceptor phase/CI reagents, CP-MIMS-LEI/CI was shown to quantify and resolve PAH isomers from direct soil analyses via diagnostic PAH adduct ions: [M+CH2Cl+CH3OH-HCl]+ or [M+CHCl2-HCl]+. Using these selective ions, CP-MIMS-LEI/CI was again shown to be rapid (15 soils/hr), sensitive (ng/g detection limits) and quantitatively comparable to gas chromatography-MS for PAH measurements (average percent difference of -9% across 9 PAHs in 8 soil samples). The results across this thesis present a compelling argument for direct, quantitative screening from complex samples using CP-MIMS-LEI/CI, particularly given the simple workflow and short analytical duty cycle. / Graduate

<p>Crude oil is a mixture of hydrocarbons so complex that it is predicted to comprise as many compounds as there are genes in the human genome. Developing methods to not only recover crude oil from the ground but also to convert crude oil into desirable products is challenging due to its complex nature. Thus, the petroleum industry relies heavily on analytical techniques to characterize the oil in reservoirs prior to enhanced oil recovery efforts and to evaluate the chemical compositions of their crude oil based products. Mass spectrometry (MS) is the only analytical technique that has the potential to provide elemental composition as well as structural information for the individual compounds that comprise petroleum samples. The continuous development of ionization techniques and mass analyzers, and other instrumentation advances, have primed mass spectrometry as the go-to analytical technique for providing solutions to problems faced by the petroleum industry. The research discussed in this dissertation can be divided into three parts: developing novel mass spectrometry-based methods to characterize mixtures of saturated hydrocarbons in petroleum products (Chapters 3 and 5), exploring the cause of fragmentation of saturated hydrocarbons upon atmospheric pressure chemical ionization to improve the analysis of samples containing these compounds (Chapter 4), and developing a better understanding of the chemical composition of crude oil that tightly binds to reservoir surfaces to improve chemically enhanced oil recovery (Chapter 6). </p>

Lipids from the fat body of queens of Bombus terrestris species in different life stages were studied using chromatographic methods. High-performance liquid chromatography - mass spectrometry with electrospray ionization was used to analyze all lipids from the tissue. Semi- preparative thin-layer chromatography was used to isolate triacylglycerols (TGs) from the fat body tissue. The TGs were subsequently analyzed by high-performance liquid chromatography - atmospheric pressure chemical ionization mass spectrometry. Quantitative differences between different life stages have been found. Qualitative composition has not been changing significantly. Only minor differences have been found in the substances, which were present in amount less than 1%.