<p>High-resolution mass spectrometry (MS) and tandem mass spectrometry (MS/MS) are powerful tools for the characterization of the molecular structures of components of both simple and complex mixtures. MS and MS/MS have played key roles in many fields, including proteomics, metabolomics, and petroleomics. This thesis focuses on the development of tandem mass spectrometric methods for the structural characterization of asphaltenes and small isomeric molecules. In addition, this thesis also presents a method to address a sampling bias in asphaltene analysis. </p>

<p>Mass spectrometry-based techniques have been widely used in reaction monitoring due to their high sensitivity and ability to offer structure information by tandem mass spectrometry. We applied nanoelectrospray mass spectrometry (nanoESI-MS) to simultaneously monitor pre-catalysts, catalytic intermediates, reagents, and products of palladium catalyzed Suzuki-Miyaura cross-coupling reactions. A set of Pd cluster ions related to the monoligated Pd (0) active catalyst is detected, and its deconvoluted isotopic distribution reveals contributions from two neutral molecules. One is assigned to the generally accepted Pd (0) active catalyst, seen in MS as the protonated molecule, while the other is suggested to correspond to a deactivated form of Pd catalyst. Oxidative stress testing of the synthetic model catalyst XPhos Pd cyclo-octadiene, performed using oxygen and Fe(III), supported this assignment. Thus, the make-up of the monoligated set of Pd (0) ions appears to indicate the oxidation state of the system. The formation and removal of the oxidative addition intermediate during the catalytic cycle was monitored to provide information on the progress of the transmetalation step. </p> <p> </p> <p><a>Recently, microdroplets created by ambient ionization source have been used as reaction vessels to accelerate organic reactions. Field desorption mass spectrometry under ambient conditions is applied to study solution-phase organic reactions in micro-volumes. Compared to nanoelectrospray, it is noteworthy that radical cations and formation of radical cation products are observed. Three reactions, the hydrazone formation by phenyl hydrazine and indoline-2,3-dione, the Katritzky reaction between a pyrylium salt and anisidine, and the Hantzsch synthesis of 1,4-dihydropyridine, were investigated by this system and reaction acceleration was observed to different extents. The increase in rate relative to that for the corresponding bulk reactions is attributed to solvent evaporation which increases concentration, and to the increase of surface-to-volume ratio with enhanced interfacial reaction rate constants. Later work in this thesis describes explicit solvent calculations to study the energies and structures of the hydrazone formation reaction from phenylhydrazine and indoline-2,3-dione in acidic methanol with density functional tight binding (DFTB) methods. Additionally, the thesis covers MS based methods for determination of isoaspartate and aspartate in peptide by gas-phase chemistry and detection of S-nitrosoglutathione in exhaled breath condensate sample.</a></p>

<div> <div> <div> <p>Mycobacteriophages are the viruses that infect mycobacteria. Due to the high death rate and antibiotic-resistant strains, phage therapy is considered to be a promising treatment of tuberculosis. Current understanding of phage-bacteria interaction is abstracted as phage lytic and lysogenic life cycles. However, bacterial physiology may impact phage life cycles and bacterial cells with different physiology may have different responses to phage infection. In order to improve the understanding of phage-bacteria interaction and update phage therapy strategy, the impact of mycobacterial physiology on mycobacteriophage life cycles was studied in this research. In this research, a mass spectrometry-based method was first developed to study phage proteins in phage-bacteria mixture. Then five mycobacteriophages isolated at Purdue University were selected to infect exponential and stationary <i>Mycobacterium smegmatis</i> (<i>M. smegmatis</i>) cell cultures. Growth curves of the <i>M. smegmatis</i> cell cultures infected by the five phages were determined. Proteomics and lipidomics of the <i>M. smegmatis</i> cells cultures infected by phages FrenchFry and MrGordo were analyzed by mass spectrometry. The correlations between individual proteins/lipids and the experimental factors (bacterial growth phases, phages and phage infection time) were studied by developing linear regression models using SAS. The mass spectrometry-based method was proved to be able to detect phage proteins other than the structural proteins. It also verified the phage protein annotation that had been accomplished <i>in silico</i>. X! Tandem and a database consisting of six frame translation of the phage genome and the annotated proteins of <i>M. smegmatis</i> were the optimal option for analyzing mass spectra data of phage-bacteria mixture. The growth curves of the <i>M. smegmatis</i> infected by the phages displayed that growth of exponential <i>M. smegmatis</i> cell cultures were depressed by phages (except FrenchFry) and stationary <i>M. smegmatis</i> cell cultures were not actively lysed by any of the phages. The proteomics results showed that MrGrodo infection impacted more proteins than other factors did. Exponential phase up-regulated proteins involved in cell division. Stationary phase up-regulated proteins that may change cell surface properties. FrenchFry up-regulated LuxR protein. Infection time up-regulated the proteins associated with mycobacterial virulence. The lipidomics results indicated that growth phases impacted the most lipids. Phage infection time increased the amount of the lipids related to mycobacterial virulence. In summary, the mass spectrometry-based method developed in this research can be employed to study phage proteins in phage-bacteria mixture and verify phage genome annotation. Mycobacterial physiology alters mycobacteriophage life cycles. Phage-bacteria interaction is the interaction between the two populations instead of between an individual phage particle and an individual bacterial cell. Virulence of <i>M. smegmatis</i> improves as a response to phage infection.</p></div></div></div>

<div>Mass spectrometry (MS) is a powerful and versatile analytical tool that is extensively used for the identification and analysis of complex mixtures. The ability to couple MS to atmospheric pressure ionization techniques and high-performance liquid chromatography (HPLC) or gas chromatography (GC) provides a high degree of experimental flexibility. MS is based on the analysis of gas-phase ions. Gas-phase ions are manipulated within the mass spectrometer and separated for detection based on their mass-to-charge (m/z) ratio.</div><div>One of the most commonly used techniques for complex mixture analysis is tandem mass spectrometry (MSⁿ). MSⁿ involves the isolation of the desired ion and allowing it to undergo reactions, such as collision-activated dissociation (CAD) or ion-molecule reactions. Based on the generated product ions, structural information can be obtained for unknown analytes in complex mixtures. In addition, MSⁿ methods based on diagnostic gas-phase ion-molecule reactions have been demonstrated to provide a general and predictable tool to identify specific functional groups in unknown ionized analytes and to classify unknown analytes into different compound classes depending on their functionalities.</div><div>The research described in this dissertation mainly focuses on the development of tandem mass spectrometric methods based on gas-phase ion-molecule reactions and/or CAD for the identification of the <i>N</i>-nitroso functionality, which is present in some potentially mutagenic drug impurities. Furthermore, the dissertation discusses combining machine learning and MSⁿexperiments based on diagnostic ion-molecule reactions of 2-methoxypropene to predict reaction outcomes in a semiautomated fashion for protonated analytes containing specific functional groups. Lastly, chemical characterization and gas-phase reactivity of the boron-centered radical dianion [B₁₂I₁₁]^2-• toward some organic molecules are discussed.</div>

<p>Mass spectrometry (MS) is a versatile analytical tool that is especially useful for identification of unknown compounds in mixtures when coupled with chromatography. In MS experiments, the analytes are ionized, separated based on their mass-to-charge (<i>m/z</i>) ratios, and detected. The molecular weight of the analyte can often be derived from the mass spectrum if stable molecular ions (M^•+) or stable protonated/deprotonated analyte molecules ([M+H]⁺ or [M-H]^–) are generated. Further, MS can also be used to obtain structural information for the ionized analytes via their fragmentation reactions. Tandem mass spectrometry (MSⁿ) experiments are powerful for the characterization of unknown compounds in mixtures without the need for coupling them with chromatography. In MSⁿ experiments, the analytes are ionized, the ions of interest are isolated and subjected to reactions, such as collision-activated dissociation (CAD) or ion-molecule reactions with neutral reagent molecules. The fragmentation pattern or the diagnostic ion-molecule reaction product ions can be utilized to elucidate the structures of the analytes. The fragment ions or diagnostic product ions can further be subjected to CAD to obtain more structural information. Besides analytical purposes, MSⁿ also provides a powerful tool for exploring the reactivities of reaction intermediates that are elusive, such as phenylcarbyne anions and phenylcarbene anions.</p> <p>The research described in this dissertation mainly focuses on the development of MSⁿ methods based on diagnostic gas-phase ion-molecule reactions followed by CAD for (1) the characterization of differently substituted ureas and (2) the differentiation of sulfonate esters from their isomeric analogs, such as sulfite esters and sulfones. HPLC was coupled with the MSⁿ methods discussed above to demonstrate its usefulness in the identification of compounds in mixtures. Additionally, a gas-phase reactivity study on phenylcarbyne anions is discussed in this dissertation. The phenylcarbyne anions were generated by CAD of two nitrogen molecules from negatively charged phenyl tetrazole precursors. Their reactivities towards various reagents were explored and rationalized with the help of quantum chemical calculations.</p>

La photothérapie dynamique (PDT) consiste à injecter un photosensibilisateur (PSr) au patient, puis à illuminer sa tumeur. En présence d’oxygène, le PSr activé entraîne la formation d’oxygène singulet cytotoxique. Nos collaborateurs à l’Institut Curie ont synthétisé des dérivés porphyriniques glycoconjugués(TPP) pour traiter le rétinoblastome par PDT.Des études de caractérisation de ces TPP in vitro ont montré une internalisation dans la cellule par voie passive. C’est dans ce contexte que nous avons analysé l’interaction de certaines TPP avec les lipides membranaires.Dans un premier temps, cette interaction a été étudiée par une approche chromatographique sur des colonnes C18/C8, PolarTec, HILIC et IAM. Nous avons démontré une variation de l’interaction selon la structure des TPP. Par la suite, nous avons mis en évidence par DSC, les changements d’organisation de bicouches phospholipidiques produits par deux TPP d’intérêt, et déterminé par FTIR-ATR, la localisation de la perturbation au niveau des têtespolaires ou des chaines aliphatiques des lipides.Cette approche a été poursuivie par l’évaluation de la localisation des TPP à l’échelle cellulaire,par microspectroscopie IR couplée au rayonnement synchrotron. Une discrimination des TPP a été mise en évidence par des outils chimiométriques pour les cellules Y79, mais pas pour les lignées WERI-Rb1 ni ARPE-19. Afin de développer un modèle membranaire artificielde rétinoblastome, nous avons réalisé par spectrométrie de masse (Orbitrap) une analyse lipidomique approfondie des phospholipides des membranes plasmiques et mitochondriales des lignées Y79 et ARPE-19,. Nous avons analysé les propriétés visco-élastiques des extraits membranaires et proposé un modèle artificiel complexe mimant au moins partiellement ces propriétés. Ce modèle pourrait permettre le criblage in vitro des TPP. / Photodynamic therapy (PDT) is atreatment modality in which a photosensitizer(PSr) is injected to a patient. Then the tumor isilluminated with a laser. The excited PSrinduces the production of cytoxic singletoxygen. Our collaborators at the Institut Curiehave synthesized glycoconjugated tetraphenylporphyrins(TPP) for the treatment ofretinoblastoma by PDT. These compoundswere characterized in vitro and studies showedthat the most promising porphyrin crossed thecell membrane by passive transport. It is in thiscontext that this research was developed: theobjective was to study the interaction of aseries of porphyrins with membrane lipids.Firstly, porphyrin interaction with lipids wasstudied by a chromatographic approach onC18/C8, PolarTec, HILIC and IAM columns.Results showed a variation in the interactionaccording to porphyrin structures.Then, we demonstrated the effect of two TPPson phospholipid bilayers organization by DSC,and determined the localization of thisinteraction (polar heads or lipid aliphaticchains) by FTIR-ATR. The effect of TPPs onlipids and proteins was studied at the cellularlevel by IR microspectroscopy coupled withsynchrotron radiation. A discrimination ofporphyrins could be made by chemometrictools for Y79 cells but not for WERI-Rb1 norARPE-19 ones. In order to develop an artificialmembrane model, we performed lipidomicanalysis by mass spectrometry (Orbitrap) ofplasma and mitochondrial lipid membranes ofY79 and ARPE-19 cells. We determined theviscoelastic properties of lipid extracts andproposed an artificial lipid model partiallymimicking these viscoelastic properties. Thismodel could allow TPP screening in vitro.

L'aérosol atmosphérique a des effets sur le changement climatique global et un impact sanitaire non-négligeables. Dans l'aérosol atmosphérique terrestre, les composés organiques représentent une fraction importante. Du fait de l'extrême complexité de cette fraction organique et des processus dynamiques qui l'animent, une fraction non négligeable de celle-ci n'est pas clairement identifiée à ce jour malgré des techniques d'analyses toujours plus nombreuses. Dans cette thèse, nous avons voulu explorer la richesse d'information fournie par une technique innovante : la spectrométrie de masse à haute résolution (HRMS). La haute résolution du LTQ-Orbitrap fournit une extrême précision sur la masse des molécules analysées et permet d'en identifier les formules brutes. Tout d'abord, nous avons utilisé cette nouvelle méthode de caractérisation afin d'élucider en laboratoire des mécanismes de production de l'aérosol se déroulant en phase aqueuse. Associée à une caractérisation par RMN, la HRMS nous permet d'identifier des voies de fabrication de composés de faible poids moléculaires (acides carboxyliques, aldéhydes, cétone) ainsi que des composés à haut poids moléculaire : les oligomères formés se transforment en HULIS au cours de leur vieillissement. Le fait que la méthacroléine (MACR) et la méthyl-vinyl-cétone (MVK), les deux principaux produits d'oxydation de l'isoprène, forment des AOS en phase aqueuse avait été précédemment montré. Ce travail montre que les précurseurs des AOS sont différents selon l'isomère et que les séries d'oligomères formées atteignent 1400 Da.. L'étude HRMS des produits permet de proposer un mécanisme radicalaire d'oligomérisation de la MVK. L'analyse HRMS des produits de la MACR montre qu'en plus du mécanisme valable pour la MVK, la réactivité de la MACR engendre co-polymérisation et production d'Hulis. Une signature HRMS des Hulis a été mise en évidence. Ensuite, nous avons utilisé les méthodes de traitement de données HRMS pour tenter de les appliquer à l'identification d'aérosol ambiant. Les composés organiques représentent la fraction majeure des particules de l'aérosol atmosphérique ; une grande partie reste mal identifiée. Une compréhension détaillée des sources et des procédés de transformations est nécessaire. L'investigation de la composition chimique des particules de matière fine et ultrafine peut être apporter par HRMS. L'ESI-Orbitrap apporte une description moléculaire qui détermine les propriétés chimiques et physiques de l'aérosol organique. Les particules ont été échantillonnées selon leur taille respective. Les prélèvements ont été fait à Grenoble en été et en hiver. Une comparaison saisonnière permet d'identifier des signatures chimiques différentes. Enfin, une intercomparaison est établie avec des échantillons d'une troisième campagne prélevées en proximité routière: MOCOPO. / Atmospheric aerosol has an important impact on the radiative balance of Earth. Organics compounds represent the major fraction of atmospheric aerosol particles; a large part is still not well characterized. A detailed understanding of the sources, transformations processes and fates of organics aerosols is needed. This work investigates the ability of the ESI-Orbitrap to characterize organics molecules of aerosol. Firstly, experimental and analytical methods were developed to unveil mechanistic ambiguities that were previously shown. Methacrolein (MACR) and methyl vinyl ketone (MVK) (the two main gas phase atmospheric oxidation products of isoprene) were known to form oligomers and secondary organic aerosol (SOA) upon aqueous phase OHoxidation and subsequent water evaporation. For the two precursors, ESI-MS analysis of the reacting solutions brought clear evidence for the formation of oligomer systems having a mass range of up to 1400 Da.. Taking advantage of the regularities observed in the oligomer systems, the ESI-HRMS data were used to propose stoichiometries for more than 75% of the observed signal. Moreover, we show here that MACR oligomers aging give rise to HULIS production. In addition, global estimates of secondary organic aerosol (SOA) formation flux show that current descriptions miss a large fraction of the sources. This gaping underestimation has been linked to a poor understanding of aerosol functionalization in the atmosphere and lead to the formation of a new conceptual framework for the description of the aerosol, based on volatility versus polarity plots. This new framework is almost exclusively based on High Resolution Time of Flight Aerosol Mass Spectrometer(HR-Tof-AMS) data, as this instrument gives access to average H:C, N:C and O:C ratios for the bulk aerosol. The AMS estimates for O:C and H:C ratios are thus based on heavy fragmentation of organics followed by stoichiometry attribution on those fragments. Given the resolution of the HR-ToF-AMS, such an attribution is not feasible above a certain mass, making fragmentation a necessary aspect of the measurement. Conversely, Orbitrap-HRMS provide a resolution of 100,000 at m/z 400, with a mass range 50 – 2000 amu, enabling stoichiometry retrieval up to higher masses than the AMS. Coupled to a “soft” electrospray ionization method, Orbitrap-HRMS gives O:C and H:C ratios on entire molecules in the analysed mixture. We used samples from three contrasted field campaigns: the two first at an urban kerbside site in summer and in winter, the third one in the roadway vicinity (Grenoble, France). Accelerated Solvent Extraction provides a clear overview of the chemical composition of organic extracts from aerosol particles collected at different season at an urban site. The elemental composition was obtained within 2-5 ppm, on the range 150-300 m/z. However, this study shows that both ionization polarity were needed to get a complete picture of the chemical composition of the samples. We showed that Esi-Orbitrap-HRMS allows to compute a statistical distribution of the elementary ratios that is different from a simple average value. Keywords: HRMS, SOA.