A espectrometria de massas baseada na tecnologia MALDI-TOF (do inglês, matrix-assisted laser desorption ionization-time of flight) (MALDI-TOF MS) tem sido cada vez mais incorporada à rotina de identificações microbiológicas nos laboratórios farmacêuticos de controle de qualidade, principalmente para as atividades do Programa de Monitoramento Ambiental de Salas Limpas. Isso porque o longo tempo necessário para a obtenção dos resultados por meio de métodos convencionais tem incentivado a procura por técnicas que permitam métodos rápidos. O objetivo deste trabalho foi avaliar a adequação da técnica MALDI-TOF MS para a identificação de bactérias isoladas do ambiente de salas limpas utilizadas em algumas etapas da produção de uma vacina viral. Treze espécies bacterianas conhecidas, normalmente isoladas das salas limpas estudadas, e cinco cepas ATCC foram identificadas pela técnica MALDI-TOF MS e por uma técnica bioquímica (BBL Crystal®). O desempenho da técnica MALDI-TOF MS foi superior ao da técnica bioquímica na identificação correta das espécies bacterianas (88,89% e 38,89%, respectivamente) e produziu menos identificações não confiáveis (5,55% e 22,22%, respectivamente). Os resultados evidenciaram que a técnica MALDI-TOF MS pode ser implementada para identificação rotineira de bactérias em um laboratório de controle de qualidade farmacêutico. Entretanto, a dependência de bases de dados exige estudos adicionais de isolados não identificados e, se apropriado, a adição destes a uma base de dados interna. O aperfeiçoamento de métodos de identificação microbiana é muito relevante no contexto de salas limpas, pois permitem ações corretivas e proativas essenciais para garantir a segurança microbiológica do processamento asséptico. / Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been increasingly introduced in routine microbiological identifications of pharmaceutical quality control laboratories, mainly for the activities of the Environmental Monitoring Program of Clean Rooms. The long time needed to obtain the results through conventional methods has stimulated the search for techniques that allow rapid methods, as MALDI-TOF MS. Thus, the objective of this work was to evaluate the suitability of the MALDI-TOF MS technique for the identification of bacteria isolated from the environment of clean rooms used in some stages of the production of a viral vaccine. Thirteen bacterial species commonly isolated from clean rooms studied and five strains ATCC were identified by MALDI-TOF MS technique and by a biochemical technique (BBL Crystal® System). Performance of MALDI-TOF MS was better than biochemical technique for correct species identifications (88.89% and 38.89%, respectively) and produced fewer unreliable identifications (5.55% and 22.22%, respectively). MALDI-TOF MS can be implemented for routine identification of bacteria in a pharmaceutical quality control laboratory. However, as a database-dependent system, maybe some isolated not identified by this technique must be additionally studied and, if appropriate, added to an in-house database.

This PhD project investigated the ramifications of air-cured and nitrogen-cured manufacturing processes during silicone hydrogel contact lens manufacture in terms of lens surface characterisation and clinical performance. A one-hour contralateral clinical study was conducted for ten subjects to compare the clinical performance of the two study lenses. The main clinical findings were reduced levels of subjective performance, reduced surface wettability and increased deposition. Contact angle analysis showed the air-cured lenses had consistently higher advancing and receding contact angle measurements, in comparison with the nitrogen-cured lens. Chemical analysis of the study lens surfaces in the dehydrated state, by x-ray photoelectron spectroscopy (XPS) and time-of-flight mass spectrometry (ToF-SIMS), showed no difference due to surface segregation of the silicone components. Analysis of frozen lenses limited surface segregation and showed a higher concentration of silicone polymer components and lower concentration of hydrophilic polymer components at the surface of the air-cured lens, in comparison with the nitrogen-cured lens. Scanning electron microscope (SEM) imaging showed the nitrogen-cured lens to have a surface typical of a hydrogel material, whereas the air-cured lens had regions of apparent phase separation. In addition, atomic force microscopy (AFM) showed the air-cured lens to have a rougher surface associated with greater adherence of contaminants (often observed in materials with reduced polymer cross-linking). In conclusion, clinical assessment of the study lenses confirmed the inferior performance of the air-cured lens. Surface analysis suggested that the non-wetting regions on the air-cured lenses were associated with elevated level of silicone components, reduced polymer cross-linking and polymer phase separation.

Capillary electrophoretic (CE) separations were successfully coupled to time-of-flight mass spectrometric (TOFMS) detection for the analysis of three families of biological compounds that act as mediators and/or indicators of disease, namely, catecholamines (dopamine, epinephrine, norepinephrine) and their O-methoxylated metabolites (3-methoxytyramine, norepinephrine, and normetanephrine), indolamines (serotonin, tryptophan, and 5-hydroxytryptophan), and angiotensin peptides. While electrophoretic separation techniques provided high separation efficiency, mass spectrometric detection afforded specificity unsurpassed by other types of detectors. Both catecholamines and indolamines are present in body fluids at concentrations that make it possible for them to be determined by capillary zone electrophoresis coupled to TOFMS without employing any preconcentration scheme beyond sample work up by solid phase extraction (SPE). Using this hyphenated approach, submicromolar levels of catecholamines and metanephrines in normal human urine and indolamines in human plasma were detected after the removal of the analytes from their biological matrices and after preconcentration by SPE on mixed mode cation-exchange sorbents. The CE-TOFMS and SPE methods were individualized for each group of compounds. While catecholamines and metanephrines in urine samples were quantitated using 3,4-dihydroxybenzylamine as an internal standard, deuterated isotopes, considered ideal internal standards, were used for the quantitation of indolamines. Because the angiotensin peptides are present in biological fluids at much lower concentrations than the previous two families of analytes, their analysis required the application of additional preconcentration techniques. In this work, the coupling of either of two types of electrophoretic preconcentration methods - field amplified injection (FAI) and isotachophoresis (ITP) - to capillary zone electrophoresis with both UV and MS detection was evaluated. Using FAI-CE-UV, angiotensins were detected at ~1 nM concentrations. Using similar conditions but TOFMS detection, the detection limits were below 10 nM. ITP was evaluated in both single-column and two-column comprehensive arrangements. The detection limits achieved for the ITP-based techniques were approximately one order of magnitude higher than for the FAI-based preconcentration. While the potential usefulness of these techniques was demonstrated using angiotensins standards, substantial additional research would be required to allow these approaches to be applied to plasma as part of clinical assays.

To investigate the influence of the internal micellar structure on the course of enzymatic cross-linking especially in the initial phase of the reaction, casein micelles isolated from raw milk via ultracentrifugation were incubated with microbial transglutaminase (mTG) in comparison with non-micellar sodium caseinate. Reactive lysine and glutamine residues were identified using a label-free approach, based on the identification of isopeptides within tryptic hydrolysates by targeted HRMS as well as manual monitoring of fragmentation spectra. Identified reactive sites were furthermore weighted by tracking the formation of isopeptides over an incubation time of 15, 30, 45 and 60 min, respectively. Fifteen isopeptides formed in the early stage of mTG cross-linking of caseins were identified and further specified concerning the position of lysine and glutamine residues involved in the reaction. The results revealed lysine K176 and glutamine Q175 of β-casein as the most reactive residues, which might be located in a highly flexible region of the molecule based on different possible reaction partners identified in this study. Except for the isopeptide αₛ₁ K34–αₛ₂ Q101 in sodium caseinate (SC), all reactive sites were detected in micellar and in non-micellar casein, indicating that the initial phase of enzymatic cross-linking is not affected by micellar aggregation of caseins.

Fatty acids (FAs) represent an important class of metabolites, impacting on membrane building blocks and signaling compounds in cellular regulatory networks. In nature, prokaryotes are characterized with the most impressing FA structural diversity and the highest relative content of free fatty acids (FFAs). In this context, nitrogen-fixing bacteria (order Rhizobiales), the symbionts of legumes, are particularly interesting. Indeed, the FA profiles influence the structure of rhizobial nodulation factors, required for successful infection of plant root. Although FA patterns can be assessed by gas chromatography—(GC-) and liquid chromatography—mass spectrometry (LC-MS), sample preparation for these methods is time-consuming and quantification suffers from compromised sensitivity, low stability of derivatives and artifacts. In contrast, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) represents an excellent platform for high-efficient metabolite fingerprinting, also applicable to FFAs. Therefore, here we propose a simple and straightforward protocol for high-throughput relative quantification of FFAs in rhizobia by combination of Langmuir technology and MALDI-TOF-MS featuring a high sensitivity, accuracy and precision of quantification. We describe a step-by-step procedure comprising rhizobia culturing, pre-cleaning, extraction, sample preparation, mass spectrometric analysis, data processing and post-processing. As a case study, a comparison of the FFA metabolomes of two rhizobia species—Rhizobium leguminosarum and Sinorhizobium meliloti, demonstrates the analytical potential of the protocol.

Antalet monoklonala antikroppar som används i läkemedel ökar kraftigt. Dessa läkemedel är dyra och risken för förfalskning är stor. Behovet att utveckla en metod för snabb och precis identifiering av monoklonala antikroppar är därför brådskande. För identifiering utfördes analyser med Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-ToF-MS), Capillary Gel Electrophoresis (CGE) and Capillary Zone Electrophoresis (CZE) på nio monoklonala antikroppar. Fokuset var att undersöka huruvida signifikanta fysiokemiska egenskaper och unika aminosyrasekvenser var närvarande och kunde urskiljas. Olika analyser med MALDI-ToF-MS användes till att både separera de monoklonala antikropparna baserat på dess fysiokemiska egenskaper, och annotera aminosyrasekvenser innehållande nyckelfragment. Med metoderna baserade på kapillärelektrofores uppnåddes också separation. CZE föredras framför CGE då mängden data som erhålls från CZE är större och provberedningen är enklare. Sammanfattningsvis utformades ett protokoll för identifieringsprocessen, vilket inleds med MALDI-ToF-MS-analyser av monoklonala antikroppar på reducerad form mot kända referenser. Därefter är en hypotes formulerad utifrån vilka antikroppar som ser mest lika ut. Slutligen analyseras dessa med CZE för fastställning av den monoklonala antikroppens identitet. / The number of monoclonal antibodies used in pharmaceuticals is increasing sharply. These medicines are expensive, and the risk of counterfeiting is high. The need to develop a method for rapid and precise identification of monoclonal antibodies is therefore urgent. For identification, analyses were performed with Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-ToF-MS), Capillary Gel Electrophoresis (CGE) and Capillary Zone Electrophoresis (CZE) on nine monoclonal antibodies. The focus was to investigate whether significant physiochemical features and unique amino acid sequences were present and could be distinguished. Various analyses with MALDI-ToF-MS were used to both separate the monoclonal antibodies based on their physicochemical properties and annotate amino acid sequences containing key fragments. With the methods based on capillary electrophoresis, separation was also achieved. CZE is preferred over CGE as the amount of data obtained from CZE is greater and sample preparation is simpler. In summary, an identification process protocol was designed and is initiated with MALDI-ToF-MS analyses of reduced-form monoclonal antibodies against known references. A hypothesis is then formulated based on which antibodies look the most similar. Finally, these are analysed by CZE to determine the identity of the monoclonal antibody.

Phospholipids are dominant components of bacterial cell membranes, where they create double layers. Bacteria differ in their phospholipid composition determination of which can help in identification of important groups of microorganisms. Phospholipid composition of bacteria is influenced by many environmental factors, therefore its variation can be observed within one bacterial stem also. Because of its simplicity, thin layer chromatography is usually applied to identification and determination of bacterial phospholipids. Disadvantage of this method are the high demands of time, carefulness and skills of the analytical personnel. The increasing interest in the phospholipid double-layer promotes the detailed investigation of their fatty acid composition because the more detailed analyses allows for more information yield about bacteria. Gas chromatography hyphenated with mass spectrometry seems to be the best choice for these purposes. Fatty acid identity and total fatty acid content in phospholipid molecules could be determined by this method. Additionally, number, position and isomerism of double bonds and presence of other functional groups on hydrocarbon chain could be determined. Whereas a suitable and...

Le Lebanese Atomic Energy Commission (LAEC) poursuit un programme de développement des techniques analytiques pour compléter l’analyse par faisceau d’ions (IBA). Il a décidé de s’équiper d’un spectromètre de masse couplée à l’imagerie 2D puis récemment 3D avec l’acquisition d’un spectromètre de masse IONTOF V™ équipé de deux colonnes ioniques délivrant des faisceaux d’agrégats de bismuth et d’argon. Dans ce cadre, mon sujet de thèse a porté sur l'optimisation de l’instrument nouvellement acquis pour l’analyse d’échantillons contenant des composés organiques. Les premiers sujets de recherche sont la mise au point du protocole d’analyse quantitative de médicaments en utilisant la technique « cluster-SIMS-imaging » et l’analyse de la météorite Paris pour localiser la matière organique et déterminer sa composition. Dans les deux cas une approche multi-technique a été utilisée : IBA au LAEC, µ-Raman et µ-IR autour des équipements de Soleil et µPIXE réalisée auprès de l’accélérateur AGLAE (Centre de recherche et de restauration des musées de France, C2RMF).L’analyse de médicaments a été initiée au Liban en collaboration avec un fabricant local de produits pharmaceutiques (Mediphar Laboratories) dans le but d’établir de nouveaux procédés de contrôle qualité de produits finis. Mon étude a montré la complexité du dosage de médicament due à la présence de plusieurs molécules actives (Principe Actif, PA) et de substances organiques et minérales inactives (excipients) mélangées dans des conditions secrètes. Les effets de matrice sont dominants et modifient l’émission ionique conduisant à des erreurs systématiques importantes. Cette complexité a été analysée avec l’étude du Fludinium™ possédant deux PAs. Les résultats de cette étude ont permis d’obtenir la première courbe d’étalonnage du rapport des deux PAs et de quantifier ceux-ci dans les conditions du médicament commercial. Le protocole pour effectuer cette courbe d’étalonnage et les contrôles « qualité » ont été déterminés. Ceux-ci incorporeront une analyse en profil pour contrôler l’homogénéité des échantillons et l’obtention d’étalons produits par le fabricant en suivant ses processus de fabrication. En effet, les expériences ont montré que la réalisation du médicament en laboratoire à partir de ses éléments (PAs et excipients) ne donnait pas la même réponse ionique que le médicament commercial. L’analyse de la météorite Paris a été initiée par une collaboration avec une équipe de l’Institut d’Astrophysique Spatial d’Orsay impliquée dans l’exobiologie et la recherche des premières molécules pré-biotiques dans des échantillons extraterrestres. Le but des recherches est de caractériser la matière organique représentant quelques pourcents en poids dans une matrice minérale complexe, sans utiliser des méthodes chimiques pouvant induire une modification de ces molécules. Cette étude a démontré l’intérêt de l’approche multi-technique centrée autour de la spectrométrie de masse couplée à l’imagerie ionique pour déterminer les éléments principaux de la matrice minérale et organique. L’analyse par µPIXE avec une cartographie micrométrique a permis d’attribuer les distributions d’ions moléculaires et agrégats des spectres de masse aux différents composés minéraux. Ces attributions se poursuivent avec la constitution d’une base de données de spectres de référence. La composante organique a été extraite et les premières hypothèses de composition ont été envisagées autour des HAPs (Hydrocarbure Aromatique Polycyclique), MOI (Matière Organique Insoluble) et analogues de carbone amorphe produits par irradiation UV de glaces dont les compositions en gaz représentent différentes hypothèses pour les nuages interstellaires. Les protocoles d’analyses multi-techniques établis (incorporant un suivi de l’échantillon par spectrométrie de masse et imagerie ionique) permettent le démarrage d’analyse d’autres échantillons extra-terrestres collectés sur terre ou dans l’espace. / The Lebanese Atomic Energy Commission (LAEC) is incorporated in a development program of the analytical techniques in order to complete the Ion Beam Analysis (IBA). It was decided to get a mass spectrometer coupled to 2D and recently to 3D imaging, by acquiring an ION TOFVTM system equipped with two ionic columns delivering bismuth and argon cluster beams.In this context, my thesis is focused on the optimization of the instrument, recently purchased, for the analysis of samples containing organic compounds. The first subjects of research are the development of a protocol for quantitative analysis of drugs using the « cluster-SIMS-imaging » technique and the Paris meteorite analysis to determine its composition and to localize the organic matter. In the last case a multi-techniques approach was used : IBA in LAEC, µ-Raman et µ-IR around the Soleil synchrotron equipments and µPIXE carried with the AGLAE accelerator (Centre de recherche et de restauration des musées de France, C2RMF).The drug analysis was initiated in Lebanon in collaboration with a local pharmaceutical manufacturer (Mediphar Laboratories) in order to establish new processes for quality control of the final products. My study showed the complexity of the drug quantification which is due to the presence of several active ingredients (AI) and inactive organic and minerals components (excipients) mixed in secret conditions. Matrix effects are dominant and modify the ionic emission leading to significant systematic errors. This complexity has been analyzed with the study of FludiniumTM with two active ingredients. The results of this study allowed to obtain the first calibration curves of the ratio between the two AIs and to quantify them in the commercial drug. The protocol to perform the calibration curve and the « quality» controls were determined. These incorporate a profile analysis to control the homogeneity of the samples and the obtaining standards produced by the pharmaceutical manufacturer following the same process used for the commercial drug. Indeed, the experiments have shown that the preparation of the drug in the laboratory from its elements (AIs and excipients) doesn’t give the same ionic emission as for the commercial drug.The Paris meteorite analysis was initiated by a collaboration with the Institut d’Astrophysique Spatiale d’Orsay team involved in the exobiology and the research of the first prebiotic molecules in the extraterrestrial samples. The work objective is to characterize the organic matter representing few percents in mass in a complex mineral matrix, without any chemical extraction that can induce a modification of these molecules. This study has demonstrated the interest of the multi-techniques approach centered on the mass spectrometry coupled to the ionic imaging for the determination of the main mineral and organic elements of the matrix. µPIXE analysis coupled to the micrometric mapping permits to attribute the distribution of molecular ions and clusters of the mass spectra with different mineral compounds. These attributions continue with the creation of the data base of standard spectra. The organic component was determined and the first hypotheses were considered concerning PAHs (Polycyclic Aromatic Hydrocarbon), IOM (Insoluble Organic Matter) and analogues of amorphous carbon produced par UV irradiation of ices with a gas composition representing different hypotheses for the interstellar clouds. The establish protocols for multi-techniques (incorporating a follow of the sample by mass spectrometry and ion imaging) permits to start the analysis of other extra terrestrial samples collected on earth or in space.

<p>This dissertation focused on the development of mass spectrometric methodologies, separation techniques, and engineered devices for the optimal analysis of complex mixtures relevant to the energy sector, such as alternative fuels, petroleum-based fuels, crude oils, and processed base oils. Mass spectrometry (MS) has been widely recognized as a powerful tool for the analysis of complex mixtures. In complex energy samples, such as petroleum-based fuels, alternative fuels, and oils, high-resolution MS alone may not be sufficient to elucidate chemical composition information. Separation before MS analysis is often necessary for such highly complex energy samples. For volatile samples, in-line two-dimensional gas chromatography (GC×GC) can be used to separate complex mixtures prior to ionization. This technique allows for a more accurate determination of the compounds in a mixture, by simplifying the mixture into its components prior to ionization, separation based on mass-to-charge ratio (<i>m/z</i>), and detection. A GC×GC coupled to a high-resolution time-of-flight MS was utilized in this research to determine the chemical composition of alternative aviation fuels, a petroleum-based aviation fuel, and alternative aviation fuel candidates and blending components as well as processed base oils.</p> Additionally, as the cutting edge of science and technology evolve, methods and equipment must be updated and adapted for new samples or new sector demands. One such case, explored in this dissertation, was the validation of an updated standardized method, ASTM D2425 2019. This updated standardized method was investigated for a new instrument and new sample type for a quadrupole MS to analyze a renewable aviation fuel. Lastly, the development and evaluation of a miniaturized coreflood device for analyzing candidate chemically enhanced oil recovery (cEOR) formulations of brine, surfactant(s), and polymer(s) was conducted. The miniaturized device was used in the evaluation of two different cEOR formulations to determine if the components of the recovered oil changed.

Anthropogenic emissions into the troposphere can impact air quality, leading to poorer health outcomes in the affected areas. Volatile organic compounds (VOCs) are a group of chemical compounds, including some which are toxic, that are precursors in the formation of ground-level ozone and secondary organic aerosols. VOCs have a variety of sources, and the distribution of atmospheric VOCs differs significantly over time and space. Historically, the large number of chemical species present at low concentrations (parts-per-trillion to parts-per-billion by volume) have made VOCs difficult to measure in ambient air. However, with improvements in analytical instrumentation, these measurements are becoming more common place. Direct mass spectrometry (MS), such as membrane introduction mass spectrometry (MIMS) and proton-transfer reaction time-of-flight mass spectrometry (PTR-ToF-MS) facilitate real-time, continuous measurements of VOCs in air, with full scan mass spectral data capturing changes in chemical composition with high temporal resolution. Operated on-road, mobilized direct MS has been used for quantitative mapping of VOCs at the neighborhood scale, but identifying VOC sources based on the observed mixture of molecules in the full scan MS dataset has yet to be explored. This dissertation describes the use of chemometric techniques to interrogate full scan MS data, and the progression from discriminating VOC samples of known chemical composition based on full scan MIMS data through to the apportionment of VOC sources measured continuously with a PTR-ToF-MS system operating in a moving vehicle. Lab‐constructed VOC samples of known chemical composition and concentration demonstrated the use of principal component analysis (PCA) to discriminate, and k-nearest neighbours to classify, samples based on normalized full scan MIMS data. Furthermore, multivariate curve resolution-alternating least squares (MCR-ALS) was used to resolve mixtures into molecular component contributions. PCA was also used to discriminate ‘real-world’ VOC mixtures (e.g., woodsmoke VOCs, headspace above aqueous hydrocarbon samples) of unknown chemical composition measured by MIMS. Using vehicle mounted MIMS and PTR-ToF-MS systems, full scan MS data of ambient atmospheric VOCs were collected and PCA was applied to the normalized full scan MS data. A supervised analysis performed PCA on samples collected near known VOC sources, while an unsupervised analysis using PCA followed by cluster analysis was used to identify groups in a continuous, time series PTR-ToF-MS dataset measured between Nanaimo and Crofton, British Columbia (BC). In both the supervised and unsupervised analysis, samples impacted by emissions from different sources (e.g., internal combustion engines, sawmills, composting facilities, pulp mills) were discriminated. With PCA, samples were discriminated based on differences in the observed full scan MS data, however real-world samples are often impacted by multiple VOC sources. MCR-weighted ALS (MCR-WALS) was applied to the continuous, time series PTR-ToF-MS data from three field campaigns on Vancouver Island, BC for source apportionment. Variable selection based on signal-to-noise ratios was used to reduce the mass list while retaining the observed m/z that capture changes in the mixture of VOCs measured, improving model results, and reducing computation time. Both point (e.g., anthropogenic hydrocarbon emissions, pulp mill emissions) and diffuse (e.g., VOCs from forest fire smoke) VOC sources were identified in the data, and were apportioned to determine their contributions to the measured samples. The data analyzed captured fine scale changes in the ambient VOCs present in the air, and geospatial maps of each individual source, and of the source apportionment were used to visualize the distribution of VOC sources across the sampling area. This work represents the first use of MCR-WALS to identify and apportion ambient VOC sources based on continuous PTR-ToF-MS data measured from a moving vehicle. The methods described can be applied to larger scale field campaigns for the source apportionment of VOCs across multiple days to capture diurnal and seasonal variations. Identifying spatial and temporal trends in the sources of VOCs at the regional scale can help to identify pollution ‘hot spots’ and inform evidence-based public policy for improving air quality. / Graduate / 2022-08-17