Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Algae “super blooms” are a commonly encountered environmental issue in fresh and brackish water that occurs due to the buildup of cyanobacteria. Many of the commonly encountered cyanobacteria such as Mycrocystis aeruginosa (M. aeruginosa) produce potent cyanotoxins (microcystins) that pose serious health threats and even death to local wild life and humans. Microcystin contaminated fresh-water that empties into the ocean has been shown to lethally affect marine life in the area of contamination. Human consumption of tainted sea life and other routes of mycrocystin exposure can lead to serious liver damage and even death. Thus, a method was developed for forensic postmortem analysis of microcystins RR, LR and YR by Two-Dimensional (2D) Liquid Chromatography (LC) - tandem Mass Spectrometry (MS/MS). A final 2D LC-MS/MS method was selected from 6x6 automated method development experiments. Each microcystin were subjected to a total of 36 methods, which were completed over an 18hr period. The extraction process was performed using a reverse-phase sorbent (Oasis HLB, Waters Corporation, Milford, MA) with a 3cc solid phase extraction (SPE) barrel using sequential elution. From acetonitrile (ACN) and methanol (MeOH) stock solutions, 10 μL of the internal standard (IS) Nodularin was added to the final extract. The concept of sequential micro extraction was designed to capture the retention behaviour of the target analyte in response to various extraction parameters (sorbent strength, elution polarity, and solubility). Therefore, optimized conditions were selected to excise the region of interest during extraction. The elution solvents chosen for the microcystins were acetonitrile, methanol and acetone with 10 % sequential increments. Since microcystins exhibit a zwitterionic structure, three sets of elution solutions were created to evaluate their elution profile (pH 3, pH 7, pH 10). When the elution profile for low pH and high pH are compared, microcystin RR was eluted over the 40% to 70% methanol fractions under low pH conditions with a slight shift towards higher organic % (50%-70% fractions) under high pH. This elution behaviour suggests that the basic moieties of the structure demonstrate a stronger retention for the stationary phase. Microcystin LR and YR however, eluted at a higher organic solvent percentage under low pH conditions and at a lower organic solvent percentage under high pH conditions, indicates that the acidic moieties of the structures have stronger retention. The urine sample gave recovery values for all three microcystins in the 80-90% range, as to be expected with type of complexity associated with biological samples. The sequential extraction protocol produced an extraction method that delivered a clean extract after a 30 min workflow using a single and optimized 2D LC-MS/MS method. The total analytical run time was set at 10 minutes.

The new field of ‘omics’ has spawned the development of metaproteomics, an approach that has the ability to identify and decipher the metabolic functions of a proteome derived from a microbial community that is largely uncultivable. With the development and availabilities of high throughput proteomics, high performance liquid chromatography coupled to mass spectrometry (MS) has been leading the field for metaproteomics. MS-based metaproteomics has been successful in its’ investigations of complex microbial communities from soils to the human body. Like the environment, the human body is host to a multitude of microorganisms that reside within the skin, oral cavity, vagina, and gastrointestinal tract, referred to as the human microbiome. The human microbiome is made up of trillions of bacteria that outnumber human genes by several orders of magnitude. These microbes are essential for human survival with a significant dependence on the microbes to encode and carryout metabolic functions that humans have not evolved on their own. Recently, metaproteomics has emerged as the primary technology to understand the metabolic functional signature of the human microbiome. Using a newly developed integrated approach that combines metagenomics and metaproteomics, we attempted to address the following questions: i) do humans share a core functional microbiome and ii) how do microbial communities change in response to disease. This resulted in a comprehensive identification and characterization of the metaproteome from two healthy human gut microbiomes. These analyses have resulted in an extended application to characterize how Crohn’s disease affects the functional signature of the microbiota. Contrary to measuring highly complex and representative gut metaproteomes is a less complex, controlled human-derived microbial community present in the gut of gnotobiotic mice. This human gut model system enhanced the capability to directly monitor fundamental interactions between two dominant phyla, Bacteroides and Firmicutes, in gut microbiomes colonized with two or more phylotypes. These analyses revealed membership abundance and functional differences between phylotypes when present in either a binary or 12-member consortia. This dissertation aims to characterize host microbial interactions and develop MS-based methods that can provide a better understanding of the human gut microbiota composition and function using both approaches.

Novel psychoactive substances (NPS) represent a great challenge to toxicologists due to the ability of illicit drug manufacturers to alter NPS chemical structures quickly and with ease to circumvent legislation regulating their use. Each time a new structure is introduced, there is a possibility that it has not been previously recorded in law enforcement or scientific databases. Many toxicology laboratories use targeted analytical methods that rely on libraries of known compounds to identify drugs in samples. However, these libraries do not include large numbers of NPS which could result in non-identification or detection. High-resolution mass spectrometry (HRMS) has been suggested as a method for screening a wide variety of analytes due to its higher sensitivity and mass accuracy as compared to some other forms of mass spectrometry. This technique can generate characteristic MS/MS spectral data for use in compound identification. The main goal of this research was to create a high-resolution mass spectrometry (HRMS) library of NPS and metabolites, as well as validate a method for screening and confirmation of these substances. The study consisted of three main tasks which included; the development of a large high-resolution MS/MS spectral library and database, validation of a method for screening and confirmation of over 800 NPS and metabolites, and screening of blind-spiked and authentic urine specimens to determine real-world applicability of the HRMS library and method. During validation, several isomeric and structurally related NPS were observed which could not be adequately separated using traditional LC methods. A fourth task was therefore added to investigate improved separation using two-dimensional liquid chromatography (2D-LC). Increased resolving power is achieved in 2D-LC through the coupling of multiple orthogonal separation systems. Ultimately, an on-line, comprehensive method was developed using orthogonal reversed-phase columns in each dimension (RP x RP) for improved separation of co-eluting and isomeric synthetic cannabinoids. This work can aid laboratories in the identification of NPS through the use of a validated LC-QTOF-MS method for screening and confirmation and HRMS spectral library. In instances where isomeric and structurally related NPS are not sufficiently separated, RP x RP methods can be explored.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Alors que le protéome de l'ovocyte isolé, aux stades VG et MII a déjà été étudié, celui du follicule en croissance n'a jamais été décrit.Dans cette étude, nous avons cherché à identifier, comparer et caractériser les profils protéiques de follicules ovariens de souris à trois stades de leur développement in vitro distincts morphologiquement : follicules secondaires en début de culture - stade initial (IS), follicules avec une rupture complète de la membrane de Slavjanski (RMS) et follicules avec une cavité similaire à l'antrum (FA).Après un préfractionnement par IEF et une analyse LC-MS/MS en deux configurations (1D et 2D), 1403 protéines ont pu être identifiées dans le follicule ovarien de souris. 43,4 % (609) des protéines identifiées étaient communes aux trois stades et d'autres ont été identifiées uniquement à un stade : 71 au stade IS, 182 au stade RMS et 193 au stade FA. De plus, on a identifié 365 protéines qui n'avaient pas été décrites antérieurement dans le protéome de l'ovocyte ce qui pourrais indiquer qu'elles sont exprimées dans les cellules somatiques du follicule. Des analyses qualitatives et quantitatives complémentaires ont démontré une surreprésentation pour 44 fonctions biologiques par rapport aux fonctions biologiques des gènes constituant le génome de Mus musculus et mis en évidence des différences d'expression et d'abondance des protéines liées au cycle cellulaire, à la fixation des ions de calcium et à la glycolyse selon le stade de développement. Ces résultats représentent un point de départ pour beaucoup d'autres études de caractérisation moléculaire du développement folliculaire. / Until now only the proteome of isolated oocyte from fully grown follicle were described with the aim of oocyte maturation characterization. However the ability of oocyte to mature is acquired during its development within the follicle. Thus in this study we proposed a protein identification and characterization of whole mice ovarian follicle at three morphological stages during in vitro development: early secondary stage, described as initial stage (IS), follicles with a complete Slavjanski membrane rupture (RMS) and follicles with an antrum like cavity formation (FA). Using an IEF pre fractionation before protein digestion and two configurations of LC-MS/MS analysis (1D and 2D), 1403 proteins were successfully identified in the murine ovarian follicle. From those, 43.4 % (609) were commonly identified in the three stages and some were identified only at one single stage: 71 at IS stage, 182 at RMS stage and 193 at FA stage. Compared to the proteomes of isolated oocyte previously described, 365 proteins were only identified in our samples indicating that those ones were probably expressed in the somatic cells of the follicle. Additional qualitative and quantitative analysis highlighted 44 biological processes over represented in our samples when compared to Mus musculus gene database and different expressions and protein abundance implicated in cell cycle, calcium ion binding and glycolysis, throughout in vitro follicle development. This report represents so far the most complete catalogue of follicle proteins and could be an important milestone in the proteomic study of the follicle metabolism throughout in vitro development.

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Impact Polypropylene Copolymers (IPCs) are extremely complex materials, consisting of a mixture of polypropylene homopolymer and copolymers having different comonomer (ethylene) contents and chemical composition distributions. IPC can only be effectively analysed by multidimensional analytical approaches. For this, initially, the individual components have to be separated according to any of their molecular characteristics, either by chemical composition distribution (CCD) or molar mass distribution (MMD), followed by further analysis of these separated fractions with conventional analytical techniques. The combination of preparative temperature rising elution fractionation (TREF) with several other analytical techniques have been reported for the thorough characterization of this material. However, even the combinations of these methods were of limited value due to the complex nature of this polymer. Therefore, novel analytical approaches are needed for a more detailed compositional analysis of IPCs. This work describes a number of multidimensional analytical techniques that are based on the combination of fractionation and hyphenated techniques. Firstly, preparative TREF was combined with high temperature size exclusion chromatography-FTIR (HT SEC-FTIR), HT SEC-HPer DSC (High Performance Differential Scanning Calorimetry) and high temperature two-dimensional liquid chromatography (HT 2D-LC) for the comprehensive analysis of a typical impact polypropylene copolymer and one of its midelution temperature TREF fractions. HT SEC-FTIR analysis provided information regarding the chemical composition and crystallinity as a function of molar mass. Thermal analysis of selected SEC fractions using a novel DSC method - High Speed or High Performance Differential Scanning Calorimetry (HPer DSC) - that allows measuring of minute amounts of material down to micrograms, yielded the melting and crystallization behaviour of these fractions which is related to the chemical heterogeneity of this complex copolymer. High temperature 2D-LC analysis provided the complete separation of this TREF fraction according to the chemical composition of each component along with its molar mass distribution. In a second step, the compositional characterization by advanced thermal analysis (HPer DSC, Flash DSC 1, and solution DSC) of the TREF-SEC fractions was extended to all semi-crystalline and higher temperature TREF fractions. By applying HPer DSC at scan rates of 5−200°C/min and Flash DSC 1 at scan rates of 10−1000°C/s, the metastability of one of the fractions was studied in detail. DSC measurements of TREF-SEC cross-fractions at high scan rates in p-xylene successfully connected reversely to the slow scan rate in TREF elution, if corrected for recrystallization. Finally, the exact chemical structure of all HT HPLC separated components was determined by coupling of HT HPLC with FTIR spectroscopy via an LCTransform interface. This novel approach revealed the capability of this hyphenated technique to determine the exact chemical composition of the individual components in the complex TREF fractions of IPCs. The HT HPLC–FTIR results confirmed the separation mechanism in HPLC using a solvent gradient of 1-decanol/TCB and a graphitic stationary phase at 160°C. FTIR analysis provided information on the ethylene and propylene contents of the fractions as well as on the ethylene and propylene crystallinities. / AFRIKAANSE OPSOMMING: Impak Polipropileen Kopolimere (IPKe) is uiters komplekse materiale, bestaande uit 'n mengsel van polipropileen homopolimeer en kopolimere met verskillende komonomeer (etileen) inhoud en chemiese samestelling verspreiding. IPKe kan slegs doeltreffend ontleed word deur multidimensionele analitiese benaderings te volg. Hiervoor moet die individuele komponente aanvanklik eers geskei word volgens enige van hul molekulêre eienskappe, hetsy deur die chemiese samestelling verspreiding (CSV) of molêre massa verspreiding (MMV), gevolg deur 'n verdere ontleding van hierdie geskeide fraksies met konvensionele analitiese tegnieke. Die kombinasie van voorbereidings temperatuur-verhogings eluasie fraksionering (TVEF) met verskeie ander analitiese tegnieke is gerapporteer vir die deeglike karakterisering van hierdie materiaal. Maar selfs die kombinasies van hierdie metodes was van beperkte waarde as gevolg van die komplekse aard van hierdie polimeer. Daarom word nuwe analitiese benaderings benodig vir 'n meer gedetailleerde komposisionele ontleding van IPKe. Hierdie studie beskryf 'n aantal multidimensionele analitiese tegnieke wat gebaseer is op die kombinasie van fraksionering en gekoppelde tegnieke. Eerstens is voorbereidings TVEF gekombineer met hoë temperatuur grootte-uitsluitingschromatografie-FTIR (HT GUC-FTIR), HT GUC-HPer DSK en hoë temperatuur twee-dimensionele vloeistof chromatografie (HT 2D-VC) vir die omvattende ontleding van 'n tipiese impak polipropileen kopolimeer en een van sy mid-eluasie temperatuur TVEF fraksies. HT GUC-FTIR analiese het inligting verskaf met betrekking tot die chemiese samestelling en kristalliniteit as 'n funksie van molêre massa. Termiese analiese van geselekteerde GUC fraksies deur gebruik te maak van 'n nuwe-DSK metode - Hoë Spoed of Hoë Prestasie Differensïele skandeer kalorimetrie (HPer DSK) - wat die meting van klein hoeveelhede materiaal tot by mikrogram hoeveelhede toelaat, het die smelt en kristallisasie gedrag van hierdie fraksies bepaal wat verwant is aan die chemiese heterogeniteit van hierdie komplekse kopolimeer. Hoë temperatuur 2D-LC analiese het die volledige skeiding van hierdie TVEF fraksie volgens die chemiese samestelling van elke komponent saam met die molêre massa verspreiding moontlik gemaak. In 'n tweede stap, is die komposisionele karakterisering deur gevorderde termiese analiese (HPer DSK, Flash DSK 1 en oplossing DSK) van die TVEF-GUC fraksies uitgebrei na alle semi-kristallyne en hoër temperatuur TVEF fraksies. Deur die gebruik van HPer DSK, teen ’n skandeerspoed van 5-200°C / min, en Flash DSK 1, teen ’n skandeerspoed van 10-1000°C / s, is die meta-stabiliteit van een van die fraksies in detail bestudeer. DSK metings van TVEF-GUC kruis-fraksies by 'n hoë skandeeerspoed in p-xyleen het suksesvol omgekeerd verbind aan die stadige skandeerspoed in TVEF eluasie, wanneer gekorrigeer vir dekristallisatie. Ten slotte is die presiese chemiese struktuur van al die HT HPVC geskeide komponente bepaal deur die koppeling van HT HPVC met FTIR spektroskopie deur middel van 'n LC-transform-koppelvlak. Hierdie nuwe benadering het die vermoë van die gekoppelde tegniek om die presiese chemiese samestelling van die individuele komponente in die komplekse TVEF fraksies of IPKe te bepaal aan die lig gebring. Die HT HPVC-FTIR resultate het die skeidingsmeganisme in HPVC bevestig deur die gebruik van ’n oplosmiddelgradiënt van 1-dekanol/TCB en 'n graphitiese stasionêre fase by 160°C. FTIR analiese verskaf inligting in verband met die etileen en propileen inhoud van die fraksies sowel as die etileen en propileen krystalliniteit.

Alors que le protéome de l'ovocyte isolé, aux stades VG et MII a déjà été étudié, celui du follicule en croissance n'a jamais été décrit.Dans cette étude, nous avons cherché à identifier, comparer et caractériser les profils protéiques de follicules ovariens de souris à trois stades de leur développement in vitro distincts morphologiquement : follicules secondaires en début de culture - stade initial (IS), follicules avec une rupture complète de la membrane de Slavjanski (RMS) et follicules avec une cavité similaire à l'antrum (FA).Après un préfractionnement par IEF et une analyse LC-MS/MS en deux configurations (1D et 2D), 1403 protéines ont pu être identifiées dans le follicule ovarien de souris. 43,4 % (609) des protéines identifiées étaient communes aux trois stades et d'autres ont été identifiées uniquement à un stade : 71 au stade IS, 182 au stade RMS et 193 au stade FA. De plus, on a identifié 365 protéines qui n'avaient pas été décrites antérieurement dans le protéome de l'ovocyte ce qui pourrais indiquer qu'elles sont exprimées dans les cellules somatiques du follicule. Des analyses qualitatives et quantitatives complémentaires ont démontré une surreprésentation pour 44 fonctions biologiques par rapport aux fonctions biologiques des gènes constituant le génome de Mus musculus et mis en évidence des différences d'expression et d'abondance des protéines liées au cycle cellulaire, à la fixation des ions de calcium et à la glycolyse selon le stade de développement. Ces résultats représentent un point de départ pour beaucoup d'autres études de caractérisation moléculaire du développement folliculaire.

Here we report the identification and approximate quantification of cytochrome P450 (CYP) proteins in human liver microsomes as determined by nano-LC-MS/MS with application of the exponentially modified protein abundance index (emPAI) algorithm during database searching. Protocols based on 1D-gel protein separation and 2D-LC peptide separation gave comparable results. In total, 18 CYP isoforms were unambiguously identified based on unique peptide matches. Further, we have determined the absolute quantity of two CYP enzymes (2E1 and 1A2) in human liver microsomes using stable-isotope dilution mass spectrometry, where microsomal proteins were separated by 1D-gel electrophoresis, digested with trypsin in the presence of either a CYP2E1- or 1A2-specific stable-isotope labeled tryptic peptide and analyzed by LC-MS/MS. Using multiple reaction monitoring (MRM) for the isotope-labeled tryptic peptides and their natural unlabeled analogues quantification could be performed over the range of 0.1-1.5 pmol on column. Liver microsomes from four individuals were analyzed for CYP2E1 giving values of 88-200 pmol/mg microsomal protein. The CYP1A2 content of microsomes from a further three individuals ranged from 165 to 263 pmol/mg microsomal protein. Although, in this proof-of-concept study for CYP quantification, the two CYP isoforms were quantified from different samples, there are no practical reasons to prevent multiplexing the method to allow the quantification of multiple CYP isoforms in a single sample.