Thesis (MSc)--University of Stellenbosch, 2005. / Bibliography. Also available via the Internet.

abstract: Signal processing techniques have been used extensively in many engineering problems and in recent years its application has extended to non-traditional research fields such as biological systems. Many of these applications require extraction of a signal or parameter of interest from degraded measurements. One such application is mass spectrometry immunoassay (MSIA) which has been one of the primary methods of biomarker discovery techniques. MSIA analyzes protein molecules as potential biomarkers using time of flight mass spectrometry (TOF-MS). Peak detection in TOF-MS is important for biomarker analysis and many other MS related application. Though many peak detection algorithms exist, most of them are based on heuristics models. One of the ways of detecting signal peaks is by deploying stochastic models of the signal and noise observations. Likelihood ratio test (LRT) detector, based on the Neyman-Pearson (NP) lemma, is an uniformly most powerful test to decision making in the form of a hypothesis test. The primary goal of this dissertation is to develop signal and noise models for the electrospray ionization (ESI) TOF-MS data. A new method is proposed for developing the signal model by employing first principles calculations based on device physics and molecular properties. The noise model is developed by analyzing MS data from careful experiments in the ESI mass spectrometer. A non-flat baseline in MS data is common. The reasons behind the formation of this baseline has not been fully comprehended. A new signal model explaining the presence of baseline is proposed, though detailed experiments are needed to further substantiate the model assumptions. Signal detection schemes based on these signal and noise models are proposed. A maximum likelihood (ML) method is introduced for estimating the signal peak amplitudes. The performance of the detection methods and ML estimation are evaluated with Monte Carlo simulation which shows promising results. An application of these methods is proposed for fractional abundance calculation for biomarker analysis, which is mathematically robust and fundamentally different than the current algorithms. Biomarker panels for type 2 diabetes and cardiovascular disease are analyzed using existing MS analysis algorithms. Finally, a support vector machine based multi-classification algorithm is developed for evaluating the biomarkers' effectiveness in discriminating type 2 diabetes and cardiovascular diseases and is shown to perform better than a linear discriminant analysis based classifier. / Dissertation/Thesis / Ph.D. Electrical Engineering 2012

Orientadores: Marcos Nogueira Eberlin, Maria Cristina Marcucci Ribeiro / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-07T02:59:35Z (GMT). No. of bitstreams: 1 Sawaya_AlexandraChristineHelenaFrankland_D.pdf: 1255664 bytes, checksum: 590eb73bc0e239bc517bb37afcab9c89 (MD5) Previous issue date: 2006 / Resumo: A própolis é uma resina obtida de plantas que as abelhas utilizam, acrescida de cera, para proteger sua colméia contra a entrada de correntes de ar, de predadores e de microrganismos. A composição química e fontes vegetais de própolis obtida das abelhas Apis mellifera de regiões de clima temperado como Europa e América do Norte, já foi estudada, constando da literatura pesquisada. Com o objetivo de determinar a composição química e fontes vegetais de própolis brasileira, foram feitos vários estudos, utilizando a espectrometria de massas com ionização por eletrospray (ESI-MS). Inicialmente, extratos etanólicos de própolis (EEP) de Apis mellifera do sul, sudeste e nordeste do Brasil, bem como EEP provenientes da Bulgária, Inglaterra, Finlândia, América do Norte e Moçambique, foram analisados diretamente por ESI-MS e seus espectros comparados por quimiometria. A seguir, EEP de A. mellifera do sul e sudeste do Brasil foram analisados por ESI-MS e comparados com extratos de plantas sugeridas como fontes vegetais de própolis destas regiões. Cromatografia liquida foi acoplada a espectrometria de massas para isolar e identificar compostos encontrados nos EEP e nos extratos de plantas. Em outro estudo, amostras de um tipo de própolis de A mellifera do nordeste brasileiro foram analisadas, permitindo identificar uma fonte vegetal e alguns compostos com atividade antioxidante. Dois estudos foram realizados com própolis de abelhas nativas. Inicialmente, EEP da abelha nativa brasileira (Tetragonisca angustula) provenientes do sul, sudeste e nordeste do Brasil foram comparados entre si, com EEP de A. mellifera destas regiões e com extratos de plantas visitadas por T. angustula, permitindo a identificação da fonte vegetal desta própolis. Depois, EEP de diversas espécies de abelhas nativas sem ferrão de cinco regiões do Brasil foram comparadas entre si e com extratos de plantas e EEP de A. mellifera das mesmas regiões, determinando padrões na composição de própolis de abelhas nativas. Os resultados obtidos contribuíram para um melhor conhecimento da variável composição química de própolis brasileira e de suas fontes vegetais / Abstract: Propolis is a resin, collected from plants, which bees mix with wax and use to protect their hives against air currents, predators and microorganisms. The chemical composition and plant origins of propolis obtained from Apis mellifera bees from temperate regions such as Europe and North America, have already been studied and can be found in literature. With the objective of determining the chemical composition and plant origins of Brazilian propolis, several studies were carried out, using electrospray ionization mass spectrometry (ESI-MS). Initially, ethanolic extracts of propolis (EEP) of Apis mellifera bees from the south, southeast and northeast of Brazil, as well as EEP from Bulgaria, England, Finland, North America and Mozambique, were analyzed by direct insertion ESI-MS and the results analyzed by chemometric analysis. Next, EEP from A. mellifera from the south and southeast of Brazil were analyzed by ESI-MS and their MS fingerprints compared to those of extracts of plants that were previously indicated as plant sources of propolis from those regions. Liquid chromatography was used in-line with mass spectrometry to isolate and identify components of the EEP and plant extracts. In another study, samples of one type of A mellifera propolis from the northeast of Brazil were analyzed, identifying their main plant source and some compounds with antioxidant activity. Two studies were carried out with propolis from native Brazilian stingless bees. Initially EEP of the native bee (Tetragonisca angustula) from the south, southeast and northeast of Brazil were compared with each other, with EEP of A. mellifera from the same regions and with extracts of plants visited by T. angustula, allowing us to identify the main plant source of this type of propolis. Next, EEP of several species of native stingless bees from five regions in Brazil were also compared with plant extracts and EEP of A. mellifera from the same regions, identifying patterns in the composition of propolis from native Brazilian stingless bees. The results obtained contributed to a grater understanding of the variable composition of Brazilian propolis and its plant sources / Doutorado / Quimica Analitica / Doutor em Ciências

No description available.

By using two electrospray emitters containing different solutions (“dual-spray”) we have recently conducted in-source hydrogen/deuterium exchange (HDX) reactions and synthesized organometallic species. For dual-spray HDX reactions, peptide and protein solutions were electrosprayed through one emitter and the deuterating agent D2O through the secondary electrospray emitter. Clear shifts in isotope distributions indicated hydrogen-deuterium exchange occurring within the ion source. By ion mobility, simultaneous deuterium exchange for two isobaric species, the oxytocin monomer and dimer, was observed. Lysozyme has a linear relation between the charge state and the average number of exchanges, indicating that lysozyme becomes increasingly unfolded as the charge state increases. Based on deuterium uptake data and the lack of a temperature dependence, the dual-spray HDX reaction is thought to occur mostly in the gas phase. Tris(2,2’-bipyridine)ruthenium(II) and similar complexes containing the 1,10-phenanthroline ligand were formed by spraying a ligand solution and the ruthenium trichloride solution through two independent ESI emitters. This was confirmed by comparing ion mobility drift time, mass spectra, and CID fragmentation with the reference standard compounds. Tris(2,2’-bipyridine)iron(II), tris(1,10-phenantroline)iron(II) and mixed ligand complexes of iron(II) formed by dual-spray showed two additional hydrogens bonded to the complex. By CID, these unique gas phase complexes showed similar initial ligand loss to the reference standards however the secondary ligand loss showed dissimilar dissociation channels and energetics. Using DFT calculations, geometry optimizations for the [Fe(phen)3 + 2H]2+ complex and its fragment ions were done. After the initial ligand loss, the additional hydrogens are believed to transfer to the central iron atom. The relative energy of the dissociation channels showed good agreement with experimental breakdown curves.

In this thesis, the reactivity and synthesis of methylalumoxane (MAO) via electrospray ionization mass spectrometry (ESI-MS) was investigated. The olefin polymerization catalyst [Cp2Zr(μ-Me)2AlMe2]+ [B(C6F5)4]− was also used to evaluate the efficacy of a nitrogen generator as a source for desolvation gas for ESI-MS analysis. The same catalyst was then used to study catalyst deactivation after 1-hexene addition. MAO ionizes very selectively in the presence of octamethyltrisiloxane (OMTS) to generate [Me2Al·OMTS]+ [(MeAlO)16(Me3Al)6Me]−. The advantage of this transformation was used to examine the reactivity and synthesis of MAO. The reactivity of this ion pair with other trialkyl aluminum (R3Al) components was studied both offline and in real-time. The exchanges are fast and reversible, and the methyl groups on the cation are also observed to exchange with the added R3Al species. MAO is also famously intractable to structural elucidation, consisting as it does of a complex mixture of oligomers generated from hydrolysis of pyrophoric trimethylaluminum (TMA). Synthesis of MAO was probed in real-time by ESI-MS, and the principal activated product of the benchtop synthesis was found to be the same as that observed in industrial samples, namely [(MeAlO)16(Me3Al)6Me]–. Computationally, a new sheet structure for this ion was proposed. The increasing competitiveness of nitrogen generators, which provide gas purity levels that vary inversely with flow rate, prompted an investigation of the effect of gas-phase oxygen on the speciation of ions by ESI-MS. The most reactive species studied, the reduced titanium complex [Cp2Ti(NCMe)2]+[ZnCl3]− and the olefin polymerization pre-catalyst [Cp2Zr(μ-Me)2AlMe2]+[B(C6F5)4]−, only exhibited detectable oxidation when they were rendered coordinatively unsaturated through in-source fragmentation. The catalyst [Cp2Zr(μ-Me)2AlMe2]+[B(C6F5)4]− was further studied by ESI-MS to understand better the complexities of catalyst deactivation in the polymerization of 1-hexene. I also contributed to other projects, namely the interaction of neutral donors with MAO, saturation problems in ESI-MS, and ligand substitution reaction in ruthenium complexes, and my work on all these projects are summarized in this thesis. / Graduate

Electrospray ionization mass spectrometry (ESIMS) is widely used to characterize neutral and ionic species in solvents. Typically, electrical, thermal, and pneumatic potentials are applied to create electrosprays from which charged ionic species are ejected for downstream analysis by mass spectrometry. Most recently, ESIMS has been exploited to investigate ambient proton transfer reactions at air-water interfaces in real time. We assessed the validity of these experiments via complementary laboratory experiments. Specifically, we characterized the products of two reaction scenarios via ESIMS and proton nuclear magnetic resonance (1H-NMR): (i) emulsions of pH-adjusted water and isoprene (C5H8) that were mechanically agitated, and (ii) electrosprays of pH-adjusted water that were collided with gas-phase isoprene. Our experiments unambiguously demonstrate that, while isoprene does not oligomerize in emulsions, it does undergo protonation and oligomerization in electrosprays, both with and without pH-adjusted water, confirming that C-C bonds form along myriad high-energy pathways during electrospray ionization. We also compared our experimental results with some quantum mechanics simulations of isoprene molecules interacting with hydronium at different hydration levels (gas versus liquid phase). In agreement with our experiments, the kinetic barriers to protonation and oligomerization of isoprene were inaccessible under ambient conditions. Rather, the gas-phase chemistries during electrospray ionization drove the oligomerization of isoprene. Therefore, we consider that ESIMS could induce artifacts in interfacial reactions. These findings warrant a reassessment of previous reports on tracking chemistries under ambient conditions at liquid-vapor interfaces via ESIMS. Further, we took some high-speed images of electrosprays where it was possible to observe the main characteristics of the phenomena, i.e. Taylor cone, charge separation, and Coulomb fission. Finally, we took the freedom to speculate on possible mechanisms that take place during electrospray ionization that affected our system and possibly may influence other common analytical techniques on ESIMS.

Image-charge detection is emerging as an important tool to analyze heavy and heterogeneous samples because of its unique advantages in measuring highly charged microparticles. Conventional image-charge detection instruments include at least three fundamental components: an ionization source, an aerodynamic particle delivery system, and an image-charge detector. Here I report research efforts that investigated the mechanisms of image-charge detection and proposed some instrumental developments of these components to suit specific research purposes. In Chapter 2, I report an investigation of the electrospray ionization (ESI) mechanism based on an observation that a certain portion of charged particles generated with an ESI source carried charges opposite to the needle which is biased with a high voltage. Both biological and non-biological samples were used to shed a light on the complex process of droplet evolution in ESI. In Chapter 3, I present two novel designs of printed circuit board (PCB) based image-charge detectors. With these detectors, not only the charge and velocity of each microparticle were investigated, but also the two dimensional trajectories, with applications in aerosolized particle beam diagnostics. Chapter 4 shows several designs of the microparticle delivering system aiming to achieve a faster acceleration of sample microparticles. Finally, Chapter 5 presents some thoughts on future directions for these projects.

Over the past decades, electrospray ionization for mass spectrometry (ESI-MS) has become one of the most commonly employed techniques in analytical chemistry, mainly due to its broad applicability to polar and semipolar compounds and the superior selectivity which is achieved in combination with high resolution separation techniques. However, responsiveness of an analytical method also determines its suitability for the quantitation of chemical compounds; and in electrospray ionization for mass spectrometry, it can vary significantly among different analytes with identical solution concentrations. Therefore, we investigated the ESI-response behavior of 56 nitrogen-containing compounds including aromatic amines and pyridines, two compound classes of high importance to both, synthetic organic chemistry as well as to pharmaceutical sciences. These compounds are increasingly analyzed employing ESI mass spectrometry detection due to their polar, basic character. Signal intensities of the peaks from the protonated molecular ion (MH+) were acquired under different conditions and related to compound properties such as basicity, polarity, volatility and molecular size exploring their quantitative impact on ionization efficiency. As a result, we found that though solution basicity of a compound is the main factor initially determining the ESI response of the protonated molecular ion, other factors such as polarity and vaporability become more important under acidic solvent conditions and may nearly outweigh the importance of basicity under these conditions. Moreover, we show that different molecular descriptors may become important when using different types of instruments for such investigations, a fact not detailed so far in the available literature.

Chemical substances that are either produced by nature or by humankind have a consequence on the environment when they are accumulated to a great extent. One of nature’s major problem is that of the eutrophication of surface waters, which is caused by inorganic and organic phosphorus compounds and, in particular, from a group known as Inositol Phosphates. There are six different forms of these inositols and are commonly found in soil and sediment samples. The conducted project was aimed to develop an analytical method that could efficiently analyze and separate all six with repeatable results. As such, soil samples were collected two times from two forest locations and two crop field locations. The first time the soil samples were left overnight to dry in a drying oven while on the second time, the samples left to dry at room temperature. When the samples were considered dry enough, they processed to reach grain size and extracted with a mixture of NaOH and Titriplex® III. The extracted soil samples, the standard solutions containing inositols, and the spiked extracted soil samples with inositol solution were all analyzed with an instrumental combination of a Capillary Electrophoresis instrument coupled manually to an Electrospray mass spectrometer, where the first was operated at reversed mode and the second at negative mode. To achieve the best feasible separation, several background electrolyte solutions were created along with a large number of sheath liquids regulated by an LC pump, two Capillary Electrophoresis methods, and twenty-five distinct MS methods, all tested through extensive screening to obtain the best possible combination of parameters. Out of the obtained results from the runs, four background electrolyte solutions, two MS methods, one sheath liquid controlled by one specific flow rate, and one Capillary Electrophoresis method exhibited promising potentials with a satisfying outcome. However, the intense pulsation of the spray cone observed for many of the runs, the manual protrusion of the Capillary Electrophoresis fused silica capillary, and some random errors, the repeatability of the method is called into question.