A crescente demanda por água doce de boa qualidade, associada ao aumento na frequência de florações tóxicas de cianobactérias em reservatórios utilizados para consumo humano, levou à publicação da Portaria nº. 518/04 pelo Ministério da Saúde. Entre outros parâmetros de potabilidade, as empresas fornecedoras de água tratada devem realizar o monitoramento de cianotoxinas. Para tanto, métodos analíticos rápidos e precisos para a determinação destes compostos são imprescindíveis. Neste contexto, o presente trabalho teve como objetivo empregar a cromatografia líquida acoplada à espectrometria de massas para o estudo das principais cianotoxinas em território nacional: microcistinas, anatoxina-a(s), cilindrospermopsina e saxitoxinas. Os resultados obtidos estão distribuídos em capítulos específicos dedicados a cada grupo de toxinas. Dessa forma, o primeiro capítulo apresenta um estudo de fragmentação na fase gasosa de ânions de microcistinas em um equipamento do tipo orbitrap. É demonstrado que o modo negativo de ionização por electrospray fornece informações estruturais importantes e complementares ao modo positivo de ionização. Uma abertura seletiva do peptídeo cíclico é proposta e mecanismos discutidos, o que facilita a interpretação de resultados durante a caracterização de variantes desconhecidas. O modelo de fragmentação desenvolvido foi utilizado para identificar a variante [Leu1]MC-LR em um extrato de Microcystis spp. O segundo capítulo descreve metodologias qualitativas de LC/MS para o monitoramento e identificação do organofosforado natural anatoxina-a(s), cuja análise é prejudicada pela ausência de padrões comerciais. A cromatografia de interação hidrofílica foi empregada e mecanismos de fragmentação na fase gasosa propostos, discutindo-se os íons característicos desta estrutura química. Tal modelo permitiu a identificação desta toxina nas cepas de Anabaena oumiana ITEP-25 e ITEP-26 pela primeira vez. O terceiro capítulo disserta sobre os mecanismos de fragmentação na fase gasosa da toxina cilindrospermopsina quando ionizada por electrospray na forma de aduto com metais alcalinos. Diferenças nas vias de fragmentação são demonstradas de acordo com o raio atômico do metal formador do aduto, com implicações práticas na sua determinação cromatográfica. Já o quarto capítulo discute os mecanismos de fragmentação de variantes sulfatadas de saxitoxinas (GTX1e4, GTX2e3, dcGTX2e3, GTX5) após ionização por electrospray no modo positivo e negativo. É demonstrado pela primeira vez que uma conformação estrutural específica do grupamento sulfato explica a intensa eliminação de SO3 observada para as variantes GTX1, GTX2 e dcGTX2 no modo positivo de ionização. Por outro lado, o modo negativo de ionização apresenta vantagens uma vez que a dissociação na fonte é insignificante se comparada à dissociação observada no modo positivo. Como resultado, métodos quantitativos no modo negativo podem apresentar maior sensibilidade, permitindo a detecção destas toxinas em amostras ambientais em quantidades mais baixas. De maneira geral, conclui-se que a cromatografia líquida acoplada à espectrometria de massas é ferramenta poderosa para a análise quali e quantitativa das principais cianotoxinas, podendo ser amplamente empregada para o monitoramento de água para consumo humano. / The increasing occurrence of toxic cyanobacterial blooms in reservoirs used to supply drinking water for human consumption has prompted the publication of resolution 518/04 by the Brazilian Ministry of Health. Among other quality requirements, the monitoring of cyanotoxins in treated water is mandatory for companies responsible for potable water distribution. Therefore, precise and rapid analytical methods are essential. In this context, the aim of this work is to employ liquid chromatography coupled to mass spectrometry to study the most important cyanotoxins in our country: microcystins, anatoxin-a(s), cylindrospermopsis and saxitoxins. The obtained results are distributed in four chapters, each one dedicated to a single group of toxins. In this way, chapter one presents the gas-phase fragmentation behavior of deprotonated microcystins in an Orbitrap instrument. It is demonstrated that electrospray negative ionization can provide significant structural information about microcystins. These results are complementary to the positive ionization mode. A selective ring opening process is proposed and possible mechanisms are discussed, which may facilitate data interpretation when unknown variants are considered. The general fragmentation model was further applied to the characterization of [Leu1]MC-LR in a Microcystis spp. cell extract. The second chapter describes qualitative analytical methods for the identification of anatoxin-a(s), a natural organophosphate whose determination is hampered by the lack of commercial standards. Hydrophilic interaction liquid chromatography was employed and fragmentation mechanisms proposed, identifying the characteristic product ions of this toxin. The developed methods were further used to identify anatoxin-a(s) for the first time in Anabaena oumiana strains ITEP-25 and ITEP-26. The third chapter presents data related to the gas-phase fragmentation behavior of cylindrospermospin when this toxin is ionized as metal adducts. Different fragmentation pathways are accessed depending on the atomic radius of the metal cation involved. Practical implications for the chromatographic analysis of this toxin are presented. The last chapter describes the fragmentation behavior of sulphate-containing saxitoxin variants (GTX1&4, GTX2&3, dcGTX2&3, GTX5) after electrospray ionization in both the positive and negative modes. A mechanism for the intense SO3 elimination from [M+H]+ ions from GTX1, GTX2 and dcGTX2 is proposed for the first time and relies on a specific structure conformation. On the other hand, the negative ionization mode shows much less in-source dissociation when compared to the positive mode. As a consequence, methods based on negative ionization might be more sensitive for sulfate-containing variants, allowing the detection of lower amounts of these toxins in environmental samples. At the end, it can be concluded that liquid chromatography is a well-suited and powerful technique for the qualitative and quantitative analysis of cyanotoxins, being an invaluable contribution to water safety evaluation.

Electrospray ionization is a technique widely used in mass spectrometry. Almost every material, specifically large molecules like proteins or polymers can be ionized directly out of solution. During the ionization process molecules are not fragmented. In this work a prototype apparatus for creating three-dimensional patterns in a ultra high vacuum environment using an electrospray ion source was optimized for higher ion currents hence deposition rate by improving the core component of the apparatus, an electrodynamic ion funnel. The major improvements are a redesigned heated vacuum inlet, modified gas flow inside the ion funnel because of sealing the ion funnel against perpendicular gas flow and a better measurement setup for the transmitted current. The transmission of the ion funnel was improved from 25% to 82% resulting in ion currents of up to 7nA (500pA before advancements) focused through the ion funnel. At this rate an area of 1 cm² can be coated with a molecular monolayer of Cytochrome C in 64 minutes.

Interest in microfluidic platforms has surged as an alternative for sample preparation in the past two decades, with the potential for miniaturization, portability, automation, integration and parallelism driving this research. However, it is still very challenging to develop an integrated microfluidic device for proteomic preparation for mass spectrometry analysis. My thesis work is focused on the development of a valve-based microfluidic platform interfaced with electrospray ionization mass spectrometry for multiplexed proteomic analysis. First, techniques are developed for the fabrication and packing of multiple beds in a polydimethylsiloxane (PDMS) microdevice, which is compatible with the integration of multilayer microvalves. A soft lithography technique was used to fabricate stable weirs in microchips and new bead introduction techniques were explored for the elimination of bead introduction channels in the design. Such a combination provides a convenient, efficient and effective way for multiple bed preparation in a complex design. Next, detailed studies were carried out on the design parameters and performance of multilayer PDMS microvalves in the presence of high electric fields. These studies guided the integration of electrophoresis methods with valve-based fractionation. Finally, a coupled CE-fractionation-SPE-ESIMS peptide analysis on a totally integrated valve-based microchip is presented. We show the design and operation of a system that performs electrokinetic separation, followed by fractionation into multiple channels, SPE extraction and sample cleanup on packed reaction beds, using a multiplexed, hydraulically valved system, with subsequent mass spectral (MS) analysis. This coupled multiple channel CE-Fractionation-SPE-ESIMS platform on valve-based microchip was successfully applied to peptide analysis.

The research presented in this thesis involves the application of chiral cationic and anionic surfactants for simultaneous enantioseparation of structurally similar compounds in capillary electrophoresis (CE) and CE coupled to mass spectrometry (CE-MS). The first chapter briefly introduces the fundamentals of CE and CE-MS, emphasizing the micellar electrokinetic chromatography (MEKC) and MEKC-MS techniques, as well as ionic liquids (ILs) and affinity CE (ACE). In chapter 2, a mixture of five racemic profen (PROF) drugs are simultaneously separated with the combined use of 2,3,6-tri-O-methyl-β-cyclodextrin (TM-β-CD) and IL-type surfactant, N-undecenoxycarbonyl-L-leucinol bromide (L-UCLB). Enantioseparations of these PROFs are optimized using a standard recipe containing 35.00 mM TM-β-CD, 5.00 mM sodium acetate at pH 5.0, and varying the concentration as well as chain length of the IL surfactants. The batch-to-batch reproducibility of L-UCLB is found to be acceptable in terms of enantiomeric resolution, and migration time. A competitive inhibition mechanism is proposed to investigate the ternary interactions among TM-β-CD, ILs, and PROFs. The apparent binding constant of TM-β-CD to L-UCLB is estimated by nonlinear and linear plotting methods. The binding constants of one representative PROF (e.g., fenoprofen) to TM-β-CD and to L-UCLB are estimated by a secondary plotting approach. The R- and S-fenoprofen having different binding constant values, resulting in the enantioseparation due to the synergistic effect of TM-β-CD and L-UCLB. The R- and S-configurations of barbiturates display differences in potency and biological activity. In Chapter 3, a multivariate MEKC-ESI-MS approach for the simultaneous analysis of the racemic mixture of three barbiturates is presented. The chiral selector employed is the polymeric surfactant polysodium N-undecenoxycarbonyl-L-isoleucinate. The central composite design is used to optimize the chiral resolution, decrease the total analysis time, and improve the ESI-MS signal-to-noise ratio for these barbiturates. In preliminary experiments, the ranges of the factors investigated in the multivariate approaches are determined. Then the multivariate optimizations are conducted to determine the best overall chiral resolution with shortest possible run times for barbiturates. The limit of detection of ESI-MS is several folds higher compared to the UV detection. The predicted optimum results are in good agreement with the experimental data.

Since the introduction of electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI), there has been an unprecedented growth of biomolecule analysis using mass spectrometry (MS). One of the most popular applications for mass spectrometry is the field of proteomics, which has emerged as the next scientific challenge in the post-genome era. One critical step in proteomic analysis is sample preparation, a major bottleneck that is attributed to many time consuming and labor-intensive steps involved. Microfluidics can play an important role in proteome sample preparation due to its ability to handle small volumes of sample and reagent, and its capability to integrate multiple processes on a single chip with the potential for high-throughput analysis. However, to utilize microfluidic systems for proteome analysis, an efficient interface between microfluidic chip and mass spectrometry is required. This thesis presents several methods for coupling of microfluidic chips with ESI-MS and MALDIMS. III Three microfluidic-ESI interfaces were developed. The first interface involves fabricating a polymer based microchannel at the rectangular corners of the glass substrates using a single photolithography step. The second interface was build upon the previous interface in which a digital microfluidic platform was integrated with the microchannel in a “top-down” format. The integrated microfluidic system was used for inline quantification of amino acids in dried blood spots that have been processed by digital microfluidics. The third interface was formed by sandwiching a pulled glass capillary emitter between two digital microfluidic substrates. This method is a simpler and more direct coupling of digital microfluidics with ESI-MS as compared to the method used for second interface. Finally, a strategy using a removable plastic “skin” was developed to interface digital microfluidics with MALDI-MS for offline sample analysis. We demonstrated the utility of this format by implementing on-chip protein digestion on immobilized enzyme depots.

Since the introduction of electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI), there has been an unprecedented growth of biomolecule analysis using mass spectrometry (MS). One of the most popular applications for mass spectrometry is the field of proteomics, which has emerged as the next scientific challenge in the post-genome era. One critical step in proteomic analysis is sample preparation, a major bottleneck that is attributed to many time consuming and labor-intensive steps involved. Microfluidics can play an important role in proteome sample preparation due to its ability to handle small volumes of sample and reagent, and its capability to integrate multiple processes on a single chip with the potential for high-throughput analysis. However, to utilize microfluidic systems for proteome analysis, an efficient interface between microfluidic chip and mass spectrometry is required. This thesis presents several methods for coupling of microfluidic chips with ESI-MS and MALDIMS. III Three microfluidic-ESI interfaces were developed. The first interface involves fabricating a polymer based microchannel at the rectangular corners of the glass substrates using a single photolithography step. The second interface was build upon the previous interface in which a digital microfluidic platform was integrated with the microchannel in a “top-down” format. The integrated microfluidic system was used for inline quantification of amino acids in dried blood spots that have been processed by digital microfluidics. The third interface was formed by sandwiching a pulled glass capillary emitter between two digital microfluidic substrates. This method is a simpler and more direct coupling of digital microfluidics with ESI-MS as compared to the method used for second interface. Finally, a strategy using a removable plastic “skin” was developed to interface digital microfluidics with MALDI-MS for offline sample analysis. We demonstrated the utility of this format by implementing on-chip protein digestion on immobilized enzyme depots.

We have previously used a two-dimensional fluorescence difference gel electrophoresis protein expression with matrix-assisted laser desorption ionization of mass spectrometry to identify the serum proteomic profiles before and after the Tai Chi exercise in normal adults (Yang & Chang, et al. Clin Chem 56:127, 2010). However, the high abundant serum proteins in seyal samples might interfere the discovery of low abundance proteins in two-dimensional electrophoresis, but these low abundant proteins may play an important role on human physiology. Therefore, we looked for another way to resolve this complex issue. After multiple attempts, we chose a commercial affinity column to exclude 14 kinds of high-abundance proteins before analyses of serum proteomic displays. This column could be fit into a fast liquid chromatography separation of purified proteins and eluted for low abundant proteins. The low abundant proteins were first expressed by one-dimensional gel electrophoresis of proteins followed by a series of gel cut down for in-gel digestion by trypsin and subject to nano-liquid chromatography with electrospray ionization tandem mass spectrometry analysis (nano-LC ESI MS/MS ). The results obtained by software analysis were subject to its functional pathways analysis. We analysed 3 comparisons of the protein displays including differences between normal adults before and after exercise, differences of normal adults and diabetic patients before and after exercise. Experiments were next performed to validate the most significant difference of proteins between each category by enzyme-linked immunoassay. Results showed that dipeptidyl peptidase 4 (DPP4) and neutrophil gelatinase-associated lipocalin (NGAL) proteins were significantly higher in diabetic patients than in normal adults ( P values were 0.011 and less than 0.001), while the prolactin-inducible protein (PIP) was higher in normal adults than in diabetic patients after exercise (P value of 0.042). To our knowledge, decrease of DPP4 in type 2 diabetes has been shown to reduce blood sugar and improve the immunity; and NGAL has been confirmed to be an indicator for early diagnosis of acute kidney injury. Therefore, we have identified certain functional proteomic markers in normal and diabetic patients after Tai Chi exercise. This study model with exclusion of high-abundance serum proteins is a useful mode for identifying immune and metabolic marker with and without.

Ambient ionization mass spectrometry, which has witnessed a flurry of recent developments, is a set of useful techniques for the analysis of samples under open-air conditions. It allows direct, rapid, real-time, high-throughput analysis with little or no sample pretreatment for the chemicals in solids or liquids. In this study, thermal desorption electrospray ionization mass spectrometry ( TD-ESI/MS ) involving direct insertion probe ( DIP ), thermal desorption ( TD ) and electrospray ionization ( ESI ) was used for the rapid screening of various types of samples. The source mainly consists of the sampling probe device, thermal desorption heating device, electrospray ionization device, ion source and temperature controller. A novel strategy involved in TD-ESI/MS processes where sampling, desorption, and ionization are separated as three independent events. The sampling probe is first used for the sampling of analytes and then inserted into a heat unit for thermal desorption. The desorbed analytes are finally carried into a reaction region with a stream of nitrogen gas, where charged methanol droplets were generated continuously by electrospray for post-ionization. Total analysis time is less than 10 seconds. Traditionally, three standard methods are used for the analysis for pesticide residues, biochemical, immunoassay and instrument. And, the instrument analysis is the most widely used because it provides lots of advantages in particularly accurate quantitative approach. However, its complicated steps take a long period of time for preparation. Here, we used TD-ESI/MS to rapidly screen the pesticide residues on the surface of fruits and vegetables. The MS/MS analysis was also performed to confirm those detected compounds. The experimental results of the standard deviation for reproducibility is 13.2% (n = 10), and the detection limit is approximately 10 ppb. Furthermore, several fruits and vegetables purchased from local market were used as test samples and pesticide residues on the surface of samples can be successfully detected via TD-ESI/MS. In addition, the TD-ESI/MS technique was also applied to the analysis of illegal additives or phthalates in food. In this study, the TD-ESI/MS technique emerges lots of advantages such as direct, rapid, real-time analysis of sample surface and sample pretreatment is not necessary, and shows highly potential for rapid screening of chemicals in food safety.

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The focus of this Ph.D. thesis is the theoretical, computational, and experimental analysis of electrohydrodynamics and ionization in the Array of Micromachined UltraSonic Electrospray (AMUSE) ion source. The AMUSE ion source, for mass spectrometry (MS), is a mechanically-driven, droplet-based ion source that can independently control charge separation and droplet formation, thereby conceptually differing from electrospray ionization (ESI). This aspect allows for low voltage soft ionization of a variety of analytes and flexibility in the choice of solvents, providing a multifunctional interface between liquid chromatography and mass spectrometry for bioanalysis. AMUSE is a versatile device that operates in an array format, enabling a wide range of configurations, including high-throughput and multiplexed modes of operation. This thesis establishes an in-depth understanding of the fundamental physics of analyte charging and electrokinetic charge separation in order to enhance droplet charging and ionization efficiency. A detailed electrohydrodynamic (EHD) computational model of charge transport during the droplet formation cycle in the AMUSE ion source is developed, coupling fluid dynamics, pressure and electric fields, and charge transport in multiphase flow. The developed EHD model presents a powerful tool for optimal design and operation of the AMUSE ion source, providing insight into the microscopic details of physicochemical phenomena, on the microsecond time scale. Analyte charging and electrohydrodynamics in AMUSE are characterized using dynamic charge generation measurements and high-spatial-resolution stroboscopic visualization of ejection phenomena. Specific regimes of charge transport, which control the final droplet charging, have been identified through experimental characterization and simulations. A scale analysis of the ejection phenomena provides a parametric regime map for AMUSE ejection modes in the presence of an external electric field. This analysis identifies the transition between inertia-dominated (mechanical) and electrically-dominated (electrospraying) ejection, where inertial and electric forces are comparable, producing coupled electromechanical atomization. The understanding of analyte charging and charge separation developed through complimentary theoretical and experimental investigations is utilized to improve signal abundance, sensitivity, and stability of the AMUSE-MS response. Finally, these tools and fundamental understanding provide a sound groundwork for the optimization of the AMUSE ion source and future MS investigations.