Ce travail de thèse a été focalisé sur le développement d’approches MS et IM-MS supramoléculaires pour la caractérisation fine des interactions protéine/ligand et pour l’analyse de mélanges protéiques complexes. La maîtrise des instruments de MS supramoléculaire ainsi que les optimisations instrumentales et méthodologiques réalisées ont permis d’étendre le potentiel des approches MS et IM-MS pour la caractérisation d’assemblages moléculaires particulièrement complexes. Nous avons ainsi pu suivre la cinétique de formation de complexes protéine/ligand ainsi que les changements conformationnels qui y sont associés, montrant l’intérêt du couplage IM-MS en recherche pharmaceutique. De plus, ce travail a porté sur l’étude de complexes de très hauts poids moléculaires et l’évaluation de l’IM-MS pour obtenir des informations structurales sur ces complexes. Nous avons ainsi permis de repousser certaines limites de la MS et de placer cette technique au cœur des études de biologie structurale. / The aim of this thesis was the development of different supramolecular approaches, like MS and IM-MS, to characterize precisely protein/ligand interaction and to analyze complex mixtures of proteins. Understanding of supramolecular MS instruments and instrumental and methodological optimizations were allowed the development of MS and IM-MS to characterize very high mass supramolecular assembly. Thus, we were able to follow by kinetic the formation of protein/ligand interaction as well as associated conformational modifications, showing the interest of IM-MS coupling in pharmaceutical research. Furthermore, this work deals with the study of high mass complexes and assessment of IM-MS to obtain structural information on these complexes. As a consequence, we have pushed away some limits of MS allowing the use of this technique in structural biology.

Um método para determinação de praguicidas das classes organofosforados, carbamatos, triazinas e ureias por HPLC-MS/MS em urina de pessoas expostas em decorrência de atividades agrícolas é proposto neste trabalho. O modo de eluição isocrática e gradiente em cromatografia líquida de fase reversa com a coluna Synergi Max RP (150 x 4,6 mm, 4 µm) foram experimentados para a separação dos componentes da amostra. O modo isocrático de eluição nas condições 45:55, 60:40 e 70:30 de ACN/água foram insuficientes para eluição dos componentes da amostra com fatores de retenção aceitáveis entre 0,5 e 20. Em modo gradiente, os efeitos do tempo de gradiente (30 a 100 min), a concentração inicial de ACN (8 a 14%), vazão da fase móvel (0,5 a 1,0 mL min-1) e temperatura (30 a 40 °C) foram verificados para aumento de resolução e diminuição do tempo de análise. Em composições distintas de fase móvel (ACN/água), o logaritmo dos fatores de retenção foi colocado em gráfico em função da acidez (α) e a basicidade (β) da ligação de H, constante dielétrica (ε) e parâmetro de solubilidade de Hildebrand (δH). Dimetoato e metomil tiveram comportamentos diferenciados, ambos explicados pelas ligações de H intramoleculares. Através de um planejamento fatorial completo de dois níveis, usando-se as funções COF e CRS como resposta, variáveis como vazão da fase móvel, tempo de gradiente, concentração inicial de ACN e temperatura foram investigados. A melhor resposta experimental forneceu como condições de análise: 0,5 mL min-1, 40 °C, 75 min e 5% de ACN, para vazão, temperatura, tempo de gradiente e concentração inicial de ACN, respectivamente. Em um sistema LC-MS/MS usando o ion trap como analizador de massas, a infusão direta dos padrões de praguicidas, para conhecimento do pico do íon molecular e das transições MS/MS, foi estudada. Experimentos de quantificação em UPLC-MS/MS foram baseados na separação em fase reversa com a coluna ACQUITY UPLC HSS T3 (50 x 2,1 mm, 1,8 µm), espectrômetro de massas equipado com analizador de massas triplo quadrupolo e modo positivo de ionização. Transições MRM de quantificação e de confirmação foram monitoradas para cada praguicida. O método apresentou respostas lineares no intervalo de 0,25 a 50 µg L-1 para todos os praguicidas com coeficiente de determinação maiores que 0,999. O LD do método variou de 0,192 a 3,19 µg L-1. O LQ do método variou entre 0,582 e 13,6 µg L-1, com coeficiente de variação inferior a 20% CV. As recuperações em amostras fortificadas em 0,75 µg L-1 variaram entre 55,7 e 72,6% e a precisão em termos de %CV entre 1,94 e 19,1%. As recuperações em amostras fortificadas em 10 µg L-1 variaram entre 99,1 a 105% e a precisão entre 0,751 e 8,98% CV. As recuperações em amostras fortificadas em 50 µg L-1 variaram entre 99,5 a 101% e a precisão entre 0,877 e 5,94% CV. Das 25 amostras quantificadas, 13 apresentaram concentrações dos praguicidas na faixa linear da curva de calibração. Estes valores de concentração variaram entre 10 e 50 µg L-1. / In this work a method for determination of different chemical groupes of pesticides (organophosphorus, carbamates, triazines, organochlorine and ureas) is proposed using HPLC-MS/MS in samples from occupational exposed agriculture workers. Isocratic and gradien elution in reversed-phase chromatography using a Synergi Max RP (150 x 4,6 mm, 4 µm) column were investigated for separation proposal. Isocratic elution conditions 45:55, 60:40, 70:30 ACN/water provided unsatisfactory results with retention factor from 0.5 to 20. In gradient elution, effects of gradient time (30 to 100 min), initial concentration of ACN (8 to 14%), flow rate (0.5 to 1 mL min-1) and temperature (30 to 40 °C) were studied for increasing resolution and decreasing analysis time. For different proportion of ACN in the mobile phase, the logarithm of retention factor has been ploted against solvent hydrogen-bond donor (α), solvent hydrogen-bond acceptor (β), dieletric constant (ε) and Hildebrand solubility (δH). Dimethoate and methomyl presented different behaviour in relation to others, explained by H intramolecular bond. Applying a two level experimental design having as response functions COF and CRS, combined factors such as flow rate, gradient time, ACN initial concentration and temperature were investigated. Optimal conditions were obtained in 0.5 mL min-1, 40 °C, 75 min e 5% CAN, for flow rate, temperature, gradient time and ACN initial concentration, respectively. Applying a LC-MS/MS system equipped with an ion trap mass analyzer, direct infusion of standard solutions of pesticides for knowledge of ion molecular peak and their MRM transitions was obtained. Quantitative experiments using UPLC-MS/MS were based in reversed-phase separation with a Acquity UPLC HSS T3 (50 x 2,1 mm, 1,8 µm) column, mass spectrometry instrument equipped with triple quadrupole mass analyzer at positive ion polarity. Quantifying and confirming ion transitions were monitored for each pesticide compound. Linearity in range of 0.25 to 50 µg L-1 was established for all pesticides with high coefficients determination R2 0.999 were obtained. The method LOD varied between 0.192 to 3.19 µg L-1. LOQ varied from 0.582 to 13.6 µg L-1, with coefficient variation below 20% CV. Recoveries for samples spiked at 0.75 µg L-1 concentration level varied from 55.7 to 72.6% and precision in terms of CV between 1.94 and 19.1% CV. Spiked samples at 10 µg L-1 concentration level varied from 99.1 to 105% and precision between 0.751 and 8.98% CV. Recoveries for samples spiked at 50 µg L-1 concentration level varied from 99.5 to 101% and precision from 0.877 to 5.94% CV. From 25 samples quantified, 13 presented concentration values in linear range of the calibration curve. These values varied from 10 to 50 µg L-1.

This thesis deals with the content of adaptogens in vegetable Schizandra chinensis. The theoretical part deals with the plant Schisandra chinensis, its occurrence, characteristics, uses and cultivation. Location of plants Schisandra chinensis are classified according to Köppen climate classification and compared with the climate in the Czech Republic, due to possible prediction of growing plants in the country. Further are described adaptogens (bioactive substances) contained in this plant and to methods for their extraction and analysis. The experimental part of the thesis deals with the identification of schisandrin in the plant Schisandra chinensis grown in our conditions. The assessment was performed by ultra-performance liquid chromatography (UPLC), high-performance liquid chromatography (HPLC) and direct injection into tha mass spectrometry (MS). Schisandrin was successfully identified in all the samples.

Glycosaminoglycans (GAGs) such as hyaluronan (HA) and chondroitin sulfate (CS) are important, natural polysaccharides which occur in biological (connective) tissues and have various biotechnological and medical applications. Additionally, there is increasing evidence that chemically (over)sulfated GAGs possess promising properties and are useful as implant coatings. Unfortunately, a detailed characterization of these GAGs is challenging: although mass spectrometry (MS) is one of the most powerful tools to elucidate the structures of (poly)saccharides, MS is not applicable to high mass polysaccharides, but characteristic oligosaccharides are needed. These oligosaccharides are normally generated by enzymatic digestion. However, chemically modified (particularly sulfated) GAGs are extremely refractive to enzymatic digestion. This study focuses on the investigation of the digestibility of GAGs with different degrees of sulfation by bovine testicular hyaluronidase (BTH). It will be shown by using an adapted spectrophotometric assay that all investigated GAGs can be basically digested if the reaction conditions are carefully adjusted. However, the oligosaccharide yield correlates reciprocally with the number of sulfate residues per polymer repeating unit. Finally, matrix-laser desorption and ionization (MALDI) MS will be used to study the released oligosaccharides and their sulfation patterns.

The goal of my diploma thesis was finding a suitable method for unifying score values from various protein identification search tools in MS/MS mass spectrometry into one single score value. Data coming from the output of mass spectrometer are processed in two independent search tools Mascot and X!Tandem. These were selected especially for their wide usage in proteomic labs. Both results are evaluated through newly designed function and unified by single valued score clearly identifying found proteins. Newly designed scoring value is called Matascore and function producing this score was implemented in MATLAB. Function and its results were successfully tested by real data available in public databases on the Internet.

<p>This thesis concerns the development and validation of high performance liquid chromatography (HPLC) methods aimed for two industrially important areas: (i) analysis of biotechnological synthesis and (ii) determination of adsorption isotherm parameters. There is today a lack of detailed recommendations for analytical procedures in the field of biotechnological production of drugs. Therefore, guidelines were given for analytical development and validation in this field; the production of 9α-hydroxyprogesterone was used as model. In addition, a rapid method using HPLC coupled with diode-array-detection (DAD) and mass spectrometry (MS), was developed for the preliminary identification and quantification of the product. In addition, requirements and recommendations were developed for the selection of the internal standard and for its inclusion in the process liquid. By using this approach the precision and accuracy of the quantitative method were considerably improved. </p><p>Preparative chromatography is a powerful separation method for the purification of pure compounds from more or less complex sample mixtures. One such mixture can be the process liquid from a fermentation, another example can be a racemic mixture of compounds whose enantiomeric constituents must be isolated. Computer-assisted modeling can be used to optimize preparative chromatography. However, competitive adsorption isotherm parameters are required as input data for the computer simulations. In this thesis, a new injection technique, based on a firm theoretical basis, was developed for the peak perturbation (PP) method allowing the determination of binary competitive adsorption isotherm parameters from a broad concentration range. With the new method the determination of adsorption isotherm parameters from a quaternary mixture could be done for the first time. The profiles simulated with these parameters showed excellent agreement with the corresponding experimental profiles, validating the accuracy of the adsorption isotherm parameters derived by the new method.</p>

<p>The analysis of low abundant biological molecules is often challenging due to their chemical properties, low concentration and limited sample volumes. Neuropeptides are one group of molecules that fits these criteria. Neuropeptides also play an important role in biological functions, which makes them extra interesting to analyze. A classic chemical analysis involves sampling, sample preparation, separation and detection. In this thesis, an enhanced solid supported microdialysis method was developed and used as a combined sampling- and preparation technique. In general, significantly increased extraction efficiency was obtained for all studied peptides. To be able to control the small sample volumes and to minimize the loss of neuropeptides because of unwanted adsorption onto surfaces, the subsequent analysis steps were miniaturized to a micro total analysis system (µ-TAS), which allowed sample pre-treatment, injection, separation, manipulation and detection. </p><p>In order to incorporate these analysis functions to a microchip, a novel microfabrication protocol was developed. This method facilitated three-dimensional structures to be fabricated without the need of clean room facilities. </p><p>The sample pre-treatment step was carried out by solid phase extraction from beads packed in the microchip. Femtomole levels of neuropeptides were detected from samples possessing the same properties as microdialysates. The developed injection system made it possible to conduct injections from a liquid chromatographic separation into a capillary electrophoresis channel, which facilitated for advanced multidimensional separations. An electrochemical sample manipulation system was also developed. In the last part, different electrospray emitter tip designs made directly from the edge of the microchip substrate were developed and evaluated. The emitters were proven to be comparable with conventional, capillary based emitters in stability, durability and dynamic flow range. Although additional developments remain, the analysis steps described in this thesis open a door to an integrated, on-line µ-TAS for neuropeptides analysis in complex biological samples.</p>

<p>Advances in life science require knowledge of active molecules in complex biological systems. These molecules are often only present for a certain time and at limited concentrations. Integrated micro-analytical tools for sampling, separation and mass spectrometric (MS) detection would meet these requests and are therefore continuously gaining interest. An on-line coupling of analytical functions provides shorter analysis time and less manual sample handling. In this thesis, improved compatibility of microdialysis sampling and multidimensional separations coupled to MS detection are developed and discussed.</p><p>Microdialysis was used <i>in vitro</i> for determination of the non-protein bound fraction of the drug ropivacaine. The sampling unit was coupled on-line to capillary column liquid chromatography (LC) followed by ultraviolet or MS detection. For MS detection, the system was extended with a desalting step and an addition of internal standard. A method for MS screening of microdialysates, collected <i>in vivo,</i> was also developed. The method involved sampling and measurements of the chemical pattern of molecules that generally are ignored in clinical investigations. Chemometric tools were used to extract the relevant information and to compare samples from stimulated and control tissues.</p><p>Complex samples often require separation in more than one dimension. On-line interfaces for sample transfer between LC and capillary electrophoresis (CE) were developed in soft poly(dimethylsiloxane) (PDMS). MS detection in the LC-CE system was optimised on frequent sampling of the CE peak or on high resolution in mass spectra using time-of-flight (TOF)MS or Fourier transform ion cyclotron resonance (FTICR)MS, respectively. Aspects on electrode positioning in the LC-CE interface led to development of an on-column CE electrode. A successful method for deactivation of the PDMS surface using a polyamine polymer was also developed. The systems were evaluated using peptides and proteins, molecules that are gaining increased attention in bioscience, and consequently also in chemical analysis. </p>

This thesis concerns the development and validation of high performance liquid chromatography (HPLC) methods aimed for two industrially important areas: (i) analysis of biotechnological synthesis and (ii) determination of adsorption isotherm parameters. There is today a lack of detailed recommendations for analytical procedures in the field of biotechnological production of drugs. Therefore, guidelines were given for analytical development and validation in this field; the production of 9α-hydroxyprogesterone was used as model. In addition, a rapid method using HPLC coupled with diode-array-detection (DAD) and mass spectrometry (MS), was developed for the preliminary identification and quantification of the product. In addition, requirements and recommendations were developed for the selection of the internal standard and for its inclusion in the process liquid. By using this approach the precision and accuracy of the quantitative method were considerably improved. Preparative chromatography is a powerful separation method for the purification of pure compounds from more or less complex sample mixtures. One such mixture can be the process liquid from a fermentation, another example can be a racemic mixture of compounds whose enantiomeric constituents must be isolated. Computer-assisted modeling can be used to optimize preparative chromatography. However, competitive adsorption isotherm parameters are required as input data for the computer simulations. In this thesis, a new injection technique, based on a firm theoretical basis, was developed for the peak perturbation (PP) method allowing the determination of binary competitive adsorption isotherm parameters from a broad concentration range. With the new method the determination of adsorption isotherm parameters from a quaternary mixture could be done for the first time. The profiles simulated with these parameters showed excellent agreement with the corresponding experimental profiles, validating the accuracy of the adsorption isotherm parameters derived by the new method.

In analytical chemistry the main goal is normally to determine the identity and/or concentration of one or more species in a sample. The samples analyzed are often natural samples, containing numerous different species in a complex matrix and the choice of technique for multi-elemental detection is in general inductively coupled plasma spectrometry. The chemical forms of an element can affect many of its characteristics e.g. toxicity, which makes speciation analysis important. Therefore, determination of the identity and quantity of an element is still important, but for many applications measurements of total element concentration provides insufficient information. To be able to perform speciation analysis, separation, identification and/or characterization of the various forms of elements in the sample has to be accomplished. Speciation analysis has been employed in a wide range of disciplines, including for example environmental science, biology and clinical chemistry. This thesis describes work to improve and understand the elemental speciation analysis with liquid chromatography coupled to plasma spectrometry and also highlights the importance and potential of the synergy between atomic spectrometry and molecular mass spectrometry. The combination of the matrix tolerant, robust and very sensitive plasma spectrometry used together with molecular mass spectrometry, which provides structural information and the possibility to identify unknown species, is demonstrated to be a very powerful tool for speciation analysis. In this thesis methods are developed for on-line sample clean-up and pre-concentration coupled to liquid chromatography and plasma spectrometry, which makes handling of small sample volumes easier and also decreases the risk of contamination. The problems associated with organic modifiers in plasma spectrometry are also addressed. Applications of speciation analysis are exemplified by analysis of aluminium-chelated siderophores in field-soil solutions and organic phosphorous species in aquatic sediments. The possibility to analyze un-dissolved samples as slurries with minimal sample preparation is also discussed.