No / The structural and functional diversity of lipids accounts for their involvement into a wide range of homeostatic processes and disease states, including lifestyle-related diseases as well as genetic conditions. Challenges presented by this diversity have been addressed to a great extent by the development of lipidomics, a platform that makes possible the detailed profiling and characterisation of lipid species present in any cell, organelle, tissue or body fluid, and allows for a wider appreciation of the biological role of lipid networks. Progress in the field of lipidomics has been greatly facilitated by recent advances in MS and includes a range of analytical platforms supporting applications spanning from qualitative and quantitative assessment of multiple species to lipid imaging. Here we review these MS techniques currently in routine use in lipidomics, alongside with new ones that have started making an impact in the field. Recent applications in health, disease and nutrition-related questions will also be discussed with a view to convey the importance of lipidomics contributions to biosciences and food technology.

Proteomic characterization of human NK cell membrane microdomains. (in Czech) Bc. Alan Kádek (Department of Biochemistry, Faculty of Science, Charles University in Prague, Czech Republic) Natural killer (NK) cells are one of the important components of innate immune system. Their main function is to fight against tumors, virally infected or otherwise malformed cells. Plasma membranes of NK cells contain regions with specific lipid composition compared to the surrounding membrane (called membrane microdomains or rafts). Because of their lipid composition, microdomains preferentially accommodate some immunologically relevant proteins and play a role during cellular polarization and signalization. Characteristic feature of membrane microdomains is their partial resistance to solubilization by mild non-ionogenic detergents. In this thesis, microdomains were isolated in a detergent-resistant membrane fraction (DRM) from human NK-92MI cell line and from NK cells immunomagnetically enriched from peripheral blood of non-leukemic donors. For the isolation, Triton X-100 or Brij-98 detergent solubilization and ultracentrifugation in a sucrose density gradient was used. Protein composition of isolated DRMs was analyzed by mass spectrometry employing an LC-MALDI-TOF/TOF method. Protein lists generated in these...

This thesis investigates the development of new methodology for the identification and quantification of organic phosphorus compounds in environmental samples. Phosphorus is a vital element for primary production and one of the factors contributing to eutrophication. Eutrophication of aquatic systems leads to algal blooms, changes in ecological balance and deteriorating water quality. Difficulties in studying organic phosphorus stem from the fact that organic phosphorus is present in the environment in a variety of forms and each form may have different degradation and turnover time, having very different effects on eutrophication. New methods for the quantification of phosphorus derived from three groups of organic phosphorus compounds were developed. For the determination of phosphorus derived from DNA and phospholipids selective extraction was combined with digestion and colorimetric determination of the extracted phosphate. For quantification of inositol phosphates high performance liquid chromatography was coupled with tandem mass spectrometry using electrospray ionization.   The methods were applied to studying the distribution of these compounds in a small catchment and in the case of DNA-P and phospholipid-P, the degradation of the fractions in lake sediments. The studies showed that phosphorus bound to DNA, phospholipids and inositol phosphates constitute a sizeable part of the total phosphorus in different environmental samples. The phospholipid-P fraction was the smallest one, accounting for, on average, only a few percent of the total phosphorus in the sample. Inositol phosphates were most prevalent in the soils, with inositol hexakisphosphate accounting for over 10% of the total phosphorus content. The highest content of DNA-P was found in sediments and it was shown that DNA-P degrades more rapidly than phospholipid-P and therefore plays a more critical role in internal loading.

No / A novel ion trap time-of-flight hybrid mass spectrometer (qIT-TOF MS) has been applied for peptide sequencing in proteolytic digests generated from spore mixtures of Bacilli. The method of on-probe solubilization and in situ proteolytic digestion of small, acid-soluble spore proteins has been recently developed in our laboratory, and microorganism identification in less than 20 min was accomplished.1 In this study, tryptic peptides were generated in situ from complex spore mixtures of B. subtilis 168, B. globigii, B. thuringiensis subs. Kurstaki, and B. cereus T, respectively. MALDI analysis of bacterial peptides generated was performed with an average mass resolving power of 6200 and a mass accuracy of up to 10 ppm using a trap-TOF tandem configuration. Precursor ions of interest were usually selected and stored in the quadrupole ion trap with their complete isotope distribution by choosing a window of ±2 Da. Sequence-specific information on isolated protonated peptides was gained via tandem MS experiments with an average mass resolving power of 4450 for product ion analysis, and protein and bacterial sources were identified by database searching.

Analysis of biological samples can be a difficult task. This thesis covers a broad aspect of the analytical areas of capillary electrophoresis (CE) and capillary electrochromatography (CEC) in combination with mass spectrometry (MS) that are of great importance for achieving fast, accurate and sensitive bioanalyses. A significantly time reduced and automated system for sample cleanup was developed to greatly simplify the pretreatment process of biological samples with a complex matrix. Desalting and preconcentration of species in urine was conducted and the limit of detection for the antidepressant escitalopram was lowered 10 times. This extraction devise was also successfully incorporated in a chip based platform for the possibility to be a part of multidimensional separation systems. The reduced risk of sample loss leads to improved detection limits, which are usually one the most challenging parts when working with bioanalyses. In the area of separation, a monomer surface with tailored hydrophobicity was developed to achieve rapid, high efficient separations of complex mixtures. Within five minutes a tryptic digest of a protein could be separated and then identified by a Mascot search. The applications addressed have been focused on medical conditions which are of highest interest for both physicians and patients. A high throughput analysis of the kynurenine metabolites with CE-MS offers a new method to rapidly examine samples from patients with neurological disorders. A screening study of possible biomarkers for the two different types of appendicitis, gangraenous and phlegmonous was conducted. Indicative patterns were found for both pre and post surgery of the two types of inflammation as well as between them. The divergences were traced back to the MS peaks obtained in the CE- and CEC-MS setups as possible biomarkers for the two forms of appendicitis. A preliminary study of polycystic ovary syndrome also offered some valuable results for future biomarker identification.

Soluble guanylyl cyclase (sGC) is the receptor for nitric oxide and a highly sought-after therapeutic target for the management of cardiovascular diseases. New compounds that stimulate sGC show clinical promise, but where these stimulator compounds bind and how they function remains unknown. Here, using a photolyzable diazirine derivative of a novel stimulator compound, IWP-051, and MS analysis, we localized drug binding to the 1 heme domain of sGC proteins from the hawkmoth Manduca sexta and from human. Covalent attachments to the stimulator were also identified in bacterial homologs of the sGC heme domain, referred to as H-NOX domains, including those from Nostoc sp. PCC 7120, Shewanella oneidensis, Shewanella woodyi, and Clostridium botulinum, indicating that the binding site is highly conserved. The identification of photoaffinity-labeled peptides was aided by a signature MS fragmentation pattern of general applicability for unequivocal identification of covalently attached compounds. Using NMR, we also examined stimulator binding to sGC from M. sexta and bacterial H-NOX homologs. These data indicated that stimulators bind to a conserved cleft between two subdomains in the sGC heme domain. L12W/T48W substitutions within the binding pocket resulted in a 9-fold decrease in drug response, suggesting that the bulkier tryptophan residues directly block stimulator binding. The localization of stimulator binding to the sGC heme domain reported here resolves the longstanding question of where stimulators bind and provides a path forward for drug discovery.

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.

<p>This thesis describes the current status and novel aspects of the analysis of the molecules of life, i.e. peptides and proteins, using capillary electrophoresis (CE) coupled to mass spectrometry (MS) via (sheathless) electrospray ionization (ESI). Early reports of sheathless CE-ESI-MS were plagued by limited lifetimes of the electrospray emitter. In this thesis, two new approaches, the Black Dust and the Black Jack methods, utilizing polymer-embedded graphite instead of noble metals are presented. These emitters have shown improved long-term stability and proven excellent for sheathless electrospray operation. Failure of an emitter is often caused by electrochemical reactions occurring at the emitter-liquid interface. The electrochemical properties of the graphite coated emitters were therefore evaluated by classical electrochemical methods, such as cyclic voltammetry and chronoamperometry. The graphite coated emitters showed excellent electrochemical stability and properties compared to noble metal and polymer configurations.</p><p>Analyte-wall interactions have long been known to cause problems in the CE analysis of biomolecules. This can be circumvented by internal modification of the capillary walls. Additionally, it is of outermost importance to have a stable and sufficiently high electroosmotic flow (EOF) to sustain the electrospray, when using a sheathless approach. New monomer and polymer coatings are presented for rapid and high-efficient CE-ESI-MS separations of peptides and proteins.</p><p>Furthermore, the use of CE-ESI coupled to Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) shows great potential for rapid proteomic probing of human cerebrospinal fluid. The results are comparable with more established techniques, such as liquid chromatography and two-dimensional gel electrophoresis coupled to MS. However, the CE-ESI-FTICRMS analysis has significantly lower sample consumption and faster analysis time compared to the other techniques. The applications and use of CE-ESI-MS is expected to have a bright future with continued growth as current trends of multidimensional hyphenation and microfabricated devices are further developed and explored.</p>

This thesis describes the current status and novel aspects of the analysis of the molecules of life, i.e. peptides and proteins, using capillary electrophoresis (CE) coupled to mass spectrometry (MS) via (sheathless) electrospray ionization (ESI). Early reports of sheathless CE-ESI-MS were plagued by limited lifetimes of the electrospray emitter. In this thesis, two new approaches, the Black Dust and the Black Jack methods, utilizing polymer-embedded graphite instead of noble metals are presented. These emitters have shown improved long-term stability and proven excellent for sheathless electrospray operation. Failure of an emitter is often caused by electrochemical reactions occurring at the emitter-liquid interface. The electrochemical properties of the graphite coated emitters were therefore evaluated by classical electrochemical methods, such as cyclic voltammetry and chronoamperometry. The graphite coated emitters showed excellent electrochemical stability and properties compared to noble metal and polymer configurations. Analyte-wall interactions have long been known to cause problems in the CE analysis of biomolecules. This can be circumvented by internal modification of the capillary walls. Additionally, it is of outermost importance to have a stable and sufficiently high electroosmotic flow (EOF) to sustain the electrospray, when using a sheathless approach. New monomer and polymer coatings are presented for rapid and high-efficient CE-ESI-MS separations of peptides and proteins. Furthermore, the use of CE-ESI coupled to Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) shows great potential for rapid proteomic probing of human cerebrospinal fluid. The results are comparable with more established techniques, such as liquid chromatography and two-dimensional gel electrophoresis coupled to MS. However, the CE-ESI-FTICRMS analysis has significantly lower sample consumption and faster analysis time compared to the other techniques. The applications and use of CE-ESI-MS is expected to have a bright future with continued growth as current trends of multidimensional hyphenation and microfabricated devices are further developed and explored.

Proteomics is the global analysis of proteins that covers a broad range of technologies aimed at determining the identity and quantity of proteins expressed in the cell, their three-dimensional structure and interaction partners. In contrast to genome, proteome reflects more accurately on the dynamic state of the cell, tissue, or an organism. Therefore much is expected from proteomics to yield better disease markers for early diagnosis and therapy monitoring, as well as biomarkers that would indicate environmental exposure or provide prediction of biological age. In this thesis, I have developed and applied robust and sensitive subproteomic approaches to study the effect of aging as well as and environmental pollution using different animal models. In the first part, a high-throughput proteomic method based on liquid chromatography coupled to 2-dimensional gel electrophoresis (LC/2-DE) was developed. The usefulness of this method has been demonstrated by applying it to the assessment of marine pollution in a field experiment. Next, I have utilized this subproteomic approach to study the effect of aging in mouse kidney of both genders. As a result, a protein expression signature of aging kidney was obtained, revealing gender-dependent alterations in proteome profiles of aging mouse kidney. In order to further reduce the dynamic range of protein expression and increase the sensitivity of proteomic analysis, I have applied a shotgun mass spectrometry-based proteomic approach using isobaric tags for relative and absolute quantification (iTRAQ) coupled to liquid chromatography and tandem mass spectrometry (LC-MS/MS) to study age-related differences in peroxisome-enriched fractions from mouse liver. Only eight proteins showed statistically significant difference in expression (p&lt;0.05) with moderate folds. This study indicates that age-depended changes in the liver proteome are minimal, suggesting that its proteome is efficiently maintained until certain age. Finally, in the context of aging studies and the role of peroxisomes in aging, I have tested the utility of cell-penetrating peptides (CPPs) as agents for protein delivery into acatalasemic peroxisomes using yeast as a model. The results obtained suggest that CPPs may be suitable for the delivery of antioxidants to peroxisomes and in future could provide a tool for the protein therapy of age-related diseases. / At the time of the doctoral defense, the following publications were unpublished and had a status as follows: Paper 3: Submitted, Paper 4: Submitted.