The possibilities of differentiating linkage positions and anomeric configurations of small oligosaccharides by negative ion mode MALDI using anion attachment followed by PSD are investigated. By careful initial adjustment of the focusing mirror ratios allowing acquisition of the peaks of interest within the same PSD segment, it is possible to obtain highly reproducible relative ion abundances. Discrimination of different linkage types is achieved by analysis of structurally-informative diagnostic peaks offered by PSD spectra of chloride adducts of oligosaccharides, whereas the relative peak intensities of selected diagnostic fragment pairs make differentiation of anomeric configuration possible. F- and Ac- cannot form anionic adducts with the oligosaccharides in significant yields. However, Br-, I- and NO3- anionic adducts consistently appear in higher abundances relative to [M - H]-, just like Cl-. Mildly acidic saccharides form both deprotonated molecules and anionic adducts, making it possible to simultaneously detect neutral and acidic oligosaccharides via anion attachment. PSD of [oligosaccharide + Cl]- yields structurally-informative fragment ions that retain the charge on the sugar molecule rather than solely forming Cl-, whereas PSD of Br-, I- and NO3- adducts of oligosaccharides yield the respective anions as the main product ions without offering structural information concerning the sugar. PSD of the chloride adduct of saccharides containing 1-2 linkages also yields chlorine-containing fragment ions. MALDI-TOF-MS and LDI-TOF-MS are shown to be useful for characterization of ultra-small titania nanoparticles. Peak maxima in MALDI-TOF mass spectra are found to correlate with nanoparticle size. The size distributions of TiO2 nanoparticles, obtained from MALDI- and LDI-TOF-MS are in good agreement with parallel TEM observations. PSD analysis of inorganic x nanomaterials is performed and valuable information about the structure of analytes has been obtained. A group of inorganic nitrate and perchlorate salts of forensic and health interest are investigated by LDI- and MALDI-TOF MS. In each case, a series of characteristic cluster ions are predominant in the negative-ion mode. The number and identity of metal atoms and anions in the recorded cluster ions can be positively identified by their m/z values, distinctive isotopic patterns and characteristic PSD fragmentation patterns.

Submitted by Sara Ribeiro (sara.ribeiro@ucb.br) on 2017-09-04T12:53:05Z No. of bitstreams: 1 DielledeOliveiraMottaDissertacao2014.pdf: 3579770 bytes, checksum: 082642eeca29a044c3ecc5a70434c6bb (MD5) / Approved for entry into archive by Sara Ribeiro (sara.ribeiro@ucb.br) on 2017-09-04T12:53:20Z (GMT) No. of bitstreams: 1 DielledeOliveiraMottaDissertacao2014.pdf: 3579770 bytes, checksum: 082642eeca29a044c3ecc5a70434c6bb (MD5) / Made available in DSpace on 2017-09-04T12:53:20Z (GMT). No. of bitstreams: 1 DielledeOliveiraMottaDissertacao2014.pdf: 3579770 bytes, checksum: 082642eeca29a044c3ecc5a70434c6bb (MD5) Previous issue date: 2014-01-01 / The identification of filamentous fungiis traditionally based on morphological and biochemical criteria which are time demanding and for which results can be inaccurate. This fact motivated the evaluation of matrix-assisted laser desorption ionization ??? time of flight (MALDI-TOF) mass spectrometry for the identification of 36 brazilian isolates of Aspergillus terreus. The species is important worldwide due to its ability to produce lovastatin, a drug extremely successful in decreasing plasmatic cholesterol and consequently decreasing the risk of cardiovascular disease, main cause of death worldwide. Prior to MS analysis, the sequencing of internal transcribed spacer (ITS) allowed the identity confirmation of 94% of samples when compared GenBank database. First of all with the aim to compare the molecular biological technique with identification for MALDI-TOF was evaluated the influence of important factors in the quality of mass spectrums and then selected those more suitable to the identification of the specie. This enabled to characterize the proteic profile 30 of the 36 isolates. Nevertheless only 20% of brazilian isolates were identified as A. terreus when compared at the almost 4000 organisms of Biotyper database which may be attributed to the low representation of the specie. The results show that there are strong evidences that the technique is suitable which corroborates with this is: the similar pattern in the dendograms generated for each methodology, the ability to distinguish of the isolates comparatively higher by MALDI-TOF and the proven effectiveness of the technique evaluated by dark tests from the construction of a personal library. For these reasons the use of MALDI-TOF in the identification of isolates of A. terreus in replacing the conventional techniques is promising nevertheless requires optimizations regarding standardizing the processing of samples and inclusion of more reference spectra in the specie in database. / A identifica????o de fungos filamentosos ?? tradicionalmente baseada em crit??rios morfol??gicos e bioqu??micos que demandam tempo e cujos resultados podem ser imprecisos. Isso motivou a avalia????o do uso da t??cnica alternativa de espectrometria de massa por ioniza????o e dessor????o a laser assistida por matriz (MALDI-TOF) para a identifica????o de 36 isolados brasileiros de Aspergillus terreus. A esp??cie ?? importante mundialmente, dentre outros motivos, devido ?? habilidade de produzir lovastatina, uma droga bem sucedida na redu????o do colesterol plasm??tico com consequente redu????o do risco de doen??as cardiovasculares, principal causa mundial de ??bitos. Antes das an??lises por MALDI-TOF, o sequenciamento do espa??ador interno transcrito (ITS) permitiu a confirma????o da identidade de 94% (34/36) dos isolados quando comparado ?? base de dados GenBank. Inicialmente de forma a comparar a t??cnica de biologia molecular com a identifica????o por MALDI-TOF foi avaliado a influ??ncia de importantes fatores na qualidade dos dados e selecionado aqueles que mais se adequavam a identifica????o da esp??cie. Isso permitiu caracterizar quanto ao perfil proteico 30 dos 36 isolados. Contudo, somente 20% dos isolados brasileiros foram identificados como A. terreus quando comparado aos quase 4000 organismos da base de dados Biotyper o que pode ser atribu??do ?? baixa representatividade da esp??cie. Segundo os resultados existem fortes evid??ncias de que a t??cnica ?? adequada o que corrobora com isso ?? o padr??o semelhante observado nos dendrogramas gerados por cada uma das metodologias, a capacidade de distin????o dos isolados comparativamente maior por MALDI e a comprovada efic??cia da t??cnica avaliada pelo teste ??s escuras a partir da constru????o de uma biblioteca pr??pria. Por essas raz??es o emprego de MALDI-TOF na identifica????o de isolados de A. terreus em substitui????o as t??cnicas tradicionais ?? promissora, por??m requer otimiza????es no que diz respeito ?? padroniza????o quanto ao processamento das amostras e o incremento de mais espectros de refer??ncia da esp??cie no banco de dados.

Sialic acids are involved in many biological processes. In glycoproteins and glycolipids they are essential for signalling and mediate molecular interactions as well as being targets for many pathogens such as influenza virus. The synthesis of sialylated glycoconjugates is of great importance. The incorporation of sialic acid through chemical synthesis carries several difficulties, enzymatic strategies using glycosyltransferases are very attractive alternative strategy, and have been used on a broad range of substrates forming glycosidic linkages with regio-and stereo-specificity. The work presented herein shows the study and application of two enzymes, Photobacteriumdamselae alpha2,6-sialyltransferase (Pd2,6ST) and Trypanosoma cruzi trans-sialidase (TcTS) which are used in the synthesis of sialyloligosaccharides. Both enzymes were expressed in E.coli and purified for biotransformations. In the first application new sialylated chromogenic compounds were generated through this enzymatically by using TcTS and a Pd2,6ST. These compounds were used for the detection of neuraminidase activity in a number of biological samples and led to the discovery of neuraminidase activity from Bacillus pumilus and Arthrobacter aurescens, two different bacteria in which the presence of neuraminidases had never been described. Secondly, TcTS was used to study lipid glycosylations. Glycans in biological systems can be associated to complex lipidic microdomains and the presence of these microdomains can affect the activity of some enzymes. In case of Trypanosoma cruzi trans-sialidase, a decreased activity was detected when the acceptor substrate was part of the aggregated lipid rafts compared to activity observed when the reaction was performed using fully dispersed substrate. Thirdly, the sialylation of glycoarrays using Pd2,6ST was studied. For the first time, sialylated glycans with alpha2,6- glycosidic linkages were successfully incorporated into a gold glycoarray platform, which had been previously developed for the label-free detection of carbohydrate-protein interactions. Successful enzymatic incorporation of sialic acids onto the arrays was confirmed with commercial available lectins. Finally, by using the gold glycoarray platform containing both 2,3 and 2,6 linked sialic acids as well as other common glycans, the carbohydrate-binding properties of the surface proteins of the bacterium Lactobacillus reuteri was studied using MALDI-ToF MS techniques. For first time, strong interactions were observed between a mucus binding protein and Neu5Ac alpha2,6-linked glycans, with much weaker binding to 2,3-linked analogues. Such glycan structures have been identified in abundant manner in colon mucins and this study contributes to the understanding of complex interactions between mucins and probiotic organisms as well as pathogenic bacteria. These studies show that glycan arrays can contribute both to the understanding of probiotics as well as to the identification of glycan binding proteins as targets for new drugs.

Cellulosic biomass is the major organic matter produced in the biosphere. The biodegradation of this cellulosic material is achieved by enzymatic activities of the cellulose degrading microorganisms. These organisms usually express a complex extracellular or a membrane bound cellulolytic system comprising combination of several cellulase enzymes. Cellulases are the group of hydrolytic enzymes capable of hydrolysing insoluble cellulose to glucose. Phlebia gigantea is an aggressive white rot basidiomycete with ability to tolerate resinous extracts on freshly cut wood and higher growth rate. This helps the fungus to colonise the sapwood preventing other fungi from becoming established. Early research on the cellulase system of this organism reported the presence of a cellulase system composed of P-glucosidase, endoglucanase and a cellobiohydrolase. Based on these unpublished studies, our aim was to obtain a complete sequence of putative cellobiohydrolase I (CbhI) from this organism. Attempts to identify and isolate the cellulase gene resulted in an incomplete cDNA sequence of I 154 bp. To understand the cellulase system, expression and regulation of the cellulase enzymatic activity was examined for incubation of P. gigantea on substrates glucose, xylose, Avicel, carboxymethyl cellulose and cellobiose. The pH, total protein and biomass production results indicated that the capacity of P. gigantea to degrade cellulose is dependent upon the nature of the carbon source and the regulation of the cellulase synthesis is repressed in the presence of simple sugars like glucose and xylose. The study employed the highly effective method of purification by affinity adsorption and purified cellulase complex in large quantity. Characterisation of the kinetic properties of this cellulase complex revealed that the rate of cellulase catalysis were optimum at pH 5.0 and temperature 50GC. The purified complex was comprised of multiple proteins and demonstrated significant CMCase and CBHase activity on zymogram analysis. The purified cellulase complex was characterised by 2D gel electrophoresis and by peptide mass finger printing using MALDI-TOF massspectrometry analysis. The 2D gel analysis of the purified cellulase complex showed 15 spots within the range of pI 3.5 to pI 7 and the molecular weight between 20KDa to 100KDa. Three protein spots were selected based on the IEF and SDS zymogram and identified using MALDI-TOF MS analysis. These proteins were identified based on the peptide mass data belonging to the 6-phospho-a-glucosidase, p-glucosidase and glycosyl hydrolase family 13 a-amylase or pullulanases, suggesting the divergent evolution of specific cellulase proteins. This study showed P. gigantea as a potential cellulase source and the cellulase complex secreted by the induction of substrate, comprises a variety of enzymes related to hydrolysis of cellulose biomass. It is evident from this and previous studies that P. gigantea cellulase complex comprises of a specific set of enzymes that possess the ability to degrade crystalline cellulose and is one of the first organisms to colonise freshly cut wood. Further studies on the cellulase system of this primary colonist may open up the prospects to utilise this organism as the potential onsite bioreactor agent, pre-treating the biomass and increasing the economic feasibility of the industrial bioenergy processes.

Peptide sequencing by surface-induced dissociation (SID) on a MALDI-Ion Mobility-orthogonal-TOF mass spectrometer is demonstrated. The early version of the instrument used for proof-of-concept experiments achieves a mobility resolution of approximately 20 and TOF mass resolution better than 200. Peptide sequences of four peptides from a tryptic digest of cytochrome c (ca. 1 pmol deposited) were obtained. The advantage of IM-SID-o-TOFMS is that a single experiment can be used to simultaneously measure the molecular weights of the tryptic peptide fragments (peptide mass mapping) and partial sequence analysis, (real time tandem mass spectrometry.) Optimization of the MALDI-IM-SID-o-TOF mass spectrometer for peptide sequencing is discussed. SID spectra obtained by using stainless steel, Au grids, and fluorinated self-assembled monolayers (F-SAM) on Au are compared. Optimum collision energies differ for the various surfaces. The fragmentation patterns observed for a series of peptides and protein digests using the Nd:YAG laser (355 nm) for MALDI ion formation and an FSAM surface for ion activation is compared to the fragmentation patterns observed for CID and photodissociation. The fragmentation patterns observed in all cases are strikingly similar. Photodissociation produced a greater abundance of ions resulting from side-chain cleavages. As a general rule optimized SID spectra contain fewer immonium ions than either photodissociation or CID. Evaluation of an instrument incorporating a new hybrid drift cell is discussed. Spectra for a digest of hemoglobin is compared to that acquired with an ABI 4700 TOF-TOF. The performance of the instrument is also evaluated using a micro-crystal Nd:YAG laser (355 nm) for MALDI operated at 400 Hz. Experiments were performed to determine the sensitivity and overall performance of the instrument. The reproducibility of the MS/MS spectra for gramicidin S is shown to be 94% run-to-run. The best mobility resolution obtained for a neat deposition of the dye Crystal Violet was 60 t/∆t. Sensitivity was tested with the peptide fibrinopeptide A (m/z 1537, AA sequence ADSGEGDFLAEGGGVR). Data acquired for sixty seconds with approximately sixty femtomoles deposited. Abundant [M+H]+ ions where observed as well as [M+H]+-NH3 ions. The S/N for this short run was insufficient to identify any SID fragments

This study focuses on the application of 193-nm excimer laser (ArF) photodissociation to tandem time-of-flight mass spectrometry. In particular, it focuses on identifying the optimal experimental conditions for peptide sequencing and applying the technology to interesting systems. The early focus is on optimizing the sample preparation conditions that define the initial internal energy state of MALDI-produced ions. Subsequent chapters investigate the effect of changing photodissociation laser conditions and define conditions under which the information content of the spectrum is maximized. Later chapters compare the photodissociation experiment to technologies that represent the current state of the art in tandem mass spectrometry, illustrating both the advantages and shortcoming of photodissociation TOF methodology. Finally, we apply photodissociation to the study of interesting systems of biological relevance, including (1) peptides derived from enzymatic digestion, (2) post-translationally modified peptides, and (3) peptide-transition metal ion complexes. In the final chapter we consider the analytical implications of the work as a whole and comment on the analytical viability of the methodology and look forward to new directions for the experiments.

Hereditary Hemochromatosis (HH) is an inherited recessive autosomal disorder characterized by accumulation of excess iron. When iron binding proteins become saturated, concentrations of free, or non-transferrin-bound iron (NTBI) rise, a condition thought to be responsible for the adverse effects associated with HH. To investigate that disturbing iron homeostasis plays a role in free radical injury in HH, protein carbonyls were found to be 1-7 times higher in patients with HH than in controls, with the greatest increases being observed in untreated HH patients with high ferritin and >90% transferrin saturation with iron. An Unpaired t test revealed a P value of 0.0278 (P< 0.05), which is considered to be statistically significant. Our data showed a significant positive correlation (linear relationship) between the level of carbonyl content and ferritin concentration in plasma samples from patients with HH. In vitro oxidation of transferrin and ferritin standards with hydrogen peroxide and excess iron, followed by immobilized trypsin digestion (Poroszyme), high-resolution LC-MS/MS analysis (Q-TOF Ultima, Waters) and MS/MS data processing (PEAKS, Bioinformatics Solution), identified several tryptic peptides containing oxidized Met,Trp and His residues. Mapping of the oxidized ferritin residues showed them to be located on the inner face of each sub-unit, the face directed toward the ferritin core where iron is normally stored. Using the same methodology, oxidized residues were subsequently detected in ferritin and transferrin isolated from plasma samples of patients severely affected with HH. Comparing of MS/MS spectra of in vitro oxidized samples that have most fragment ion peaks in common with oxidized peptide MS/MS spectra from samples of patients with HH revealed a significant correlation between the two. These data show that elevated NTBI may be involved in oxidative modification of the iron binding proteins, ferritin and transferrin, and that such modifications may play a significant role in the pathophysiology of HH.

Hereditary Hemochromatosis (HH) is an inherited recessive autosomal disorder characterized by accumulation of excess iron. When iron binding proteins become saturated, concentrations of free, or non-transferrin-bound iron (NTBI) rise, a condition thought to be responsible for the adverse effects associated with HH. To investigate that disturbing iron homeostasis plays a role in free radical injury in HH, protein carbonyls were found to be 1-7 times higher in patients with HH than in controls, with the greatest increases being observed in untreated HH patients with high ferritin and >90% transferrin saturation with iron. An Unpaired t test revealed a P value of 0.0278 (P< 0.05), which is considered to be statistically significant. Our data showed a significant positive correlation (linear relationship) between the level of carbonyl content and ferritin concentration in plasma samples from patients with HH. In vitro oxidation of transferrin and ferritin standards with hydrogen peroxide and excess iron, followed by immobilized trypsin digestion (Poroszyme), high-resolution LC-MS/MS analysis (Q-TOF Ultima, Waters) and MS/MS data processing (PEAKS, Bioinformatics Solution), identified several tryptic peptides containing oxidized Met,Trp and His residues. Mapping of the oxidized ferritin residues showed them to be located on the inner face of each sub-unit, the face directed toward the ferritin core where iron is normally stored. Using the same methodology, oxidized residues were subsequently detected in ferritin and transferrin isolated from plasma samples of patients severely affected with HH. Comparing of MS/MS spectra of in vitro oxidized samples that have most fragment ion peaks in common with oxidized peptide MS/MS spectra from samples of patients with HH revealed a significant correlation between the two. These data show that elevated NTBI may be involved in oxidative modification of the iron binding proteins, ferritin and transferrin, and that such modifications may play a significant role in the pathophysiology of HH.

Hemoglobin plays an important role in transporting oxygen in human beings and other mammals. Hemoglobin is a tetrameric protein composed of two alpha and two beta subunits. The £\ and £] subunits are both necessary and the stoichiometric ratio of the two dislike subunits is critical for hemoglobin to perform its oxygen-carrying function properly. To better understand the coupling between the £\ and £] subunits and the subunit disassembly pathway, p-hydroxymercuri-benzoate (PMB) has been used to react with the cysteine residues in hemoglobin. The hemoglobin tetramer becomes unstable and disassembles into £\ and £] subunits when the cysteine sites are perturbed upon reacting with PMB. There are three kinds of cysteine residues, £]93, £\104 and £]112, in human hemoglobin. The reactivity of different cysteine residues with PMB and their reaction sequence have been studied via the Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). The resonance Raman spectroscopy has been used to investigate the structural changes of hemoglobin accompanying the PMB-modification under the oxygenated and deoxygenated conditions. At last, a hemoglobin subunit disassembly mechanism is proposed and the site-specific roles of cysteine residues in human hemoglobin are discussed in detail.

Density gradient ultracentrifugation (DGU) is a powerful method for analyzing lipoprotein particles in great detail. It yields considerable amounts of information regarding the density distribution of these particles when coupled with fluorometric analysis and is an invaluable tool in determining their relative abundance. This union allows relationships between subclasses of lipoproteins to be established that gives researchers a more focused path to aid them in developing methods to predict the early onset of coronary artery disease (CAD). The research presented here focuses on the pairing of DGU with post-separatory techniques including matrix-assisted laser desorption mass spectrometry (MALDI-MS), liquid chromatography mass spectrometry (LC-MS), capillary electrophoresis (CE), isoelectric focusing (IEF) and apoptosis studies involving cell cultures. It is becoming clearer that cholesterol concentrations themselves do not provide sufficient data to assess the quality of cardiovascular health. As a result, research is becoming more focused on identifying better markers that may be indicative of development of CAD in a patient. Of specific interest is group of particles known as high density lipoproteins (HDL). Classically, this molecule is considered the “good cholesterol”, but literature from the last decade suggests that there may be atherogenic variants to this group. By utilizing DGU as a preparatory method for secondary analyses, new dimensions can be added to the density distribution analysis to allow a better determination of markers of cardiovascular health. The aim of this work is to utilize the principles involved with these various techniques to develop a comprehensive set of methods to aid in the detection of potential risk markers. In this study, the properties of metal ion complexes of EDTA as solute systems for analysis of lipoproteins by DGU are analyzed. We show that by varying the complexing ion and counter-ion of these metal-ion complexes, we gain the ability to control the separation of lipoprotein subclasses for subsequent analyses. Qualitative and quantitative data is presented that describes the analysis of different density regions of HDL for apolipoprotein content. Trends between control and atherogenic samples are also described and a clinical link between the biological activity of these regions and the chemical analysis is discussed.