[pt] Método de identificação e quantificação de peptídeos, através da otimização de estratégias para a marcação de peptídeos com metais e subsequente separação por nano-HPLC-UV, MALDI MS. Primeiramente, peptídeos foram marcados com 3 diferentes metais lantanídeos usando um reagente funcional NHS-DOTA. Os resultados demonstraram que a reação de derivatização usando o reagente quelante DOTA foi eficiente para peptídeos simples e misturas dos mesmos, verificada através do MALDI MS a partir da relação m/z. Em paralelo, análises ambientais foram realizadas pela otimização de um procedimento de extração de metalotioneína em bílis de peixe, uma vez que esta matriz tem sido reportada como um biomarcador ambiental de contaminação por metal. Diferentes procedimentos e agentes de redução foram aplicadas para a extração de metalotioneína em bílis e fígado de peixe (Oreochromis niloticus. Análises espectrofotométricas foram realizadas a fim de quantificar os extratos de MT, e gel SDS-PAGE foi usado para avaliação qualitativa dos diferentes procedimentos usados. Cada procedimento foi avaliado estatisticamente. Metodologia de superfície de resposta foi aplicada para amostras de bílis, a fim de avaliar a resposta desta matriz. Em um contexto ambiental, concentrações de MT biliar foi mais baixa que MT do fígado, no entanto, a primeira mostrou-se mais adequada para um monitoramento ambiental. / [en] This work developed a new method for the identification and quantification of peptides, by optimizing some of the available strategies suitable for labeling peptides with lanthanide metals with subsequent separation by nano-HPLC with UV detection, matrix-assisted laser desorption ionization-mass spectrometry (MALDI MS). First, peptides were labeled with the three different lanthanide metals using a functional DOTA-based reagent. The results demonstrate that the derivatization reaction using the chelating reagent DOTA-NHS-ester was effective for single peptides and peptide mixtures, verified from the m/z relation obtained by MALDI MS. In parallel, environmental analyses were conducted, by performing the standardization of metalloprotein purification in fish bile, since this matrix has been reported as a biomarker for environmental metal contamination. Different procedures and reducing agents were applied to purify MT isolated from fish (Oreochromis niloticus) bile and liver. Spectrophotometrical analyses were used to quantify the resulting MT samples, and SDS-PAGE gels were used to qualitatively assess the different procedure results. A response surface methodology was applied for bile samples. In an environmental context, biliary MT was lower than liver MT, and, bile MT seems to be more adequate in environmental monitoring scopes. / [fr] Ce travail a développé une nouvelle méthode pour l identification et la quantification des peptides, par l optimisation de certaines stratégies disponibles appropriées pour le marquage des peptides avec des métaux lanthanide, une séparation par nano-HPLC et détection UV, et suivi par MALDI MS. Tout d abord, les peptides ont été marqués avec les trois métaux lanthanides différents et un réactif fonctionnel - DOTA. Les résultats montrent que la réaction de transformation en dérivé à l aide du réactif chélateur DOTA-NHS-ester a été efficace pour des peptides individuels et des mélanges de peptides, vérifiées à partir de la relation m/z obtenue par MALDI MS. En parallèle, nous avons effectué l optimisation pour la purification de métalloprotéine dans la bile de poisson, qui est signalée entant que biomarqueurs de contamination métallique de l environnement. Des procédures différentes et les agents réduisant ont été apliqués pour purifier les MT isolées de la bile et du foie des poissons (Oreochromis niloticus). Des analyses spectrophotométriques ont été utilisées pour quantifier les échantillons de MT, et le gel SDS-PAGE a été utilisé pour évaluer qualitativement les différents résultats de la procédure. Chaque procédure a en suíte été évaluée statistiquement, une méhtode des surfaces de réponse a été appliquée. Les MT de la bile semblent être plus adéquate pour la surveillance de l environnement en ce qui concerne l exposition récente à des xénobiotiques qui peuvent influer sur l expression protéomique et metalloproteomique de cette matrice biologique.

Lignocellulosic biomass (e.g., non food-based agricultural resides and forestry wastes) has recently been promoted for use as a source of bioethanol instead of food-based materials (e.g., corn and sugar cane), however to fully realize these benefits an improved understanding of lignocellulosic recalcitrance must be developed. The primary goal of this thesis is to gain fundamental knowledge about the surface of the plant cell wall, which is to be integrated into understanding biomass recalcitrance. Imaging mass spectrometry by TOF-SIMS and MALDI-IMS is applied to understand detailed spatial and lateral changes of major components in the surface of biomass under submicron scale. Using TOF-SIMS analysis, we have demonstrated a dilute acid pretreated poplar stem represented chemical differences between surface and bulk compositions. Especially, abundance of xylan was observed on the surface while sugar profile data showed most xylan (ca. 90%) removed from the bulk composition. Water only flowthrough pretreated poplar also represented difference chemistry between surface and bulk, which more cellulose revealed on the surface compared to bulk composition. In order to gain the spatial chemical distribution of biomass, 3-dimensional (3D) analysis of biomass using TOF-SIMS has been firstly introduced in the specific application of understanding recalcitrance. MALDI-IMS was also applied to visualize different molecular weight (e.g., DP) of cellulose oligomers on the surface of biomass.

In der vorliegenden Arbeit wird eine konvergente Synthesestrategie zum Aufbau von formstabilen dendritischen Carbosilanmolekülen mit 1,4-Phenyleneinheiten, welche als “Silicium-Silicium-Spacer” fungieren, vorgestellt. Zur Darstellung dieser Verbindungen kommen repetitive Lithiierungs-Silylierung-Zyklen zur Anwendung. Die Lithiierung von 1-Br-4-C6H4-Si(C6H4-4-Si(CH2CH=CH2)nMe3-n)3 (n = 0, 1, 2, 3) mit nBuLi und die Umsetzung von in-situ generiertem 1-Li-4-Si(CH2CH=CH2)nMe3-nC6H4 mit SiCl4 liefert Dendrimere der 0. Generation Si(C6H4-4-Si(CH2CH=CH2)nMe3-n)4 (n = 1, 2, 3). Wird 1-Li-4-Si(CH2CH=CH2)nMe3-nC6H4 mit 1-Br-4-SiCl3-C6H4 zur Reaktion gebracht, sind Dendronen der 0. Generation 1-Br-4-C6H4-Si(C6H4-4-Si(CH2CH=CH2)nMe3-n)3 (n = 0; 1; 2; 3) zugänglich. Durch repetitive Lithiierungs-Silylierungs-Zyklen können ausgehend von 1-Br-4-C6H4-Si(C6H4-4- Si(CH2CH=CH2)nMe3-n)3 Dendrimere höherer Generationen aufgebaut werden. Bringt man die lithiierte Spezies 1-Li-4- C6H4-Si(C6H4-4-Si(CH2CH=CH2)nMe3-n)3, welche ausgehend von 1-Br-4-C6H4-Si(C6H4-4-Si(CH2CH=CH2)nMe3-n)3 durch Metallierung mit tBuLi zugänglich ist, in Anwesenheit von TMEDA mit SiCl4 zur Reaktion, so erhält man die Dendrimere der 1. Generation Si(C6H4-4-(C6H4-4-Si(CH2CH=CH2)nMe3-n)3)4 (G1b, n = 1; G1c n = 2). Erfolgt die Silylierung jedoch in Abwesenheit von TMEDA, werden die Chlorsilane ClSi(C6H4-4-(C6H4-4-Si(CH2CH=CH2)nMe3- n)3)3 (D1bCl, n = 1; D1cCl, n = 2) gebildet. Die Silylierung von 1-Li-4-C6H4-Si(C6H4-4-Si(CH2CH=CH2)nMe3-n)3 mit 1-Br-4-SiCl3-C6H4 liefert die Dendronen der 1. Generation 1-Br-C6H4-4-Si(C6H4-4-(C6H4-4-Si(CH2CH=CH2)nMe3-n)3)3 (D1b, n = 1; D1c, n = 2; D1d, n = 3). Diese liegen in einem Gleichgewicht monomerer und komplementärer dimerer Spezies vor. Die Dimerisierung kann durch NMR-Untersuchungen sowie durch die Einkristallröntgenstruktur von D1bCl belegt werden. Die Darstellung von Carbosilanen des Typs PhMeSi((CH2)3B(OH)2)2 (2), Si(C6H4-4-SiMe2((CH2)3B(OH)2)4 (5), PhMeSi((CH2)3OH)2 (3) und Si(C6H4-4-SiMe3-n((CH2)3OH)n)4 (6a, n = 1; 6b, n = 2; 6c, n = 3) wird beschrieben. Die Boronsäuren 2 und 5 sind durch Umsetzung von PhMeSi(CH2CH=CH2)2 (1) und Si(C6H4-4-SiMe2(CH2CH=CH2))4 (4a) mit HBBr2·SMe2 und anschließender Hydrolyse zugänglich, während 3 und 6a - 6c durch Hydroborierung von 1 und 4a - c mit BH3·SMe2 und anschließender Oxidation mit H2O2 erhalten werden. Die Einkristallröntgenstruktur von 6a zeigt, dass das Molekül aufgrund von π-π-Wechselwirkungen und der Ausbildung von Wasserstoffbrückenbindungen Teil eines zweidimensionalen Netzwerks ist. Ein weiterer Schwerpunkt der Arbeit widmet sich der Synthese und Charakterisierung von Dendrimeren der 0. und 1. Generation mit symmetrisch substituiertem Porphyrin-Grundgerüst als multifunktionalem Kern. Hierbei werden zunächst die allyl-terminierten Bromide 1-Br-4-Si(CH2CH=CH2)nMe3-nC6H4 (n =1, 2) bzw. die Dendronen -Br-4-C6H4- Si(C6H4-4-Si(CH2CH=CH2)nMe3-n)3 (n = 0, 1, 2) in die aromatischen Aldehyde 1-HOC-4-Si(CH2CH=CH2)nMe3-nC6H4 (2b, n = 1; 2c, n = 2) bzw. 1-HOC-4-C6H4-Si(C6H4-4-Si(CH2CH=CH2)nMe3-n)3 (4a, n = 0; 4b, n = 1; 4c, n =2) überführt. Aus diesen werden nach der Methode von Lindsey durch Umsetzung mit Pyrrol, BF3·OEt2 und DDQ die entsprechenden Porphyrine H2T(-4-Si(CH2CH=CH2)nMe3-nC6H4)P (5b, n = 1; 5c, n = 2) bzw. H2T(-4-C6H4-Si(C6H4-4- Si(CH2CH=CH2)nMe3-n)P (7a, n = 0; 7b, n = 1; 7c, n =2) aufgebaut. Deren Komplexierung mit Zn(OAc)2 liefert die Zn- Porpyrine Zn(II) T(-4-Si(CH2CH=CH2)nMe3-nC6H4)P (6a, n = 1; 6b, n = 2) bzw. Zn(II) T(-4-C6H4-Si(C6H4-4- Si(CH2CH=CH2)nMe3-n)P (8a, n = 0; 8b, n = 1; 8c, n =2). Ausgehend von 5b und 5c sind Porphyrine mit terminalen Hydroxyl-Carbosilan-Einheiten via Hydroborierung- Oxidation zugänglich. Diese Verbindungen einschließlich der entsprechenden Zn-Komplexe sind aufgrund ihrer Fähigkeit zur Ausbildung von Wasserstoffbrücken-Netzwerken in hohem Maße zum Aufbau von supramolekularen Strukturen geeignet. Anhand der Einkristallröntgenstruktur-Analyse von Zn[T(4-Si((CH2)3-OH)Me2-C6H4)P] 10a ist ersichtlich, dass dieses Metalloporphyrin aufgrund von dirigierenden Wasserstoffbrücken Teil eines selbst organisierenden Porphyrin-Netzwerks darstellt und darum einzigartige strukturelle Eigenschaften aufweist. Die Einkristallröntgenstrukturen von 5b, 5c, 6b und 7b werden ebenfalls vorgestellt.

Matrix metalloproteinases (MMPs) network with other biological molecules to maintain the extracellular matrix (ECM) in normal physiology and perform different roles. Understanding and assigning specific role to each of 24 members of these endoproteinases is impeded because of lack of specific and efficient detection methods in biological samples. Moreover, MMP-based anti-cancer drug development has also been challenged because, currently, there is no robust methodology to distinguish the inactive pro-enzymes, active enzymes or those complexed with endogenous inhibitors in biological specimens. The objective of this project is to develop a chemical proteomics strategy based on Matrix assisted laser desorption ionization tandem mass spectrometry (MALDI-MS/MS) to help identify and discriminate the various MMP forms. Firstly, a triazine dye-based ligand immobilized on chromatography beads was utilized to assess whether it binds to recombinant human MMPs (rhMMPs). The results highlighted that the ligand interacts with latent forms of MMPs in agreement with the literature. Secondly, the potential of the ligand was assessed using MALDI-MS/MS based methodology in in vitro cancer models. Cell line culture supernatants were used in amounts to emulate the availability of tumour biopsies in clinical settings. The MS/MS spectral peaks specific to MMPs (MMP-2 and MMP- 14), and two endogenous inhibitors TIMP-1 and TIMP-2 were found in affinity chromatography eluates of cell culture supernatants with higher Mascot scores for the latter. While western blot detected MMP-2 in cell extracts, MALDI-MS/MS did not detect MMPs because of amounts below the limit of detection (LOD) of the instrument. Although the ligand was found to be interacting with MMPs and detergent-free salt elution buffers improved MALDI analysis, recovery of MMPs from biological samples was sub-optimal. The dye ligand was observed to bind other enzymes and despite various strategies to reduce non-specific binding of proteins or enable selective elution did not improve MMP enrichment. Further work using methodology described in this study is required after scaling up the MMP amounts in biological specimen and to resolve the issue of non-specific binding of proteins to the ligand by understanding its structure.

Characterization of post-translational modifications (PTMs) of therapeutic proteins is very important during the bioprocess development to maintain desired product quality and during the submission process to regulatory authorities for product approval. Monitoring glycosylation in pharmacokinetic studies can be useful to evaluate the dependence of clearance rates on different glycoforms. The cost and efficiency of characterization affect the speed to market of biopharmaceutical proteins. A reduction in the number of manual processing steps, cost of reagents and consumption of sample, as well as the time required for chemical analysis, is therefore necessary. The research presented in this thesis is focused on the potential of using microfluidic discs for automated, miniaturized, parallel and rapid sample preparation for PTM characterization of therapeutic monoclonal antibodies. Paper I describes the method development for N-linked glycosylation profiling. Several sample preparation steps have been performed in an integrated process in the microfluidic compact disc (CD). Paper II demonstrates the use of the method presented in paper I in combination with multivariate statistics for discrimination of glycosylation profiles of different therapeutic antibodies and simulation of a real case of quality control. Paper III is focused on a method for monitoring changes in glycosylation profiles of therapeutic antibodies in serum over time by incubation with an exoglycosidase enzyme. Paper IV describes the method for peptide mapping of therapeutic antibodies. In addition, recent work (unpublished results) assesses the potential of this method for methionine oxidation detection. The developed methods were fast, robust with low sample/reagent consumption. Generation of glycosylation profile data for one sample was established in approximately 2 h. The amount of samples and antigens loaded into the CD platform for one replicate was less than 0.3 μg and approximately 0.06 μg, respectively. Furthermore, considering the parallel function of the CD, conducting the analysis for 54 samples can be completed within a day. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.</p>

The aim of presented diploma thesis was to characterize recent knowledge in the field of beer proteomics. The main part of this work was focused on modern instrumental methods of protein analysis, especially on protein identification by mass spectrometry. In experimental part proteins from selected beer samples were isolated, purified and separated by 2-D electrophoresis. The identification was performed by MALDI MS/MS and LC-MS/MS. Identified proteins were divided into 6 groups - serpines and protein Z, trypsine/-amylase inhibitors, yeast proteins, LTP protein, hordeins and other proteins. Proteomic analysis provided identification of proteins important for final analytical and sensory characteristics of the beer - for final beer quality and taste

In der vorliegenden Arbeit wird die Synthese linearer und zyklischer Aminoketone via nucleophiler aromatischer Substitution von fluorsubstituierten aromatischen Ketonen mit sekundären, aliphatischen Diaminen vorgestellt. Durch eine Adaption der Prozessparameter konnte eine elegante Methode zur Synthese fluorendgruppentragender Oligomere sowie von definierten Makrozyklen entwickelt werden. Die Modifizierung der Oligomere erfolgte sowohl durch Endgruppensubstitution als auch durch Reaktionen an der Carbonylgruppe am Oligomerrückgrat. Als Funktionalisierungsreagenzien wurden Mercaptoessigsäure, LAWESSONs Reagenz und N,N-Dimethylanilin eingesetzt. Die Umsetzung der Makrozyklen mit N,N-Dialkylanilinen ermöglicht die Synthese zyklischer Triphenylmethanfarbstoffe. Die Untersuchung der optischen Eigenschaften dieser zyklischen Kristallviolett-Derivate in Abhängigkeit des pH-Wertes und der Natur des Lösungsmittels sowie der Sensitivität gegenüber Cyanid-Ionen erfolgte mit Hilfe der UV/Vis-Spektroskopie.

No description available.

Matrix metalloproteinases (MMPs) network with other biological molecules to maintain the extracellular matrix (ECM) in normal physiology and perform different roles. Understanding and assigning specific role to each of 24 members of these endoproteinases is impeded because of lack of specific and efficient detection methods in biological samples. Moreover, MMP-based anti-cancer drug development has also been challenged because, currently, there is no robust methodology to distinguish the inactive pro-enzymes, active enzymes or those complexed with endogenous inhibitors in biological specimens. The objective of this project is to develop a chemical proteomics strategy based on Matrix assisted laser desorption ionization tandem mass spectrometry (MALDI-MS/MS) to help identify and discriminate the various MMP forms. Firstly, a triazine dye-based ligand immobilized on chromatography beads was utilized to assess whether it binds to recombinant human MMPs (rhMMPs). The results highlighted that the ligand interacts with latent forms of MMPs in agreement with the literature. Secondly, the potential of the ligand was assessed using MALDI-MS/MS based methodology in in vitro cancer models. Cell line culture supernatants were used in amounts to emulate the availability of tumour biopsies in clinical settings. The MS/MS spectral peaks specific to MMPs (MMP-2 and MMP- 14), and two endogenous inhibitors TIMP-1 and TIMP-2 were found in affinity chromatography eluates of cell culture supernatants with higher Mascot scores for the latter. While western blot detected MMP-2 in cell extracts, MALDI-MS/MS did not detect MMPs because of amounts below the limit of detection (LOD) of the instrument. Although the ligand was found to be interacting with MMPs and detergent-free salt elution buffers improved MALDI analysis, recovery of MMPs from biological samples was sub-optimal. The dye ligand was observed to bind other enzymes and despite various strategies to reduce non-specific binding of proteins or enable selective elution did not improve MMP enrichment. Further work using methodology described in this study is required after scaling up the MMP amounts in biological specimen and to resolve the issue of non-specific binding of proteins to the ligand by understanding its structure. / Shaukat Khanam Memorial Cancer Hospital and Research Centre, Pakistan and University of Bradford

No description available.