Die Analyse von organischen Polymeren mittels Massenspektrometrie mit induktiv gekoppeltem Plasma nach Laserablation unterliegt starken Matrixeffekten. Mögliche Korrekturmodelle sollten basierend auf der tatsächlich ablatierten Elementmasse sowie der Signalintensität des Kohlenstoffisotops C-13 (13C-Korrektur) entworfen werden. Damit die 13C-Korrektur erfolgreich verlaufen kann, ist ein direkter Zusammenhang zwischen ablatiertem Kohlenstoff und gemessenem 13C-ICP-MS Signal erforderlich. Dies wurde überprüft, indem unter Anwendung der konfokalen Mikroskopie das Ablationskratervolumen bestimmt und der ablatierte Kohlenstoff berechnet wurde. Dieser Zusammenhang konnte sowohl für undotierte, wie auch für elementdotierte Polymere und die Verwendung verschiedener Ablationsgase (Helium, Argon und Sauerstoff) ermittelt werden. Eigens hergestellte polymere elementdotierte Standardmaterialien wurden hinsichtlich der Matrixeffekte charakterisiert. Als größter Einflussfaktor stellte sich die unterschiedliche Ablationsrate bei der Ablation verschiedener Polymere heraus. Unter Anwendung der tatsächlich ablatierten Elementmasse sowie unter Anwendung der 13C-Korrektur konnte die Matrixabhängigkeit deutlich verringert werden.

Herein, we report on the mechanochemical Scholl reaction of dendritic oligophenylene precursors to produce benchmark nanographenes such as hexa-peri-hexabenzocoronene (HBC), triangular shaped C60 and expanded C222 under solvent-free conditions. The solvent-free approach overcomes the bottleneck of solubility limitation in this well-known and powerful reaction. The mechanochemical approach allows tracking the reaction process by in situ pressure measurements. The quality of produced nanographenes has been confirmed by MALDI-TOF mass spectrometry and UV-Vis absorption spectroscopy. This approach paves the way towards gram scale and environmentally benign synthesis of extended nanographenes and possibly graphene nanoribbons suitable for application in carbon based electronics or energy applications.

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.

Biotechnological processes are distinguished from classical chemistry by employing bio-molecules or whole cells as the catalytic element, providing unique reaction mechanisms with unsurpassed specificity. Whole cells are the most versatile \''factories\'' for natural or non-natural products, however, the conversion of e.g. hydrophobic substrates can quickly become cytotoxic. One host organism with the potential to handle such conditions is the gram-negative bacterium Pseudomonas putida, which distinguishes itself by solvent tolerance, metabolic flexibility, and genetic amenability. However, whole cell bioconversions are highly complex processes. A typical bottleneck compared to classical chemistry is lower yield and reproducibility owing to cell-to-cell variability. The intention of this work was therefore to characterize a model producer strain of P. putida KT2440 on the single cell level to identify non-productive or impaired subpopulations. Flow cytometry was used in this work to discriminate subpopulations regarding DNA content or productivity, and further mass spectrometry or digital PCR was employed to reveal differences in protein composition or plasmid copy number. Remarkably, productivity of the population was generally bimodally distributed comprising low and highly producing cells. When these two subpopulations were analyzed by mass spectrometry, only few metabolic changes but fundamental differences in stress related proteins were found. As the source for heterogeneity remained elusive, it was hypothesized that cell cycle state may be related to production capacity of the cells. However, subpopulations of one, two, or higher fold DNA content were virtually identical providing no clear hints for regulatory differences. On the quest for heterogeneity the loss of genetic information came into focus. A new work flow using digital PCR was created to determine the absolute number of DNA copies per cell and, finally, lack of expression could be attributed to loss of plasmid in non-producing cells. The average plasmid copy number was shown to be much lower than expected (1 instead of 10-20). In conclusion, this work established techniques for the quantification of proteins and DNA in sorted subpopulations, and by these means provided a highly detailed picture of heterogeneity in a microbial population.

In der vorliegenden Arbeit wird die Synthese von Carbosiloxandendrimeren der dritten Generation durch repetitive Alkoholyse-Hydrosilylierungs-cyclen auf dem divergenten Syntheseweg beschrieben. Im Mittelpunkt der Arbeit stand jedoch die Funktionalisierung dieser Dendrimere mit einer Vielzahl metallorganischer (Ferrocenyl-, Übergangsmetallcarbonyl-verbindungen) bzw. organischer (stickstoffhaltige Ligandsysteme) Einheiten. Zudem wird die Darstellung amphiphiler und bifunktionaler Carbosiloxandendrimere vorgestellt. Die neu synthetisierten Verbindungen wurden analytisch umfassend charakterisiert, wobei die 29Si-{1H}-NMR-Spektroskopie sowie die Massenspektrometrie einen besonderen Stellenwert einnehmen.

Innerhalb der Arbeit wurden mit Hilfe eines DC-Glimmplasmas im Vakuumbereich zwischen 100 und 400 Pa auf kathodisch geschalteten, metallischen Substraten mittels silicium- und bororganischen Verbindungen Schichten abgeschieden. Unter den gewählten Bedingungen war eine Abscheidung von amorphen Hartstoffschichten bei niedriger Substrattemperatur (ca. 200–450 °C), geringem apparativen Aufwand und hohen Abscheideraten (bis zu 2.5 µm min-1) möglich. Anhand der Abscheidung mit Hexamethyldisilazan (HMDSN) und unterschiedlichen Arbeitsgasen (Wasserstoff, Argon, Stickstoff, Ammoniak, Sauerstoff, bzw. ohne Arbeitsgas) wurde der grundlegende Einfluss der Beschichtungsparameter (Plasmaleistung, Prozessdruck, Precursorfluss und Substratgröße) auf unterschiedliche Schichteigenschaften (Mikrostruktur, Ele-mentgehalt, optische und mechanische Eigenschaften) sowie auf die Abscheiderate untersucht und diskutiert. Zudem wurde das Abscheideverhalten von zwei weiteren siliciumorganischen, zwei borsiliciumorganischen und einer bororganischen Verbindung untersucht. Um Aussagen zum Wachstumsmechanismus treffen zu können, wurden mit Hilfe der differentiell gepumpten Massenspektroskopie quantitative Untersuchungen an den Reaktionsprodukten durchgeführt. Weiterhin wurde ein Beitrag zur Anwendung der IR-Spektroskopie in Reflexion zur Charakterisierung der auf nichttransparenten Substraten abgeschiedenen Schichten geleistet. Mittels einer numerischen Simulation der Spektren konnte die Schichtdicke, die Brechzahl sowie das Spektrum der Absorptionskonstante zur quantitativen, strukturellen Charakterisierung der abgeschiedenen Schichten ermittelt werden.

In der vorliegenden Arbeit wird die Synthese und die Charakterisierung von Carbosiloxandendrimeren der 1. – 3. Generation, welche periphere Me2SiH, MeSiH2 bzw. SiH3 Gruppen besitzen, vorgestellt. Ausgehend von diesen Verbindungen konnte am Beispiel eines mit einer Dimethylvinylsilyl-Einheit funktionalisierten Titanocendichlorides gezeigt werden, dass sich durch die Hydrosilylierungsreaktion metallorganische Bausteine an SiH-funktionalisierte Carbosiloxandendrimere anbinden lassen. Einen weiteren Schwerpunkt dieser Arbeit bildeten Carbosilandendrimere. Eine neue Variante der Darstellung dieser Moleküle durch die konvergente Synthesemethode mit Hilfe von kettenverlängernden, 1 zu 2 bzw. 1 zu 3 verzweigten Bausteinen konnte partiell erfolgreich durchgeführt werden. Die Anbindung von cyclischen (12-Krone-4, 15-Krone-5, 18-Krone-6, Sila-8-Krone-3, Sila-11-Krone-4) und acyclischen (Triethylenglycolmonomethylether) Polyethern an dendritische Carbosilane der 1. und 2. Generation wird ebenfalls beschrieben. Hierzu wurden Carbosilandendrimere mit peripheren SiH-Einheiten durch Hydrosilylierung mit den entsprechenden allyl- bzw. vinylfunktionalisierten Ethern zur Reaktion gebracht. Die auf diesem Weg erhaltenen Dendrimere mit endständigen cyclischen bzw. linearen Polyethern wurden mit Alkalimetallionen (Li+, Na+, K+) umgesetzt und die entstandenen Komplexe massenspektrometrisch untersucht.

Kieselalgen (Diatomee) sind eukaryotische einzellige Algen die hochspezifische Proteine (sogenannte Silaffine) erzeugen, um ‘nanopatterned’ Silica-Zellwände herzustellen. Diese Proteine zeigen geringe oder gar keine Homologie innerhalb der Diatomeen Gattung und sind ausgiebig (extensiv) posttranslatorisch modifiziert. Zum Unterschied zu konventioneller Modifikation (z.B. Phosphorylierung und Glykosylierung) weisen Lysinreste von Silaffinen einige Polyaminketten mit sehr heterogenen molekularen Strukturen auf. Diese Modifikationen sind spezifisch für Kieselalgen und spielen somit hypothetisch eine Rolle in der Biosilica-Synthese. Allerdings sind Lysin Polyamin Modifikationen, modifizierte Proteine und modifizierte Stellen kaum charakterisiert. Um diese Frage zu beantworten entwickelten wir eine Methode Polyamine zu quantifizieren und die Position von Polyamin-Modifikationen in engverwandte Proteine zu identifizieren (in morphologisch unterschiedliche Diatomeen Thalassiosira pseudonana, T. oceanica und Cyclotella cryptica). Wir zeigten, dass das Gesamtmuster von Polyaminender phylogenetischen Nähe dieser Kieselalgenarten folgt und dass diese Polyaminmodifikationen an Konsensusstellen sogar in Proteinen auftraten, die keine Sequenzähnlichkeit zeigten.:CONTENTS Summary Zusammenfassung List of figures List of tables Abbreviations 1 Introduction 1.1 Diatoms 1.2 Diatom biosilica 1.2.1 Biosilicification in nature 1.2.2 Diatom biosilica structure and cell cycle 1.2.3 The cell biology of biosilica morphogenesis 1.3 The role of polyamine PTMs in diatom biosilicification 1.3.1 Identifying biomolecules associated with diatom biosilica 1.3.2 PTM complexity of biosilica-associated proteins 1.3.3 Lysine ε-polyamine PTMs in biosilica-associated proteins 1.4 Mass spectrometry in PTM discovery 1.4.1 Modification-specific proteomics 1.4.2 Analysis of polyamine-modified lysines by MS 1.4.3 Fractionation of proteins and peptides prior to MS 1.4.4 MS/MS analysis in modification-specific proteomics 1.4.5 Bioinformatics tools for modification-specific proteomics 1.5 Rationale of the thesis 2 Aim of the thesis 3 Results and discussion 3.1 A method for analysis of ε-polyamine PTMs 3.1.1 Establishing a method to analyse ε-polyamines 3.1.2 Method applicability for lysine PTM profiling 3.1.3 Profiling of lysine PTMs in silaffin-3 3.2 Profiling lysine PTMs in biosilica extracts 3.2.1 Lysine PTM profile and characteristic fragments 3.2.2 Elucidation of phosphopolyamine structures 3.2.3 LysinePTMprofilesofAFSMextracts 3.2.4 Comparison of AFIM and AFSM profiles in T. pseudonana 3.2.5 Phylogenetic relationship across three diatom species 3.3 PTM localization and discovery of consensus motifs 3.3.1 Multiple protease strategy for mapping lysine PTMs 3.3.2 Selection of deprotection technique 3.3.3 Mapping lysine PTMs on tpSil3 using iterative search strategy 3.3.4 Deconvolution of raw MS/MS spectra 3.3.5 PTM mapping by polyamine-specific fragments 3.3.6 Identification of consensus motifs harboring lysine PTMs 4 Conclusions and Outlook 5.1 Synthesis of polyamine standards 5.2 Isolation of biosilica-associated proteins 5.3 Expression of tpSil3 from synthetic gene 5.4 HCl hydrolysis 5.5 AQC-derivatization of amino acids and polyamines 5.6 LC-MS/MS analysis of QAC-derivatives 5.7 Amino acid measurement using UV-detection 5.8 Direct infusion MS/MS analysis 5.9 Acetylation of phosphopolyamines 5.10 31P-NMR measurements 5.11 Deglycosylation with TFMS 5.12 Treatment with HF·pyridine soluble complex 5.13 Anhydrous HF-treatment 5.14 Protein analysis by GeLC-MS/MS 5.15 Proteomics data processing A Appendix B Bibliography Acknowledgments Publications Declaration / Erklärung / Diatoms are eukaryotic unicellular algae that employ highly specialized proteins called silaffins for making nanopatterned silica-based cell walls. These proteins share little or no homology across diatom species and are extensively post-translationally modified. Apart from conventional modifications (e. g., phosphorylation and glycosylation) lysine residues of silaffins bear polyamine chains with highly heterogeneous molecular structure. The latter appear to be specific for silicifying organisms and therefore hypothesized to play a key role in biosilica synthesis. However, polyamine modifications of lysines, modified proteins, and modification sites remain poorly characterized. To address these questions, we developed a method to quantify polyamines and identify sites of polyamine modifications in proteins from phylogenetically closely related, yet morphologically distinct diatoms Thalassiosira pseudonana, T. oceanica, and Cyclotella cryptica. We demonstrated that the overall pattern of polyamines followed the phylogenetic proximity across these diatom species and showed that polyamine modifications occurred at consensus sites even in proteins showing no sequence similarity.:CONTENTS Summary Zusammenfassung List of figures List of tables Abbreviations 1 Introduction 1.1 Diatoms 1.2 Diatom biosilica 1.2.1 Biosilicification in nature 1.2.2 Diatom biosilica structure and cell cycle 1.2.3 The cell biology of biosilica morphogenesis 1.3 The role of polyamine PTMs in diatom biosilicification 1.3.1 Identifying biomolecules associated with diatom biosilica 1.3.2 PTM complexity of biosilica-associated proteins 1.3.3 Lysine ε-polyamine PTMs in biosilica-associated proteins 1.4 Mass spectrometry in PTM discovery 1.4.1 Modification-specific proteomics 1.4.2 Analysis of polyamine-modified lysines by MS 1.4.3 Fractionation of proteins and peptides prior to MS 1.4.4 MS/MS analysis in modification-specific proteomics 1.4.5 Bioinformatics tools for modification-specific proteomics 1.5 Rationale of the thesis 2 Aim of the thesis 3 Results and discussion 3.1 A method for analysis of ε-polyamine PTMs 3.1.1 Establishing a method to analyse ε-polyamines 3.1.2 Method applicability for lysine PTM profiling 3.1.3 Profiling of lysine PTMs in silaffin-3 3.2 Profiling lysine PTMs in biosilica extracts 3.2.1 Lysine PTM profile and characteristic fragments 3.2.2 Elucidation of phosphopolyamine structures 3.2.3 LysinePTMprofilesofAFSMextracts 3.2.4 Comparison of AFIM and AFSM profiles in T. pseudonana 3.2.5 Phylogenetic relationship across three diatom species 3.3 PTM localization and discovery of consensus motifs 3.3.1 Multiple protease strategy for mapping lysine PTMs 3.3.2 Selection of deprotection technique 3.3.3 Mapping lysine PTMs on tpSil3 using iterative search strategy 3.3.4 Deconvolution of raw MS/MS spectra 3.3.5 PTM mapping by polyamine-specific fragments 3.3.6 Identification of consensus motifs harboring lysine PTMs 4 Conclusions and Outlook 5.1 Synthesis of polyamine standards 5.2 Isolation of biosilica-associated proteins 5.3 Expression of tpSil3 from synthetic gene 5.4 HCl hydrolysis 5.5 AQC-derivatization of amino acids and polyamines 5.6 LC-MS/MS analysis of QAC-derivatives 5.7 Amino acid measurement using UV-detection 5.8 Direct infusion MS/MS analysis 5.9 Acetylation of phosphopolyamines 5.10 31P-NMR measurements 5.11 Deglycosylation with TFMS 5.12 Treatment with HF·pyridine soluble complex 5.13 Anhydrous HF-treatment 5.14 Protein analysis by GeLC-MS/MS 5.15 Proteomics data processing A Appendix B Bibliography Acknowledgments Publications Declaration / Erklärung

The present work is the fourth (and final) contribution to an inter-laboratory collaboration that was planned at the 3rd International Summit on Organic Photovoltaic Stability (ISOS-3). The collaboration involved six laboratories capable of producing seven distinct sets of OPV devices that were degraded under well-defined conditions in accordance with the ISOS-3 protocols. The degradation experiments lasted up to 1830 hours and involved more than 300 cells on more than 100 devices. The devices were analyzed and characterized at different points of their lifetimes by a large number of non-destructive and destructive techniques in order to identify specific degradation mechanisms responsible for the deterioration of the photovoltaic response. Work presented herein involves time-of-flight secondary ion mass spectrometry (TOF-SIMS) in order to study chemical degradation in-plane as well as in-depth in the organic solar cells. Various degradation mechanisms were investigated and correlated with cell performance. For example, photo-oxidation of the active material was quantitatively studied as a function of cell performance. The large variety of cell architectures used (some with and some without encapsulation) enabled valuable comparisons and important conclusions to be drawn on degradation behaviour. This comprehensive investigation of OPV stability has significantly advanced the understanding of degradation behaviour in OPV devices, which is an important step towards large scale application of organic solar cells. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Histone post-translational modifications (PTMs), as the histone code assumes, are related with regulation of gene transcription, an important mechanism of cells in the differentiation process. Many PTMs are simultaneously present in histone proteins, and changes in the PTM stoichiometric ratios can have several effects, like changes in the chromatin structure leading to a transcriptionally active or repressive state. Significant progresses were made to map variations of histone PTMs by mass spectrometry (MS), and although many protocols were developed there are still some drawbacks. Incomplete and side reactions were identified, which can directly affect the quantification of histone PTMs, because both (incomplete and side reactions) can be misinterpreted as endogenous histone post translational modifications. Therefore, a protocol for derivatization of histones with no noticeable undesired reactions (<10%) was required. In this thesis a new chemical modification methodology is presented, which allows the improvement of sequence coverage by acylation with propionic anhydride of lysine residues and N-terminal (free ε- and α- amino groups) and trypsin digestion. more than 95% of complete reaction was achieved with the new derivatization methodology. This strategy (chemical derivatization of histones), in combination with bottom-up MS approach, allows the quantification of lysine methylation (Kme) and acetylation (Kac) in histones from Saccharomyces cerevisiae (S.cerevisiae), mouse embryonic stem cells (mESCs) and human cell lines. The results showed histone H3 PTM pattern as the most variable profile regarding histone Kme and Kac across the three different organisms and experimental conditions. Therefore, it was concluded that quantification of H3 PTM pattern can be used to examine changes in chromatin states when cells are subjected to any kind of perturbation.