Cells, whether bacterial, fungal or mammalian, are all equipped with metabolic pathways capable of producing an assortment of structurally and functionally distinct lipid species. Despite the structural diversity of lipids being recognized and correlated to specific cellular phenomena and disease states, the molecular mechanisms that underpin this structural diversity remain poorly understood. In part, this is due to the lack of adequate analytical techniques capable of measuring the structural details of lipid species in a direct, comprehensive and quantitative manner. The aim of my thesis study was to establish methodology for automated and quantitative analysis of molecular lipid species based on mass spectrometry. From this work a novel high-throughput methodology for lipidome analysis emerged. The main assets of the methodology were the structure-specific mass analysis by powerful hybrid mass spectrometers with high mass resolution, automated and sensitive infusion of total lipid extracts by a nanoelectrospray robot, and automated spectral deconvolution by dedicated Lipid Profiler software. The comprehensive characterization and quantification of molecular lipid species was achieved by spiking total lipid extracts with unique lipid standards, utilizing selective ionization conditions for sample infusion, and performing structure-specific mass analysis by hybrid quadrupole time-of-flight and ion trap mass spectrometry. The analytical routine allowed the comprehensive characterization and quantification of molecular glycerophospholipid species, molecular diacylglycerol species, molecular sphingolipid species including ceramides, glycosphingolipids and inositol-containing sphingolipids, and sterol lipids including cholesterol. The performance of the methodology was validated by comparing its dynamic quantification range to that of established methodology based on triple quandrupole mass spectrometry. Furthermore, its efficacy for lipidomics projects was demonstrated by the successful quantitative deciphering of the lipid composition of T cell receptor signaling domains, mammalian tissues including heart, brain and red blood cells, and the yeast Saccharomyces cerevisiae.

In der vorliegenden Arbeit werden Beiträge zur Entwicklung neuer qualitativer und quantitativer analytischer Methoden für die Untersuchung von Cetrorelix und anderen GnRH-Antagonisten während des Aggregationsprozesses vorgestellt. Für die qualitative Untersuchung von GnRH-Antagonisten wurden am Modellpeptid Cetrorelix massenspektrometrische Methoden entwickelt und auf weitere GnRH-Antagonisten übertragen. Eingesetzt wurde sowohl die ESI-TOF-MS als auch die MALDI-TOF-MS. Beide massenspektrometrische Verfahren zeigten für die untersuchten GnRH-Antagonisten polydisperse Verteilungen oberhalb der fluoreszenzspektroskopisch bestimmten kritischen Aggregatbildungskonzentration (cac). Bei den ESI-TOF-MS-Messungen konnte ein stark von Cetrorelix abweichendes Aggregationsverhalten für Ozarelix beobachtet werden. Für die Quantifizierung des Aggregatanteils in Cetrorelix- bzw. Ozarelixproben wurde eine Methode mit der MALDI-TOF-MS etabliert, die Untersuchungen an pharmazeutisch relevanten Peptidhormon-Formulierungen ermöglicht. Systematische Untersuchungen zum Einfluss verschiedener An- und Kationen sowie deren Konzentrationen auf die Cetrorelixaggregation erfolgten mit der Fluoreszenzspektroskopie. Die erhaltenen Ergebnisse ermöglichen eine bessere Charakterisierung der Aggregation und lassen Abschätzungen über das Aggregationsverhalten von Cetrorelix in verschiedenen Medien mit unterschiedlichen Elektrolyten zu. Mit dem Einsatz der Transmissionselektronenmikroskopie war es erstmals möglich, Aggregate von GnRH-Antagonisten visuell darzustellen.

Mass spectrometry is the primary technology of proteomics. For the analysis of complex proteomes, protein identities and quantities are inferred from their peptides that are generated by cleaving all proteins with the endopeptidase trypsin. But there is one major disadvantage that is due to biophysical differences, different peptides cause different intensities. Miscellaneous approaches have been developed to circumvent this problem based on the chemical or metabolic introduction of heavy stable isotopes. This enables to monitor protein abundance differences of two or more samples on the same tryptic peptides that differ in mass only. Absolute quantification can be achieved similar by spiking-in synthetic isotopical labeled counterparts of a sample’s tryptic peptides. However, labeling technics suffer from high prices, introduced biases, need for extensive manual control, laborious implementation and implementation restrictions. Therefore, a multiplicity of label-free approaches have been developed that profit from instrumental improvements targeting reliability of identifications and reproducibility of quantitative values. No extensive systematic comparison of label-free quantitative parameters has been published so far presumably because of the laborious implementation. An analysis of primary label-free parameters and associated normalization methods is presented here that compares dynamic and linear ranges and accuracies in the estimation of protein amounts. This facilitated the establishment of label-free procedures addressing three fundamental questions in proteomics: what is a sample’s composition, are proteins that share a specific property enriched and what are the differences between two (or more) samples. A new mathematic model is presented that defines and elucidates enrichment. The procedures were applied first to analyze and compare stem cell plasma membrane proteomes. This is an ambitious model for proteomics because of only small amounts of arduous to analyze, partial hydrophobic proteins in a complex proteomic and chemical background. It is of scientific relevance, as membrane proteins are the cell’s communication interface that enable cell type specific processes and hence can be used to define, isolate and quantify those. The success of cell surface proteome enrichment, the quantitative composition of the proteome and the proteomic difference between stem cells isolated from the dental pulp and cultivated in different media is shown. Secondly, the procedures were applied to the analysis of transient protein networks that assemble onto proteo-liposomes in a newly designed recruitment assay that fully recapitulates membrane sorting as seen in vivo. All transmembrane proteins need to be trafficked to other organelles’ membranes by vesicular trafficking. Sorting signals within the cytosolic regions of the protein cargos trigger the formation of trafficking complexes around those. The transient membrane complexes additionally recognize organelle or organelle-domain specific membrane lipids, such as phosphatidylinositol phosphates. Different trafficking ways are characterized by different trafficking complexes. The elucidation of trafficking complexes that form around a transmembrane protein of interest discloses its trafficking routes and involved signaling processes. The synthetic proteo-liposomes were prepared from chemically defined lipids and heterologous expressed cytosolic domains of type I or type II membrane receptors. The proteomic analyses of such samples are challenging because of huge proteomic backgrounds of proteins binding to the liposomes irrespective of the receptor and relatively small amounts and numbers of receptor-specific binders. Though the basic idea is to elucidate sorting machineries and study membrane trafficking processes, such experiments are untargeted and miscellaneous discoveries were achieved. We elucidated that the apical determinant crumbs 2 is a cargo of the retromer complex. This revealed a fameless level of control for the establishment of cell polarity. We found retromer along with the adapter complexes AP 4 and AP 5 trafficking the beta amyloid precursor protein APP. This confirmed recent publications and yielded new insights. Moreover, many more proteins and complexes appeared to associate with the cytosolic part of APP (AICD) in a membrane context-dependent or -independent manner. Among those, some were so far unknown to interact with AICD, like mTORC1 and the PIKFyve complex.

Despite tremendous advances in mass spectrometry instrumentation and mass spectrometry-based methodologies, global protein profiling of organellar, cellular, tissue and body fluid proteomes in different organisms remains a challenging task due to the complexity of the samples and the wide dynamic range of protein concentrations. In addition, large amounts of produced data make result exploitation difficult. To overcome these issues, further advances in sample preparation, mass spectrometry instrumentation as well as data processing and data analysis are required. The presented study focuses as first on the improvement of the proteolytic digestion of proteins in in-gel based proteomic approach (Gel-LCMS). To this end commonly used bovine trypsin (BT) was modified with oligosaccharides in order to overcome its main disadvantages, such as weak thermostability and fast autolysis at basic pH. Glycosylated trypsin derivates maintained their cleavage specifity and showed better thermostability, autolysis resistance and less autolytic background than unmodified BT. In line with the “accelerated digestion protocol” (ADP) previously established in our laboratory modified enzymes were tested in in-gel digestion of proteins. Kinetics of in-gel digestion was studied by MALDI TOF mass spectrometry using 18O-labeled peptides as internal standards as well as by label-free quantification approach, which utilizes intensities of peptide ions detected by nanoLC-MS/MS. In the performed kinetic study the effect of temperature, enzyme concentration and digestion time on the yield of digestion products was characterized. The obtained results showed that in-gel digestion of proteins by glycosylated trypsin conjugates was less efficient compared to the conventional digestion (CD) and achieved maximal 50 to 70% of CD yield, suggesting that the attached sugar molecules limit free diffusion of the modified trypsins into the polyacrylamide gel pores. Nevertheless, these thermostable and autolysis resistant enzymes can be regarded as promising candidates for gel-free shotgun approach. To address the reliability issue of proteomic data I further focused on protein identifications with borderline statistical confidence produced by database searching. These hits are typically produced by matching a few marginal quality MS/MS spectra to database peptide sequences and represent a significant bottleneck in proteomics. A method was developed for rapid validation of borderline hits, which takes advantage of the independent interpretation of the acquired tandem mass spectra by de novo sequencing software PepNovo followed by mass-spectrometry driven BLAST (MS BLAST) sequence similarity searching that utilize all partially accurate, degenerate and redundant proposed peptide sequences. It was demonstrated that a combination of MASCOT software, de novo sequencing software PepNovo and MS BLAST, bundled by a simple scripted interface, enabled rapid and efficient validation of a large number of borderline hits, produced by matching of one or two MS/MS spectra with marginal statistical significance.

The characterization of lipids is performed by mass spectrometry based on structure specific fragments or by accurate mass measurements of intact precursor ions. The latter method, termed ’top-down lipidomics’, is due to its robustness, simplicity and speed a valuable tool for medical research to elucidate the molecular background of lipid metabolic disorders. The current thesis aims to improve the established lipidomics methods. Therefore, a new top-down lipidomics method was introduced that increased the analysis throughput, lipidome coverage and accuracy of quantification, compared to previous approaches, by rapid successive acquisition of high resolution Fourier transform mass spectra in positive and negative ion modes. Furthermore, the characterization of molecular lipid species by utilizing high energy collisional dissociation was achieved on Orbitrap instruments. The mass accuracy of acquired MS/MS spectra increased the confidence in identification for unusual very-long chain polyunsaturated phosphatidylcholine species and a new lipid class, the maradolipids. Beyond that, effort was made to enhance the accuracy and comparability of MS/MS based bottom-up lipidomics data. In this respect, lipids with varying degree of unsaturation were analyzed and revealed discrete fragmentation properties. The technical refined lipidomics methods allowed insight into the lipid composition of lipoproteins and changes of the blood plasma induced by apheresis. Lipidomics screening of blood plasma uncovered an altered lipid pattern in consequence of impaired glucose metabolism and type 2 diabetes. The lipidomics characterization of islet allowed their quality assessment.

Das Problem des Missbrauchs von Erythropoietin (EPO) als Dopingsubstanz zur Steigerung der Ausdauerleistung wurde schlagartig weltweit durch den Skandal zur Tour de France 1998 bekannt. Das Internationale Olympische Komitee (IOC) führte ab 1992 Erythropoietin explizit auf der Liste der verbotenen Wirkstoffe auf, ohne des es möglich war zwischen den rekombinantem und dem körpereigene Erythropoietin zu unterscheiden. Bei der im Institut für Dopinganalytik und Sportbiochemie Kreischa durchgeführten Arbeit wurden zwei generelle Strategien verfolgt: zum einen ein indirekter Nachweis des rhEPO, basisierend auf dessen Auswirkungen auf die Erythropoese, und zum anderen der direkte Nachweis des Unterschieds zwischen rekombinantem und humanem Erythropoietin. In der ersten durchgeführten Populationsuntersuchung von 229 Leistungssportlern konnte bei der Auswertung der Daten lediglich eine signifikante Erhöhung des löslichen Transferrinrezeptors (sTfR) bei den Ausdauerathleten gefunden werden, während sich die hämatologischen Parameter nicht unterschieden. In der anschließenden Verlaufsuntersuchung von Ausdauerathleten des Deutschen Leichtathletikverbandes wurden zusätzlich zu den bereits in der Populationsstudie untersuchten Parametern erstmalig von Hochleistungs-athleten Retikulozyten und deren Reifeparameter untersucht. Bei den Hochleistungs-sportlern konnten, insbesondere für die Retikulozyten-parameter, über den Zeitraum der Studie konstante Werte gefunden werden. Die Untersuchung der zirkadianen Rhythmik zeigte lediglich für den Parameter Erythropoietin einen signifikante Veränderung mit einem Maximum in den späten Abendstunden (20:00 bis 23:00 Uhr) erreichte. Die Untersuchung der Variation der indirekten Parameter über den Zeitraum eines Jahres zeigte, dass im Gegensatz zu der Verlaufsuntersuchung der DLV-Athleten, bei der der längste Untersuchungs-zeitraum sechs Monate betrug, eine Veränderung aller Parameter, mit Ausnahme von Erythropoietin, bestand. Bei der Auswertung der Belastungsstudien wurde für die gut trainierten Athleten nur ein geringer Einfluss auf die hämatologischen Parameter gefunden, während bei einigen Retikulozytenparametern signifikante Erhöhungen durch die Belastung festgestellt werden konnten. Mit der Etablierung der direkten Nachweismethode für EPO im Urin und der Anpassung der ursprünglichen Methode an das neue Präparat ARANESP, ein modifiziertes EPO, änderte sich die Aufgabenstellung für die indirekten Parameter, da es ab sofort möglich war eine große Anzahl Proben unter Verwendung von niedrigeren Grenzwerten zu screenen. Anhand der Werte der weltbesten Ausdauerathleten wurden allgemein gültige Grenzwerte und eine globale Strategie für ein Screening aufgestellt. Bei einem auffälligen Befund würde in jedem Fall die korrespondierende Urinprobe mittels der direkten Methode untersucht und erst mit dem Nachweis des rekombinanten Erythropoietins als positiv bewertet werden. Zusätzlich zu den indirekten Parametern wurden Untersuchungen hinsichtlich des direkten Nachweis, d. h. der Anreicherung von Erythropoietin und einer massenspektrometrischen Analyse einzelner Glykanketten, durchgeführt, bei denen mit der Kombination Nanospray und TOF-MS die notwendigen Nachweisgrenzen erreicht werden konnten. Die Ergebnisse der Arbeit zeigen, dass ausgewählter Blutparameter sehr gut geeignet sind, um als Screeningmethode für erythropoesesteigernde Substanzen zu dienen. Im Gegensatz zur Methode des direkten Nachweises von EPO im Urin, die durch die Verfügbarkeit der Referenzsubstanzen limitiert ist, bietet der indirekte Nachweis über Blutparameter den Vorteil, Veränderungen des erythropoetischen Systems, verursacht durch neue Substanzen oder Methoden, erfassen zu können.