3-Jodthyronamin (3-T1AM) und Thyronamin (T0AM) sind endogene Signalmoleküle, die eine große strukturelle Ähnlichkeit zu Schilddrüsenhormonen aufweisen, allerdings die klassischen Wirkungen des aktiven Schilddrüsenhormons 3,5,3’-Trijodthyronin (T3) antagonisieren. In der vorliegenden Arbeit wurde untersucht, ob Thyronamine (TAMs) Substrate von Dejodasen (Dio1, Dio2, Dio3) sind. Die TAMs wurden mit isozymspezifischen Dio-Präparationen inkubiert. Die Dejodierungsprodukte wurden mittels Hochleistungsflüssigkeitschromatographie und Tandemmassenspektrometrie (LC-MS/MS) analysiert. Mit Präparationen der Dio1 wurden Dejodierungen von 3,3’,5’-Trijodthyronamin, 3’,5’- und 3,3’-Dijodthyronamin am phenolischen Ring sowie Dejodierungen von 3,5,3’-Trijodthyronamin und 3,5-Dijodthyronamin am Tyrosylring beobachtet. Dio2 haltige Präparationen katalysierten ebenfalls Dejodierungen von 3,3’,5’-Trijodthyronamin und 3’,5’-Dijodthyronamin am phenolischen Ring. Mit Dio3 haltigen Präparationen wurden alle TAMs mit jodiertem Tyrosylring dejodiert. In Kompetitionsversuchen inhibierten ausschließlich die TAMs, die als Substrate von Dio Isozymen identifizierten wurden, eine etablierte Dejodierungsreaktion eines bekannten Substrats. Im Gegensatz dazu interferierten TAMs, die in den LC-MS/MS Experimenten als Substrate der Dio Isozyme ausgeschlossen wurden, nicht mit der genannten etablierten Dejodierungsreaktion. Zusammenfassend wurde in der vorliegenden Arbeit gezeigt, dass TAMs Substrate aller drei Dio Isozyme sind und jedes Isozym eine eigene Substratspezifität aufweist. Diese Befunde weisen darauf hin, dass Dio Isozyme an der Biosynthese von TAMs beteiligt sein könnten. Ferner wurden die Biosynthesewege für 3-T1AM und T0AM eingegrenzt. Desweiteren gestatten die Ergebnisse neue Einblicke in die generellen strukturellen Voraussetzungen für Dio Substrate, da TAMs die bisher einzigen endogenen Dio Substrate darstellen, deren Seitenkette am Tyrosylring eine positive Ladung aufweist. / 3-iodothyronamine (3-T1AM) and thyronamine (T0AM) are novel endogenous signaling molecules that exhibit great structural similarity to thyroid hormones but apparently antagonize classical thyroid hormone (T3) actions. The present study investigated whether thyronamines (TAMs) are substrates of three Dio isozymes (Dio1, Dio2 and Dio3). TAMs were incubated with isozyme specific Dio preparations. Deiodination products were analyzed using a newly established method applying liquid chromatography and tandem mass spectrometry (LC-MS/MS). Phenolic ring deiodinations of 3,3’,5’-triiodothyronamine, 3’,5’- and 3,3’-diiodothyronamine as well as tyrosyl ring deiodinations of 3,5,3’-triiodothyronamine and 3,5-diiodothyronamine were observed with preparations containing Dio1. Preparations of Dio2 also deiodinated 3,3’,5’-triiodothyronamine and 3’,5’-diiodothyronamine at the phenolic rings. All TAMs with tyrosyl ring iodine atoms were deiodinated by Dio3 containing preparations. In functional competition assays, the newly identified TAM substrates inhibited an established iodothyronine deiodination reaction. By contrast, TAMs which had been excluded as Dio substrates in LC-MS/MS experiments, failed to show any effect in the competition assays, thus verifying the former results. In summary, all three Dio isozymes catalyzed TAM deiodination reactions with each isozyme exhibiting a unique substrate specificity. These data support a role for Dio isozymes in TAM biosynthesis and contribute to confining the biosynthetic pathways of 3-T1AM and T0AM. Furthermore, they provide new insights into the structural requirements for Dio substrates in general since TAMs represent the only endogenous Dio substrates described, so far, which possess a positively charged tyrosyl ring side chain.

Mykotoxine sind giftige Naturstoffe, die im Rahmen des Sekundärstoffwechsels von Schimmelpilzen beim Wachstum auf pflanzlichen Substraten gebildet werden. Zu den bekanntesten Mykotoxinen zählt das Ochratoxin A (OTA), welches überwiegend in Getreide und davon abgeleiteten Erzeugnissen, aber auch in Wein und Kaffee sowie Gewürzen und Bier nachgewiesen wurde. OTA ist unter anderem immunotoxisch, nephrotoxisch und besitzt teratogene sowie kanzerogene Eigenschaften. Darüber hinaus wird OTA eine hormonelle Wirkung zugesprochen. Aufgrund der Toxizität und des relativ häufigen Vorkommens in Lebensmitteln wurden für OTA Grenzwerte festgelegt. Diese liegen für Wein, Röstkaffee und diätetische Produkte zwischen 0,5 mikrogramm /kg und 10 mikrogramm /kg. Grenzwerte für Gewürze und Bier sind geplant. Im Rahmen der Methodenentwicklung zur Bestimmung von OTA in Lebensmitteln wurden verschiedene clean-up-Techniken miteinander verglichen. Dabei wurde vor allem den kombinierten Ionentauscher/reversed phase-Säulen und der LC-MS/MS wesentliche Bedeutung beigemessen. Innerhalb der Methodenvalidierung wurden die Ergebnisse mit dem entsprechenden Standardverfahren verglichen. Es konnte gezeigt werden, dass mit oben genanntem Material in Kombination mit der LC-MS/MS sehr gute Ergebnisse erzielt werden können. Diese wurden im Rahmen der Validierung durch statistische Auswertung bestätigt. Ferner wurden im Rahmen der Methodenentwicklung, speziell bei der Bestimmung von OTA in Kaffee, Extraktionstechniken miteinander verglichen. Dabei wurde die bislang kaum beachtete ASE (Accelerated Solvent Extraction, Dionex) sowie Ultraschallextraktion mit der Schüttelextraktion aus der gültigen Norm verglichen und ihre Anwendbarkeit auf weitere Lebensmittel geprüft. In diesem Zusammenhang waren die ASE und Ultraschallextraktion der konventionellen Schüttelextraktion überlegen. Darüber hinaus wurde die Ultraschallextraktion in Kombination mit dem Ionentauscher/reversed phase clean-up erfolgreich auf Weizen und Chili angewandt. Parallel zur Methodenentwicklung wurde die Stabilität und Homogenität von OTA in Wein und Röstkaffee untersucht. Sowohl die Homogenität als auch die Stabilität des Analyten sind wichtige Faktoren bei der Entwicklung neuer Verfahren, da zusammen mit Ergebnissen der Validierung, die Messunsicherheit innerhalb neuer Verfahren eingegrenzt werden. / Mycotoxins are naturally occurring toxic substances and produced as secondary metabolites by fungi which are growing on plants predominantly. One of the most interesting mycotoxins is ochratoxin A (OTA), which was found in several foods and feed stuff like wheat and its related products, wine, coffee, spices and beer. Among other things OTA is immunotoxic, nephrotoxic and has teratogenic and cancerogenic properties. Further more OTA shows hormonal effects. Because of its toxicity and common appearance in food and feed the OTA content had to be regulated in European and or national directives. The maximum values are determined between 0.5 micrograms/kg and 10 micrograms/kg for wine, roasted coffee and dietetic products. Other maximum levels for beer and spices are intended. During the investigation of analytical methods for the determination of OTA in food stuff different clean-up techniques were compared. Thereby the mixed anion exchange/reversed phase clean-up in combination with LC-MS/MS was researched intensively. Within method validation the results were compared with the corresponding standard methods. This work shows that the mixed mode clean-up in combination with LC-MS/MS gives excellent results. These results were statistically confirmed during method validation. Further more different extraction techniques were compared during the development of analytical methods, especially for the determination of OTA in coffee. Thereby the ASE (accelerated solvent extraction, Dionex) and the ultrasonic extraction were compared with the shaking technique from current standard methods. The adaptability for other food and feed products was researched as well. In this context the new extraction techniques were superior to conventional shaking techniques. In addition the ultrasonic extraction with mixed mode clean-up and LC-MS/MS detection was applied to chilli and wheat effectively. Besides the investigation of analytical methods the stability and homogeneity of OTA in wine and roasted coffee was researched. The homogeneity and stability of OTA in matrix are very important factors during the investigation of analytical methods. In combination with the relevant results of the method validation these results can be used to determine the uncertainty of the new analytical methods.

Hepcidin-25, ein 2000 entdecktes Peptidhormon, das eine Schlüsselrolle im Eisenstoffwechsel spielt, hat das Verständnis von Eisenerkrankungen revolutioniert. In dieser Studie wurde LC gekoppelt mit einem Triple-Quadrupol MS in einer schnellen und robusten Methode zur Quantifizierung von Hepcidin-25 in menschlichem Serum verwendet, welche letztlich in Routine-Laboratorien genutzt werden soll. Zu diesem Zweck wurden zwei Probenvorbereitungsstrategien und zwei komplementäre LC Bedingungen untersucht, wobei eine saure mobile Phase (0,1% TFA) mit einem neuartigen Ansatz unter der Verwendung einer basischen mobilen Phase (0,1% NH3) verglichen wurde. In einem laborinternen Vergleich beider LC-MS/MS Methoden wurde Hepcidin-25 in humanen Proben unter Verwendung der gleichen Kalibrierstandards quantifiziert und eine sehr gute Korrelation der Ergebnisse ermittelt. Hierbei wurde die Analysestrategie mit saurer mobiler Phase als hochsensitiv (LOQ von 0,5 μg/L) und präzise (CV <15%) befunden und als Kandidat einer Referenzmethoden für die Hepcidin-25 Quantifizierung in realen Proben empfohlen. Einer der neuartigen Aspekte der Methodik war die Verwendung von Amino- und Fluor-silanisierten Autosampler-Fläschchen, um die Adsorption des 25 Reste umfassenden Peptids anOberflächen zu reduzieren. Darüber hinaus wurde diese LC-MS/MS-Methode in einer internationalen Ringversuchsstudie eingesetzt, bei der ein sekundäres Referenzmaterial als Kalibrierstandard verwendet wurde, und gemäß des International Consortium for Harmonization of Clinical Laboratory Results (ICHCLR) als optimal bewertet. In dieser Arbeit wurde die Bildung von Hepcidin-Komplexen mit Kupfer(II) untersucht. Die erste Umkehrphasen-chromatographische Trennung von Hepcidin-25/Cu(II) und Hepcidin-25 (Kupfer "frei") wurde unter Verwendung von mobilen Phasen mit 0,1% NH3 erreicht. LC-MS/MS und FTICR-MS wurden für die Charakterisierung der gebildeten Hepcidin-25-Cu(II)-Spezies bei pH-Werten von 11 bzw. 7,4 verwendet. / Hepcidin-25, a key iron-regulatory peptide hormone discovered in 2000, has revolutionized the understanding of iron-related pathology. This study applied LC-MS/MS, using the triple quadrupole mass spectrometer, in a rapid and robust analytical strategy for the quantification of hepcidin-25 in human serum, to be implemented in routine laboratories. For this purpose, two sample preparation strategies and two complementary LC conditions were investigated, where the use of acidic mobile phases (0.1% TFA) was compared with a novel approach involving solvents at high pH (0.1% NH3). The application of these LC-MS/MS methods to human samples in an intra-laboratory comparison, using the same hepcidin-25 calibrators, yielded a very good correlation of the results. The LC-MS/MS employing trifluoroacetic acid-based mobile phases was selected as a highly sensitive (LOQ of 0.5 µg/L) and precise (CV<15%) method and was recommended as a reference method candidate for hepcidin-25 quantification in real samples. One of the novel aspects of the methodology was the use of amino- and fluoro-silanized autosampler vials to reduce the interaction of the 25-residue peptide to laboratory glassware surfaces. Moreover, this LC-MS/MS method was used for an international round robin study, applying a secondary reference material as a calibrator and its performance was found to be in the optimal range as defined by the International Consortium for Harmonization of Clinical Laboratory Results (ICHCLR). In this work, the formation of hepcidin-25 complexes with copper(II) was investigated. The first reversed-phase chromatographic separation of hepcidin-25/Cu2+ and hepcidin-25 (copper “free”) was achieved by applying mobile phases containing 0.1% NH3. LC-MS/MS and FTICR-MS were applied for the characterization of the formed hepcidin-25-Cu(II) species at pH values of 11 and 7.4 respectively. A new species corresponding to hepcidin-25 complexed with two copper ions was identified at high pH.

Ergotalkaloide sind sekundäre Stoffwechselprodukte des parasitären Schlauchpilzes Claviceps purpurea der auf Getreide Mutterkörner (Sklerotien) bildet. In Sklerotien sind toxische Ergotalkaloide enthalten. Durch C. purpurea werden vorrangig sechs verschiedene Ergotalkaloid-Epimerenpaare gebildet, die toxischen C8-(R)-Epimere und die biologisch nicht relevanten C8-(S)-Epimere, die ineinander umgewandelt werden können. Das Ziel der Arbeit war es, die Epimerisierung der Ergotalkaloide während der Probenvorbereitung im Vergleich zu bisher bekannten Probenaufarbeitungsverfahren zu minimieren. Dieses gelang durch den Verzicht des Zusatzes starker Säuren oder Basen. Die aufgereinigten Extrakte können bei Raumtemperatur über 96 Stunden epimerisierungsfrei in einer tensidischen Acetonitril-Wasser-Lösung gelagert werden. Die Probenaufarbeitung mit anschließender Auftrennung über die Hochleistungsflüssigchromatographie und fluorimetrischer Detektion (HPLC-FLD) wurde für Roggenmehl und Speiseöl validiert und auf diese Martices angewendet. So konnten erstmals die Ergotalkaloidgehalte auch in Weizenkeimöl quantifiziert werden. Im zweiten Teil der Arbeit wurde das Epimerisierungsverhalten von Ergotalkaloiden bei Backversuchen und in vitro Verdauexperimenten untersucht. Das Backen resultierte in eine Verschiebung des Epimerengleichgewichtes auf die Seite der (S)-Epimere. Das angewendete in vitro Verdaumodell führte für die Ergotalkaloidepimerenpaare Ergotamin und Ergosin zu einer Verschiebung des Epimerengleichgewichtes auf die Seite der toxischen (R)-Epimere. Dagegen zeigten die Ergotalkaloide der Ergotoxingruppe eine Verschiebung des Epimerengleichgewichtes auf die Seite der (S)-Epimere. Der dritte Teil der Arbeit beschäftigt sich mit Ergotalkaloid-Konjugaten, die unter dem Einfluss von UV-Licht entstehen. Es wurden sechs Ergotalkaloid-Fettsäure-Konjugate synthetisiert und in Sklerotien über die HPLC in Verbindung mit massenspektrometrischer Detektion nachgewiesen. / Ergot alkaloids are secondary metabolites of the parasitic fungus Claviceps purpurea that forms sclerotia on cereals. These sclerotia contain toxic ergot alkaloids. C. purpurea forms six epimeric pairs of ergot alkaloids predominantly the toxic C8-(R)-epimers and the biologically inactive C8-(S)-epimers. In view of the fact that both epimeric forms can be transformed into one another, the objective of this work was to develop a novel sample preparation method that minimizes the epimerization rate compared to previously published methods. The presented sample preparation procedure minimizes epimerization of ergot alkaloids, as it operates without the addition of strong acidic or alkaline modifiers for matrix removal. After sample preparation, an ergot alkaloid containing extract in a sodium hexanesulfonate solution is obtained in which no epimerization after 96 hours was observed. Thus, the sample preparation allows extract storage at ambient temperature for prolonged HPLC analysis. This novel sample preparation followed by HPLC-flourescence analysis was validated for the matrices rye flour and wheat germ oil and was applied for food samples. This is the first time that the ergot alkaloid content in wheat germ oil was quantified. The second part of this work was the study of the epimerization behaviour of ergot alkaloids during baking and in vitro digestion. Baking of cookies resulted in a shift of the epimeric ratio towards the (S)-epimers. The in vitro digestion showed an ergot alkaloid specific shift of the epimeric ratio. The initial percentage of the (R)-epimer increased for ergotamine und ergosine. In contrast, ergot alkaloids of the ergotoxine type showed an epimeric shift towards their (S)-epimers. The third part of this work was the study of ergot alkaloid derivatives that are formed in combination with UV-light. Six different ergot alkaloid fatty acid derivates were synthesized and detected in sclerotia using a HPLC-MS/MS method.

Obwohl EtG seit dem Jahr 2000 intensiv als Alkoholmarker in Haaren beforscht wird, bietet die Thematik weiterhin Raum für Forschung, insbesondere im Bereich der instrumentellen Analytik. Ziel der vorliegenden Arbeit ist die Beleuchtung dieser und weiterer Aspekte. Die Extraktion erfolgte überwiegend mittels der sogenannten Mikropulverisierung. Sie ermöglichte die simultane Mahlung der Haarmatrix und Extraktion des EtGs mit einem hohen Probendurchsatz. Die Selektion und anschließende Detektion erfolgte überwiegend durch HPLC-MS/MS. Die Sicherheit bei der Bestimmung des Analyten wurde durch die erfolgreiche Teilnahme an drei Ringversuchen der Society of Hair Testing (SoHT) belegt. Wiederholbedingungen wurden durch Herstellung von eigenen Haarreferenzmaterialien und die Verwendung von homogenen Fremdhaarmaterialien sichergestellt. Zur Evaluierung der Stabilität von EtG wurden zwei Haarmaterialien unter thermischen Stressbedingungen eingelagert und mit dem Gehalt von Referenzproben verglichen. Der Analyt zeigte außergewöhnliche Stabilität unter den gewählten Bedingungen. Ebenso erfolgte eine Beurteilung des Zerstörungsgrads von EtG im Haar durch oxidierende Substanzen, einhergehend mit der Entwicklung eines zerstörungsfreien Schnelltests mittels FTIR zur Detektion von oxidierten Cysteinspezies in Haaren. Das Modellsystem Barthaar wurde für zwei Experimentreihen etabliert: die Korrelation des EtG-Gehaltes im Barthaar nach Aufnahme definierter Alkoholmengen und den Nachweis von glucuronidierten Spezies im Barthaar nach Aufnahme der korrespondierenden Muttersubstanzen. Während keine eindeutige Korrelation zwischen aufgenommener Alkoholmenge und EtG-Gehalt im Barthaar hergestellt werden konnte, war es durchaus möglich, zwei glucuronidierte Metabolite von Arzneistoffen im Barthaar nach Konsum der Ausgangssubstanzen nachzuweisen. / Although EtG is subject to extended research since the year 2000, the topic still holds headroom for further experiments, especially when it comes to the field of instrumental analysis. The goal of the present thesis was the clarification of crucial analytical and further aspects. The extraction was mostly carried out using the so-called micropulverisation. It rendered the simultaneous milling of the hair matrix and extraction of EtG possible with a high sample throughput. Selection of the analyte and following detection was mainly carried out using HPLC-MS/MS. The quality of analysis was ensured by the successful participation in three interlaboratory tests carried out by the Society of Hair Testing (SoHT). Repetitive conditions were ensured by manufacturing of own hair reference materials as well as by the usage of homogeneous external hair materials. Two hair materials were treated under thermal stress conditions and the EtG values were compared to reference samples to verify the analytes stability. EtG showed extraordinary stability under the chosen conditions. Likewise, an assessment of the degree of EtG decay after oxidative treatment as well as the development of a nondestructive assay via FTIR to detect oxidized cysteine species were established. The model system beard hair was arranged for the conduction of two experimental series: the correlation of the EtG content in beard hair after defined oral consumption of ethanol and the detection of glucuronidation of the corresponding parent substances after consumption. Whilst no distinct correlation could be observed for the ethanol experiment, it was possible to provide evidence for the existence of two glucuronized metabolites of drugs after consumption of the parent compounds.

Cocaine abuse is a world-wide public health and social problem without a U.S. Food and Drug Administration (FDA)-approved medication. An ideal anti-cocaine medication would accelerate cocaine metabolism producing biologically inactive metabolites by administration of an efficient cocaine-specific exogenous enzyme. Recent studies in our lab have led to discovery of the desirable, highly efficient human cocaine hydrolases (hCocHs) that can efficiently detoxify and inactivate cocaine without affecting normal functions of central nervous system (CNS). Preclinical and clinical data have demonstrated that these hCocHs are safe for use in humans and effective for accelerating cocaine metabolism. However, the actual therapeutic use of a hCocH in cocaine addiction treatment is limited by the short biological half-life (e.g. 8 hours or shorter in rats) of the hCocH. In the investigation described in this thesis, we have demonstrated that mCocH and hCocH have improved the catalytic efficiency of mBChE and hBChE against cocaine by ~8- and ~2000-fold, respectively, although the catalytic efficiencies of mCocH and hCocH against other substrates, including acetylcholine (ACh) and butyrylthiocholine (BTC), are close to those of the corresponding wild-type enzymes mBChE and hBChE. In addition, we have identified the first benzoylecgonine-metabolizing enzymes that can hydrolyze benzoylecgonine and accelerate its clearance in rats. The developed LC-MS/MS method has enabled us to simultaneously determine cocaine and nine cocaine-related metabolites in whole blood samples. In development of the long-acting hCocHs, we have designed and discovered a novel hCocH form, catalytic antibody analog, which is an Fc-fused hCocH dimer (hCocH-Fc). The hCocH-Fc has not only a high catalytic efficiency against cocaine, but also a considerably longer biological half-life. A single dose of hCocH-Fc was able to accelerate cocaine metabolism in rats even after 20 days and, thus, block cocaine-induced hyperactivity for a long period of time. In consideration of the general observation that the biological half-life of a protein drug in humans is significantly longer than that in rodents, the hCocH-Fc could allow dosing once every 2-4 weeks, or longer for cocaine addiction treatment in humans.

Simvastatin is a 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitor that is used for the treatment of hyperlipidemia. Simvastatin has recently been studied for its potential use in cancer therapy. In-vitro studies have shown that simvastatin displays anticancer activity, but at concentrations unlikely to be achieved in patients being receiving typical antihyperlipidemic treatment doses. Thus, several clinical trials were conducted to study the tolerability of high dose statins in cancer patients. The maximum tolerated dose of simvastatin was determined to be 15 mg/kg/day, 25-fold higher than a typical dose. However, it is not known if simvastatin plasma concentrations can reach those found to be effective in-vitro. In this context, we initiated a clinical study to determine the pharmacokinetics of high dose simvastatin in patients with chronic lymphocytic leukemia. For this purpose, an LC-MS/MS method was developed and validated for the quantitation of simvastatin and its acid form in plasma and peripheral blood mononuclear cells obtained from CLL patients. Results show that simvastatin concentrations were dose proportional relative to the antihyperlipidemic doses, but lower than those required for in-vitro cytotoxicity against cancer cells. These findings demonstrate that the in-vitro effective concentrations of simvastatin are not achievable clinically, which might explain the limited effectiveness of high dose simvastatin in this study and in previous clinical trials. In view of these data, the use of simvastatin as a sole therapy in cancer treatment was not encouraging and led us to examine the use in combination with other anticancer drugs. After screening several chemotherapeutic agents in combination with simvastatin, we showed that tipifarnib (a farnesyltransferase inhibitor) interacts synergistically in several leukemia cell lines. Mechanistically we showed that simvastatin augments the cytotoxicity of tipifarnib by disrupting the localization of RAS in the cell membrane and by subsequent deactivation of the ERK pathway. Consistent with this observation, drug treatment led to the induction of apoptosis through the caspase cascade activation and the cleaved PARP upregulation. Notably, this synergistic effect was observed at clinically achievable concentrations of simvastatin and tipifarnib. Thus, the effectiveness of this combination should be explored further in future clinical studies.

Mining of datasets obtained from proteomics experiments was performed to investigate the dissociation pathways of protonated peptides activated in the gas phase under low energy collision-induced dissociation (CID). Intensity patterns in ion trap tandem mass spectra were exploited and different statistical approaches were employed to elucidate the dissociation mechanisms.Chapter 2 describes a study of 506 doubly-protonated tryptic peptides that shows the presence of an internal basic residue can increase the preferential fragmentation C-terminal to aspartic acid (Asp-Xxx) significantly. The degree of enhancement varies with the identity of the basic residues. The result corroborates a previously published mechanism based on studies from model peptides, and was incorporated into an existing peptide sequencing algorithm. A preliminary test on a separate dataset of 119 spectra shows that implementing rules to predict enhanced cleavages at Asp-Xxx improves the ability of the algorithm to identify the correct sequence from a list of candidates.Chapters 3-4 describe much more elaborate analyses on 28,330 peptides of different sequences and charge states. Extensive sorting based on prior knowledge was first performed to probe the correlation of fragmentation patterns with structural features. Pair-wise fragmentation maps reveal that the difference in basicity between Arg and Lys results in different dissociation patterns among singly-protonated tryptic peptides. While one dominant protonation form (proton localized) exists for Arg-ending peptides, a heterogeneous population of two or more protonated forms (proton partially-mobile) exist for Lys-ending peptides. Asp/Glu-Xxx dominates spectra from peptides that have a localized proton(s) and Xxx-Pro dominates those that have a mobile or partially mobile proton(s). When Pro is absent from peptides that have a mobile or partially mobile proton(s), cleavage at each peptide bond becomes more prominent. A fundamental dependence of gas phase peptide fragmentation on conformational constraints was found.A knowledge mining scheme was proposed in Chapter 5 to bypass the prior knowledge constraints and cluster the dissociation behaviors of 28,330 peptides into four distinct categories. The most influential factors in the fragmentation process are: the mobility of the proton(s), the presence and the location of Pro and Arg. Structural motifs responsible for each dissociation behavior are also elucidated.

N-linked glycosylation is the most common post-translational modification (PTM) of proteins that exist in nature. N-glycosylation and change in cells serve as a criterion to monitor the activity of developmental stages and diseases severity. Currently, there is an increasing application of mass spectrometry on glycoprotein for malicious, chronic or acute diseases, such as cancers, rheumatoid arthritis (RA) or influenza. In this dissertation, several mass spectrometric assays have been utilized to, quantitatively and qualitatively, characterize protein N-glycosylation at the glycan, glycopeptide and peptide levels. The goals are to identify serum-based RA biomarker (Chapter 2), or to determine possible glycan structures from monoclonal antibody (Chapter 3), or comprehensively to study one influenza glycoprotein, hemagglutinin (Chapter 4). In Chapter 2, LC-MS/MS with CID as MS 2 is the primary technique that is applied to collect raw data for RA biomarker screening; western blot is the verification method for newfound biomarkers. This mass spectrometry based comparative analysis of N-glycoprotein in RA and healthy patients’ sera reveal 41 potential biomarkers for RA that can be applied in clinical research. Chapter 3 describes another LC-MS/MS based method developed for the structural analysis of N-glycan released from the monoclonal antibody, immunoglobin G. Higher-energy collision dissociation (HCD) was the surprior technique utilized to identify glycopeptide fragments. The results show that 19 and 23 N-glycan structures were determined from standard and modified mAb samples respectively by using SimGlycan software, while 38 and 35 glycan structures were recognized by manually mapping respectively. 13 N-glycoforms, out of 26 overlapped glycan structures, were identified with significant alterations by comparing standard sample (sample A) and modified mAb (sample B) utilizing our method. In Chapter 4, we comprehensively studied hemagglutinin by using LC-MS/MS and MALDI from both proteomic perspective and glycomics prospective. After confirmed and verified protein sequence and glycosylation sites, galactose-specific quantitation was performed with exoglycosidase digestion combined HPLC with fluorescence detection. The MALDI-MS/MS based method was utilized to confirm glycan structures. The results in this dissertation provide insights into the significance of protein glycosylation alterations as RA biomarkers, and these quantitative methods can be reapplied to any other disease biomarkers screening for clinical researchers.

Lysophosphatidic acid (LPA) is a bioactive lipid with a plethora of biological functions, including roles in cell survival, proliferation, and migration. Although high-performance liquid chromatography electrospray ionization tandem mass spectrometry (HPLC ESI-MS/MS) technology has been used to measure the levels of LPA in human blood, serum and plasma, current methods cannot readily detect the minute levels of LPA from cell culture. In this study, a novel HPLC ESI-MS/MS method with enhanced sensitivity was developed which allows accurate measurements of LPA levels with a limit of quantitation at approximately 10 femtomoles. The method was validated by quantitation of LPA levels in the media of previously characterized cell lines ectopically expressing autotaxin. Autotaxin overexpression induced an increase in several subspecies of LPA while others remained unchanged. Lastly, this HPLC ESI-MS/MS method was validated via biological assays previously utilized to assay LPA production. Hence, this new HPLC ESI-MS/MS will allow researchers to measure in vitro LPA levels and also distinguish between specific LPA subspecies for the delineation of individual biological mechanisms.