<p>The comprehensive analysis of human blood plasma metabolome has been completed using derivatization gas chromatography-mass spectrometry (GC-MS) analysis, liquid chromatography-mass spectrometry (LC-MS) analysis and a comprehensive LC-GC-MS analysis approach wherein LC fractions were collected, derivatized and analyzed using GC-MS. In all cases blood plasma samples were deproteinized using solvent precipitation prior to chromatography and MS analysis.</p> <p>In GC-MS analyses, the progress of all derivatization reactions was monitored by adding 9-anthracenemethanol and 1,3-diphenylacetone to all reaction mixtures; their conversions to 9-anthracenemethanol trimethylsilyl ether and the oxime derivative of 1,3-diphenylacetone were used as measures of the completion of these derivatization reactions. Any reactions with completions less than 99% were repeated.</p> <p>GC-MS analysis of blood plasma samples detected 100 peaks; 44 were positively identified by comparing retention indices and mass spectra with those of authentic standards. LC-MS analyses were conducted on a HILIC column (aminopropyl phase) with MS detection in both negative ion and positive ion modes and resulted in the identification of 97 peaks; 47 were observed in the positive ion mode, 58 in the negative ion mode with 8 peaks observed in both modes.</p> <p>The multi-dimensional LC-GC approach was not designed as a routine analytical method; rather the purpose of this approach was to see how many compounds could be observed in the sample and to obtain better quality mass spectra and retention index values. The LC separation afforded 16 fractions which upon derivatization GC-MS analysis gave an additional 176 peaks from a total of 276 peaks. The MS data from these additional spectra can be used to develop selected ion monitoring GC-MS or tandem mass spectrometry analytical methods. This thesis has demonstrated the power of off-line comprehensive methods to identify compounds that neither the GC nor the LC methods detected.</p> / Master of Science (MSc)

Identification of disease-related alterations in molecular and cellular mechanisms may reveal useful biomarkers for human diseases including cancers. High-throughput omic technologies for identifying and quantifying multi-level biological molecules (e.g., proteins, glycans, and metabolites) have facilitated the advances in biological research in recent years. Liquid (or gas) chromatography coupled with mass spectrometry (LC/GC-MS) has become an essential tool in such large-scale omic studies. Appropriate LC/GC-MS data preprocessing pipelines are needed to detect true differences between biological groups. Challenges exist in several aspects of MS data analysis. Specifically for biomarker discovery, one fundamental challenge in quantitation of biomolecules is owing to the heterogeneous nature of human biospecimens. Although this issue has been a subject of discussion in cancer genomic studies, it has not yet been rigorously investigated in mass spectrometry based omic studies. Purification of mass spectometric data is highly desired prior to subsequent differential analysis. In this research dissertation, we majorly target at addressing the purification problem through probabilistic modeling. We propose an intensity-level purification model (IPM) to computationally purify LC/GC-MS based cancerous data in biomarker discovery studies. We further extend IPM to scan-level purification model (SPM) by considering information from extracted ion chromatogram (EIC, scan-level feature). Both IPM and SPM belong to the category of topic modeling approach, which aims to identify the underlying "topics" (sources) and their mixture proportions in composing the heterogeneous data. Additionally, denoise deconvolution model (DMM) is proposed to capture the noise signals in samples based on purified profiles. Variational expectation-maximization (VEM) and Markov chain Monte Carlo (MCMC) methods are used to draw inference on the latent variables and estimate the model parameters. Before we come to purification, other research topics in related to mass spectrometric data analysis for cancer biomarker discovery are also investigated in this dissertation. Chapter 3 discusses the developed methods in the differential analysis of LC/GC-MS based omic data, specifically for the preprocessing in data of LC-MS profiled glycans. Chapter 4 presents the assumptions and inference details of IPM, SPM, and DDM. A latent Dirichlet allocation (LDA) core is used to model the heterogeneous cancerous data as mixtures of topics consisting of sample-specific pure cancerous source and non-cancerous contaminants. We evaluated the capability of the proposed models in capturing mixture proportions of contaminants and cancer profiles on LC-MS based serum and tissue proteomic and GC-MS based tissue metabolomic datasets acquired from patients with hepatocellular carcinoma (HCC) and liver cirrhosis. Chapter 5 elaborates these applications in cancer biomarker discovery, where typical single omic and integrative analysis of multi-omic studies are included. / Ph. D.

Petit Manseng grapes harvested in 2011 and 2012 were fertilized with soil nitrogen at 0, and 30 kgN/ha, foliar nitrogen at 15kg/ha and foliar nitrogen plus sulfur at 15kg/ha and 5kg respectively. Point quadrat analysis demonstrated foliar nitrogen alone and nitrogen plus sulfur treatments increased percent gaps and lower leaf layer numbers. Berry juice samples differed in ammonia, arginine and yeast assimilable nitrogen concentration. Total glycosides were 25 percent higher in the foliar nitrogen treatment versus the control treatment. Electronic nose measurements on field clusters and laboratory berry analyses was different among treatments in volatile content. Harvest samples underwent acid or enzyme hydrolysis of precursor fractions. Solid phase microextraction (SPME) and gas chromatography-mass spectrometry (GC/MS) analysis identified 27 free aroma and flavor compounds and 52 bound compounds. Lactones and carboxylic acids were the major components of the free fractions while bound fractions had increased concentrations of alcohols, esters and terpenes compared to the free fraction. With nitrogen fertilization, acid and enzyme hydrolysis had reduced concentrations of some higher alcohols and carboxylic acids. Acid hydrolysis released more terpenes with nitrogen treatments versus enzymatic hydrolysis. Ester content was increased in both acid and enzyme hydrolysis fractions in vines receiving nitrogen treatments. For descriptive analysis, eight trained panelists described aroma, flavor, texture/mouthfeel and aftertaste attributes. Analysis of Variance (ANOVA) demonstrated that wines were a significant source of variation with 23 of the 24 attributes used. Wine principal component analysis (PCA) of aroma attributes explained 23.5% of the variation from PC1, while flavor-by-mouth and texture/mouthfeel attributes explained 26.3% of the variation due to PC1. The aim of this study was to develop descriptive terms for Petit Manseng and determine the influence of fruit nitrogen levels on the aroma and flavor profile of this cultivar. / Ph. D.

Ethoxyquin is an antioxidant commonly used to preserve vitamins and lipids in various food products and animal feeds. The extraction and determination of ethoxyquin is becoming increasingly important as products, which are labeled as "natural" are becoming more common. The present method of determination only ensures that ethoxyquin values are below 10-20 parts per million. Therefore, advances are needed in methods of extraction and analysis in order to lower the detection limits in various products. The first part of this research investigates the use of supercritical fluids in the extraction of ethoxyquin from lean beef and beef fat. Supercritical fluids offer the advantages of safety, time, expense, and selectivity over liquid extractions. Three fluids were examined: carbon dioxide, trifluoromethane, and 1,1,1,2-tetrafluoroethane. Carbon dioxide appeared to react with ethoxyquin during the extraction. Methanol modified hydrofluorocarbons provided more complete extractions over pure hydrofluorocarbon fluids. Methanol modified 1,1,1,2-tetrafluoroethane was used in the extraction of ethoxyquin from lean beef and beef fat, and provided a quantitative extraction at the 0.5 ppm level. The second part of this research centered on the separation and quantitation of the oxidation products of ethoxyquin through the use of high pressure liquid chromatography with chemiluminescence nitrogen detection (HPLC/CLND). When ethoxyquin is oxidized, the resulting products also exhibit antioxidative properties. While these oxidation products are known, no effort has been made to separate and quantify them in real or clean samples. HPLC/CLND allows all nitrogen containing compounds to be quantified without a known standard. This method is of extreme interest in the case of ethoxyquin oxidation products, or other types of metabolites, where standards are difficult to obtain or are unstable. HPLC/CLND allowed a separation of ethoxyquin and four of its oxidation products to be detected, thus making future studies of the antioxidant behavior of ethoxyquin feasible. / Master of Science

An alternative method for extraction of therapeutically beneficial compounds such as sterols, fatty acids, and tocopherols from cranberry seeds with pure SF CO2 has been provided. The supercritical fluid extraction (SFE) operating conditions such as extraction temperature, pressure of CO2, extraction time, and CO2 flow rate were optimized to maximize the extraction yield. The amount and type of SF extractables (pure CO₂) have been compared with Soxhlet extractables (hexane) to evaluate the feasibility of SFE as an alternative extraction method. The extractables obtained via hexane and SF CO₂, which were derivatized and identified by gas chromatography mass spectrometry (GC-MS), contained mostly methylated fatty acids. / Master of Science

By addressing new sample preparation techniques, the U.S. Environmental Protection Agency (EPA) has recently implemented research programs to reduce or abolish laboratory pollution. In the work reported here, EPA Method 8270, established for Priority Pollutant Organics, will be evaluated by both Soxhlet and microwave-assisted extraction (MAE) for two classifications of compounds. The common procedure for sample preparation of solids is Soxhlet extraction. This is a lengthy operation and uses abundant solvent volumes. With ever changing times, the new technology of MAE is surfacing. This technique uses far less solvent and sample preparation times are greatly reduced. The work reported here compares the recoveries of phenolic and polynuclear aromatic compounds for both Soxhlet and closed-vessel MAE. / Master of Science

No / References Citations Metrics Reprints & Permissions Get access Abstract This paper presents the observation of lipid residue, identified as beeswax, preserved in the ceramic matrix of a Late Chalcolithic (c. 3700–3000 BC) bevelled-rim bowl (BRB) from the site of Tepe Sofalin on the Tehran Plain. Gas chromatography-mass spectrometry (GC-MS) was used to separate and identify the lipid constituents preserved in the matrix of a BRB sherd. Lipid biomarkers were recovered including long-chain n-alkanes, n-alkenes, palmitic wax monoesters, fatty acids and n-alcohols characteristic of beeswax. In addition to two disaccharides, cholesterol and β-sitosterol as contaminants were retrieved by solvent soluble extraction from a number of different locations from the ceramic matrix of the analysed sherd.

Yes / Vast numbers of votive mummies were produced in Egypt during the Late Pharaonic, Ptolemaic, and Roman periods. Although millions remain in situ, many were removed and have ultimately entered museum collections around the world. There they have often languished as uncomfortable reminders of antiquarian practices with little information available to enhance their value as artefacts worthy of conservation or display. A multi-disciplinary research project, based at the University of Manchester, is currently redressing these issues. One recent aspect of this work has been the characterization of natural products employed in the mummification of votive bundles. Using gas chromatography–mass spectrometry and the well-established biomarker approach, analysis of 24 samples from 17 mummy bundles has demonstrated the presence of oils/fats, natural waxes, petroleum products, resinous exudates, and essential oils. These results confirm the range of organic materials employed in embalming and augment our understanding of the treatment of votives. In this first systematic initiative of its kind, initial findings point to possible trends in body treatment practices in relation to chronology, geography, and changes in ideology which will be investigated as the study progresses. Detailed knowledge of the substances used on individual bundles has also served to enhance their value as display items and aid in their conservation. / RCB is supported by a PhD studentship from the Art and Humanities Research Council (43019R00209). L.M. and S.A.W. are supported by a Leverhulme Trust Research Project Award (RPG-2013-143).

No / To analyze the fatty acid contents of Buddleja asiatica Lour, both the non-volatile oil and fat obtained from the n-hexane soluble sub-fraction were subjected to GC/MS using BSTFA (N,O-bis(trimethylsilyl) trifloroacetamide) derivatization. The oil showed the presence of six fatty acids including palmitic acid (46.75 %), linoleic acid (37.80 %), stearic acid (10.98 %), arachidic acid, margaric acid and lignoceric acid (< 3 %). Analysis of the fat revealed nine fatty acids including lignoceric acid (43.12 %), behenic acid (26.39 %), arachidic acid (9.29 %) and stearic acid (5.3 %). Cerotic acid, montanic acid, melissic acid and palmitic acid were found in low amounts (< 5 %) while trycosylic acid (4.83 %) was the only fatty acid with odd number of carbon atoms. The oil showed a low thermal stability. / Higher Education Commission Pakistan

Die Schwammskelette der Ordnung Verongida zeichnen sich durch das Fehlen mineralischer Komponenten aus. Stattdessen bestehen sie aus Spongin, einem kollagenartigen Protein, und Chitin. Im Rahmen der vorliegenden Arbeit wurden die aus solch einem Chitin-Protein-Komplex bestehenden Skelette der Schwammspezies Aplysina cavernicola und Ianthella basta aus der Ordnung Verongida untersucht. Aufgrund ihrer morphologischen Unterschiede wurde für jede Schwammart eine eigene Methode zur Isolierung der Schwammskelette entwickelt. Die isolierten Skelette konnten anschließend mit verschiedenen Methoden wie REM, ATR-FTIR-Spektroskopie und NMR-Spektroskopie charakterisiert werden. Weiterhin wurde eine Methode zur Extraktion und Analyse der in den Skeletten befindlichen Aminosäuren mittels GC-MS entwickelt. Die Untersuchungen zeigten deutlich, dass es sich bei Spongin um ein kollagenartiges und halogeniertes Protein handelt, welches je nach Schwammart Unterschiede in der Aminosäurezusammensetzung aufweist. Darüber hinaus gelang es zum ersten Mal das Chitin aus dem Chitin-Protein-Komplex mittels Phosphorsäure zu entfernen. Aus den gewonnenen Erkenntnissen konnte abschließend ein Modell zum Aufbau des Chitin-Protein-Komplexes in der Schwammspezies Aplysina cavernicola entwickelt werden.