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We introduce new methods for preprocessing and normalization of data acquired by gas/liquid chromatography coupled with mass spectrometry (GC/LC-MS). Normalization is desired prior to subsequent statistical analysis to adjust variabilities in ion intensities that are not caused by biological differences. There are different sources of experimental bias including variabilities in sample collection, sample storage, poor experimental design, noise, etc. Also, instrument variability in experiments involving a large number of runs leads to a significant drift in intensity measurements. We propose new normalization methods based on bootstrapping, Gaussian process regression, non-negative matrix factorization (NMF), and Bayesian hierarchical models. These methods model the bias by borrowing information across runs and features. Another novel aspect is utilizing scan-level data to improve the accuracy of quantification. We evaluated the performance of our method using simulated and experimental data. In comparison with several existing methods, the proposed methods yielded significant improvement. Gas chromatography coupled with mass spectrometry (GC-MS) is one of the technologies widely used for qualitative and quantitative analysis of small molecules. In particular, GC coupled to single quadrupole MS can be utilized for targeted analysis by selected ion monitoring (SIM). However, to our knowledge, there are no software tools specifically designed for analysis of GS-SIM-MS data. We introduce SIMAT, a new R package for quantitative analysis of the levels of targeted analytes. SIMAT provides guidance in choosing fragments for a list of targets. This is accomplished through an optimization algorithm that has the capability to select the most appropriate fragments from overlapping peaks based on a pre-specified library of background analytes. The tool also allows visualization of the total ion chromatogram (TIC) of runs and extracted ion chromatogram (EIC) of analytes of interest. Moreover, retention index (RI) calibration can be performed and raw GC-SIM-MS data can be imported in netCDF or NIST mass spectral library (MSL) formats. We evaluated the performance of SIMAT using several experimental data sets. Our results demonstrate that SIMAT performs better than AMDIS and MetaboliteDetector in terms of finding the correct targets in the acquired GC-SIM-MS data and estimating their relative levels. / Ph. D.

Vitamin C is industrially produced by the Reichstein method, which uses gluconobacters to oxidize sorbitol to sorbose then a chemical process to convert sorbose to 2-keto-L-gulonic acid (2-KLG). The establishment of a more extensive microbial process for 2-KLG production translates into a less expensive and more efficient production of vitamin C. I examined pure strains and mixed cultures for their ability to produce 2-KLG using thin layer and high performance liquid chromatography. The DSM 4027 mixed culture produced the highest yield, 25 g/L, of 2-KLG from 100 g/L of sorbose, while the gram-negative rods isolated from DSM 4027 produced 8.8 g/L, and B. megaterium isolated from DSM 4027 produced 1.4 g/L. Thus, the gram-negative rods in the mixed culture were the primary 2-KLG producer, but B. megaterium in the DSM 4027 mixture enhanced this synthesis. Authentic pure cultures of Gluconobacter oxydans IFO strain 3293 and ATCC strain 621 produced 3.4 g/L and 5.7 g/L, respectively. Attempts to co-culture the isolated B. megaterium with the isolated gram-negative rods and authentic Gluconobacter strains did not increase 2-KLG production, nor did growing the cultures on B. megaterium spent media. Bacillus megaterium produced an unidentified keto-compound detected on the TLC chromatograms, which suggested that B. megaterium converted sorbose to an intermediate that may then be converted by the gram-negative rods in DSM 4027 to 2-KLG. Limited phenotypic tests suggested that the gram-negative rods in the DSM 4027 mixture are not gluconobacters. / Master of Science

La chromatographie bidimensionnelle préparative suscite de plus en plus d'intérêt dans l'élucidation d'échantillons complexes car elle permet de collecter un grand nombre de molécules à haute pureté et quantitée récupérée. Bien que la chromatographie liquide (LC) soit souvent choisie en deuxième dimension, la chromatographie de partage centrifuge (CPC) à de multiples avantages qui en font une technique de choix pour la première dimension. Dans le but de purifier plusieurs molécules d’intérêt dans les matrices végétales, le couplage «comprehensive» CPCxLC représente une technique à fort potentiel. Après avoir expliqué son intérêt et les enjeux liés à la séparation préparative en mode «comprehensive», le développement d’une telle séparation est étudiée selon trois axes. Tout d’abord, une purification de deux molécules d’intérêt dans la plante Edelweiss est réalisée à l’échelle industrielle grâce à la réalisation de cartographies 2D au laboratoire. Cette application permet de montrer l’intérêt du couplage et de mettre en évidence les verrous liés aux conditions de transfert total des fractions en deuxième dimension. Dans une deuxième partie, la séparation CPCxLC en mode « comprehensive » est développée avec le transfert total de l’échantillon en deuxième dimension pour la purification de cinq composés cibles présents dans la plante Edelweiss. Les points clés de la séparation CPCxLC, à savoir le temps d’échantillonnage et le transfert en deuxième dimension, sont étudiés au regard du couplage LCxLC afin de garantir une qualité de séparation permettant la récupération totale des composés. Enfin, la troisième partie consiste à la mise en place d’une méthodologie de sélection des systèmes CPCxLC basée sur l’évaluation quantitative du potentiel des systèmes bidimensionnels à apporter de la distance entre les pics. Cette procédure de sélection est développée sur l’échantillon Cyclopia genistoides avec l’objectif d’isoler huit composés cibles / Preparative two-dimensional chromatography is gaining interest in the elucidation of complex samples as it allows the collection of a large number of molecules with high recovered purity and quantity. While the second dimension is often selected to be liquid chromatography (LC), centrifugal partition chromatography (CPC) is a technique with multiple advantages representing a suitable first dimension. In order to purify several molecules of interest in plant matrices, the comprehensive CPCxLC represents a technique with high potential. After explaining its interest and the issues related to the preparative separation in comprehensive mode, the development of such a separation is studied according to three axes. Firstly, a purification of two targeted molecules in Edelweiss plant is carried out at industrial scale thanks to the realization of 2D-contour plot. This application allows to expose the interest of the separation and to highlight the locks related to the conditions of total transfer of the fractions in second dimension. In a second part, the comprehensive CPCxLC separation is developed with the total transfer of the sample in second dimension applied to the purification of five target compounds from Edelweiss plant. The key points of the CPCxLC separation, namely the sampling time and the second dimension transfer, are studied with regard to the LCxLC separation in order to ensure a separation quality allowing the total recovery of the compounds. Finally, the third part consists in the implementation of a CPCxLC system selection methodology based on the quantitative evaluation of the potential of two-dimensional systems to generate distance between peaks. This selection procedure is developed on the sample Cyclopia genistoides with the objective of isolating eight target compounds

Analytical chemistry is a field with a vast variety of applications. A robust companion in the field is liquid chromatography, the method used in this thesis, which is an established workhorse and a versatile tool in many different disciplines. It can be used for identification and quantification of interesting compounds generally present in low concentrations, called analytical scale chromatography. It can also be used for isolation and purification of high value compounds, called preparative chromatography. The latter is usually conducted in large scale with high concentrations. With high concentrations it is also possible to determine something called adsorption isotherms. Determination of adsorption isotherms is a useful tool for quite a wide variety of reasons. It can be used for characterisation of chromatographic separation systems, and then gives information on the retention mechanism as well as provides the possibility to study column-column and batch-batch reproducibility. If a protein is immobilised on a solid support, adsorption isotherms can be used for pharmacological characterisation of drug-protein interactions. Moreover, they can be used for the study of unexpected chromatographic phenomena. If the adsorption isotherm is known it is also possible to simulate chromatograms, and subsequently optimise the separation process numerically. The gain of a numerically optimised separation process is higher purity or yield of valuable compounds such as pharmaceuticals or antioxidants, as well as reducing the solvent usage. Taken all together, it saves time, money and the environment. However, the process of the adsorption isotherm determination requires a number of careful experimental considerations and preparations, and these are the main focus of the thesis. Important steps along the way include the choice of separation system and of suitable analytes, preparation of mobile phases and sample solutions, calibration, determination of injection profiles and column void, and of course the adsorption isotherm determination method itself. It is also important to keep track of parameters such as temperature and pH. These issues are discussed in this thesis. At the end, a description of useful methods for processing of the raw adsorption isotherm data is presented, as well as a brief passage on methods for numerical optimisation.

<p>Liquid chromatography coupling with mass spectrometry (LC/MS) plays an important role in pharmaceutical characterization because of its ability to separate, identify, and quantify individual compounds from the mixture. Polymer brush layer bonded to the silica surface is designed as a novel stationary phase to improve the LC resolution and MS compatibility. The polymer thickness can be controlled to shield the analyte from interacting with the active silanol on the surface and reduce peak tailing. The functional group of the polymer can be changed to tune the selectivity in different separation modes. </p><p> </p><p>Two projects on LC/MS method development for biomolecule characterization using polymer-shell column are discussed in this work. In the first project, a polymer-shell column is used for disulfide bonds and free thiol subspecies identification, which is a major type of structural heterogeneities in IgG1. Compared with commercial columns, the polymer-shell column is able to resolve the free thiol variants without the presence of trifluoroacetic acid and greatly improve the MS signal. In the second project, a polymer-shell column is used for characterizing the drug-loading profile for antibody-drug-conjugates (ADC) via online LC/MS. The separation employs a mobile phase of 50 mM ammonium acetate to keep the ADC intact, and a gradient of water/isopropanol for ADC elution. MS data show that all ADC species remained intact and native on the column. Positional isomers can be separated and identified with the new method as well. Furthermore, to understand the surface chemistry and protein separation behavior quantitatively, a chromatographic simulation study is performed. The result shows that protein separation in RPLC can be described by a bi-Langmuir adsorption isotherm with mixed-mode retention of strong and weak sites. Smaller fractions and lower equilibrium constant of the strong site, which is the active silanol, give less tailing for protein separation.</p>

This dissertation contains the following sections. Chapter 1 contains a detailed description of the theory of thin layer chromatography (TLC). Chapter 2 describes the benefits and practical considerations of elevated temperatures in liquid chromatography (LC). The porous graphitic carbon (PGC) I modified as part of my work is often used in elevated temperature LC. Chapter 3 shows a thermodynamic analysis of chromatographic retention at elevated temperature, and Chapter 4 contains a closer look at the van 't Hoff equation in LC and how it can be used in retention modeling. In Chapter 5, I describe a new procedure for microfabricating TLC plates that avoids the volume/feature distortions that occurred in our first microfabrication. The primary advance of this work was the priming of the carbon nanotube (CNT) forests with chemical vapor deposition (CVD) carbon and atomic layer deposition (ALD) alumina, which permitted effective ALD-like deposition of SiO2. Chapter 6 describes advancements in the microfabrication process of TLC, which excluded the use of the CVD carbon and Al2O3 coating as described in Chapter 5. The use of ozone, to lightly oxidize the CNT surface, primed the material for direct ALD deposition. Chapter 7 gives a detailed surface analysis of the microfabrication process up to and including the CNT forest. It was noticed that a channeling effect was present during Rutherford backscattering analysis of the CNTs. Additionally, characterization of CNTs using time-of-flight secondary ion mass spectrometry in the negative ion mode showed an odd-even effect for a homologous series of carbon, where the even moieties had a stronger signal. Chapter 8 describes the functionalization of PGC with di-tert-amyl peroxide (DTAP) and its effect on increasing the chromatographic performance as seen by a reduction in the tailing factors of test analytes. Chapter 9 -- 13 are detailed X-ray photoelectron analyses of the thin films and CNTs used in producing microfabricated TLC plates.

My work has focused on a variety of different types of diamond-based, core-shell particles. These particles are formed with inert cores and poly(allylamine)/nanodiamond shells. Their intended purpose is to form an LC stationary phase that is stable from pH 1 – 14 and at elevated temperatures. At the beginning of my studies, the particles that had been made in the Linford laboratory were pH stable, but irregular and had poor mechanical stability. Since that time, I have worked to improve the particles by using more spherical zirconia and carbon cores, and I have improved their mechanical stability via chemical crosslinking with epoxides. I have performed van Deemter and van’t Hoff analyses to understand the properties of these columns. Efficiencies greater than 100,000 N/m are routinely achieved with these carbon/nanodiamond-based phases. In addition I contributed to two patents that show innovations in diamond functionalization. My contributions involved reduction of an oxidized diamond surface with LiAlH4 prior to functionalization with isocyanates. I also wrote some application notes for the Flare mixed-mode column, which was recently introduced to the market and contains particles comprised of a carbon core and a polymer/nanodiamond shell. These application notes show the gradient separations of four essential oils (lavender, melaleuca, peppermint and eucalyptus), and the isocratic separations of various triazine herbicides and a mixture of β2-agonists and amphetamines.This dissertation contains the following sections. Chapter 1 is a review of liquid chromatographic history and theory. It also includes a history of the use of diamonds in liquid chromatography. Chapter 2 is a study on a glassy carbon core - polymer/nanodiamond shell particle made in our laboratory. Stability studies at pH 11.3 and 13 were performed and different analytes were retained and/or separated on the column. Chapter 3 is a study performed on the Flare mixed-mode column. Separations of tricyclic antidepressants, β2-andrenergic receptor agonists, and linear chain alkylbenzenes were demonstrated with this phase. Van Deemter and van’t Hoff studies were also performed to probe the efficiency and selectivity of this column with different classes of analytes. Chapter 4 chronicles, via SEM and van Deemter analysis, the improvements that have taken place in our column after many iterations of improved synthetic methods and new materials. These include better particle uniformity, particle stability, and column efficiency. Three different carbon cores were analyzed, each better than the previous one. Appendices 1 – 6 are application notes published by Diamond Analytics of β2-andrenergic receptor agonists and amphetamines, triazine herbicides, and lavender, melaleuca, eucalyptus and peppermint essential oils. Appendices 7 and 8 are patents that contain ideas and research contributed by the author.