Surface structure, chemical composition, bonding configuration, film polarity, and electronic properties of InN layers grown by high pressure chemical vapor deposition (HPCVD) have been investigated. Sputtering at an angle of 50-70 degrees followed by atomic hydrogen cleaning (AHC) was successful in removing the carbon contaminants. AHC is found to be the most effective cleaning process to remove oxygen contaminants from InN layers in an ultrahigh vacuum (UHV) system and produced a well ordered surface. Auger electron spectroscopy (AES) confirmed the cleanliness of the surface, and low energy electron diffraction (LEED) yielded a 1×1 hexagonal pattern demonstrating a well-ordered surface. High resolution electron energy loss spectra (HREELS) taken from the InN layers exhibited loss features at 550 cm-1, 870 cm-1 and 3260 cm-1 which were assigned to Fuchs-Kliewer phonon, N-H bending, and N-H stretching vibrations, respectively. Assignments were confirmed by observation of isotopic shifts following atomic deuterium dosing. No In-H species were observed indicating N-termination of the surface and N-polarity of the film. Broad conduction band plasmon excitations were observed centered at 3100 cm-1 to 4200 cm-1 in HREEL spectra acquired with 25 eV electrons, for a variety of samples grown with different conditions. Infrared reflectance data shows a consistent result with HREELS for the bulk plasma frequency. The plasmon excitations are shifted about 300 cm-1 higher in HREEL spectra acquired using 7 eV electrons due to the higher plasma frequency and carrier concentration at the surface than in the bulk, demonstrating a surface electron accumulation. Hydrogen completely desorbed from the InN surface upon annealing for 900 s at 425 ºC or upon annealing for 30 s at 500 ºC. Fitting the coverage versus temperature for anneals of either 30 or 900 s indicated that the desorption was best described by second order desorption kinetics with an activation energy and pre-exponential factor of 1.3±0.2 eV and 10-7.3±1.0 cm2/s, respectively. Vibrational spectra acquired from HREEL can be utilized to explain the surface composition, chemical bonding and surface termination, and film polarity of InN layers. The explanation of evidence of surface electron accumulation and extraction of hydrogen desorption kinetic parameters can be performed by utilizing HREEL spectra.

Room-temperature chemisorption of hexacyclic aromatic hydrocarbons on the 2x1, sputtered, oxidized and H-terminated Si(100) surfaces, as well as those upon post treatments of hydrogenation, oxidization and electron irradiation have been investigated by using thermal desorption spectrometry (TDS), Auger electron spectroscopy (AES) and low energy electron diffraction (LEED). This work focuses on the effects of the functional groups (phenyl, methyl, vinyl, heteroatom, and H atom) in the chemisorbed aromatic hydrocarbons (benzene, toluene, xylene isomers, styrene and pyridine) on organic functionalization of the Si(100) surface, particularly on such surface processes as cycloaddition, dative adsorption, hydrogen abstraction, desorption, dissociation, diffusion, and condensation polymerization. Unlike the earlier notion that hydrogen evolution in the hydrocarbon/Si(100) systems is the result of hydrocarbon dissociation (into smaller hydrocarbon fragments and H atoms) on the surface, condensation polymerization of the adsorbed aromatic hydrocarbons is proposed in the present work, in order to explain the higher-temperature hydrogen evolution feature in the toluene/Si(100) system. This hypothesis is supported by our TDS results for other hydrocarbon adsorbates, especially in the pyridine/Si(100) system where electron-induced condensation polymerization has been observed at room temperature. The improved techniques in the TDS experiments developed in the present work have enabled us to observe condensation polymerization and the effect of H on the surface processes (via surface reconstruction) on Si(100) for the first time. New analysis methods have also been developed to determine the adsorption coverage from the AES data, and this work has not only improved the accuracy of the elemental-coverage evaluation, but also provided a means to estimate the rate and the order of chemisorption. By using the density functional theory with the Gaussian 98 program, the adsorption geometries and the corresponding adsorption energies of various adsorption phases have been calculated. These computational results have provided useful insights into the chemisorption structures on the Si(100) surface. The present work also presents the development of three kinetics models for hydrogen evolution in the aforementioned aromatic-hydrocarbon systems on Si(100). Based on a modified collision theory with consideration of diffusion, these theoretical models have proven to be quite successful in simulating the observed TDS profiles and in estimating the kinetic parameters for the analysis of condensation polymerization in 2-dimensional diffusion systems. The present work illustrates that TDS experiments can be used effectively with quantum computation and theoretical kinetics modelling to elucidate the intricate nature of organosilicon surface chemistry.

An investigation of binary fluid heat and mass transfer in ammonia-water absorption was conducted. Experiments were conducted on a horizontal-tube falling-film absorber consisting of four columns of six 9.5 mm (3/8 in) nominal OD, 0.292 m (11.5 in) long tubes, installed in an absorption heat pump. Measurements were recorded at both system and local levels within the absorber for a wide range of operating conditions (nominally, desorber solution outlet concentrations of 5 - 40% for three nominal absorber pressures of 150, 345 and 500 kPa, for solution flow rates of 0.019 - 0.034 kg/s.). Local measurements were supplemented by high-speed, high-resolution visualization of the flow over the tube banks. Using the measurements and observations from videos, heat and mass transfer rates, heat and vapor mass transfer coefficients for each test condition were determined at the component and local levels. For the range of experiments conducted, the overall film heat transfer coefficient varied from 923 to 2857 W/m²-K while the vapor and liquid mass transfer coefficients varied from 0.0026 to 0.25 m/s and from 5.51×10^-6 to 3.31×10^-5 m/s, respectively. Local measurements and insights from the video frames were used to obtain the contributions of falling-film and droplet modes to the total absorption rates. The local heat transfer coefficients varied from 78 to 6116 W/m²-K, while the local vapor and liquid mass transfer coefficients varied from -0.04 to 2.8 m/s and from -3.59×10^-5 (indicating local desorption in some cases) to 8.96×10^-5 m/s, respectively. The heat transfer coefficient was found to increase with solution Reynolds number, while the mass transfer coefficient was found to be primarily determined by the vapor and solution properties. Based on the observed trends, correlations were developed to predict heat and mass transfer coefficients valid for the range of experimental conditions tested. These correlations can be used to design horizontal tube falling-film absorbers for ammonia-water absorption systems.

The incidence of breast cancer became the most common female cancer, and the fourth cause of female cancer death. In this study, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/MS) have been combined with multivariate statistics to investigate breast cancer tissues and cell lines. Core needle biopsy and fine needle aspiration (FNA) are techniques largely applied in the diagnosis of breast cancer. In this study, we have established an efficient protocol for detecting breast tissue and FNA samples with MALDI-TOF/MS. With the help of statistical analysis software, we can find the lipid-derived ion signals which can be use to distinguish breast cancer tumor tissues from non-tumor parts. This strategy can differentiate normal and tumor tissue, which is potential to apply in clinical diagnoses. The analysis of breast cancer tissue is challenging as the complexity of the tissue sample. Direct tissue analyses by matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) allows us to investigate the molecular structure and their distribution while maintaining the integrity of the tissue and avoiding the loss of signals from extraction steps. Combined MALDI-IMS with statistic software, tissues can be analyzed and classified based on their molecular content which is helpful to distinguish tumor regions from non-tumor regions of breast cancer tissue. Our result shows the differences in the distribution and content of lipids between tumor and non-tumor tissue which can be supplements of current pathological analysis in tumor margins. In this study, MALDI-TOF/MS combined with multivariate statistics were used to rapidly differentiate breast cancer cell lines with different estrogen receptor (ER) and human epidermal growth factor receptor 2 (HER2) status. The protocol for efficiently detecting peptides and proteins in breast cancer cells with MALDI-TOF/MS was established, two multivariate statistics including principle component analysis (PCA) and hierarchical clustering analysis were used to process the obtaining MALDI mass spectra of six different breast cancer cell lines and one normal breast cell lines. Based on the difference of the peptide and protein profiles, breast cancer cell lines with same ER and HER-2 status were grouped in nearby region on the PCA score plot. The results of hierarchical cluster analysis also revealed high conformity between breast cancer cell protein profiles and respective hormone receptor types.

Ambient mass spectrometry (MS) is a new and growing sub-field in MS which has opened new research avenues, particularly for applications relating to the analysis of solid samples. Results on the implementation and application of ambient MS techniques including: desorption electrospray ionization (DESI) and direct analysis in real time (DART) indicated that these techniques could serve as complementary tools for the rapid qualitative screening of pharmaceuticals, allowing up to two orders of magnitude improvement in throughput compared to traditional methods such as liquid chromatography MS. The selectivity of DESI could be enhanced by performing the experiment in the reactive mode. In this mode, complexation reactions between reagents added to the spray solvent and analytes on the sample surface resulted in analyte stabilization, inhibiting fragmentation. They also resulted in a concomitant enhancement in the analyte surface activity, facilitating their evaporation from secondary droplets culminating in an improvement in sensitivity. Also for drug tablets analysis, the analyte signal dependency on DESI geometrical set-up variables could be mitigated following the careful and controlled addition of an isotopically labeled internal standard (IS) to the sample or by spraying samples with a pair of reagents with different affinities for the analyte. Either of these approaches resulted in an analyte-to-IS signal ratio (in the former) or an analyte complex ratio (in the later), which was largely independent of DESI experimental variables allowing quantitative analysis using this technique. DESI MS was also observed to be a very powerful tool for determining the 2-D distribution of various pharmaceutically important compounds on tablet and tissue surfaces. The ability to map the distribution of molecules of interest by DESI MS has very great implications in drug tablet quality control and in determining the role of chemical signals presented on tissue surfaces. DESI was observed to be limited to ionizing molecules of medium to high polarities without much limitation in terms of mass range, whereas DART was better suited for the analysis of molecules within a broader range of polarities, but within a more limited mass range (up to 800 Da approximately). These limitations were circumvented by implementing a novel multimode ambient ion source, desorption electrospray/metastable-induced ionization (DEMI), which combines various aspects of DESI and DART. Initial experiments with the DEMI ion source demonstrated its ability to enable the simultaneous analysis of molecules within a broader range of polarities and masses than DESI and DART alone.

Elucidation of the primary structure of peptides and proteins de novo by mass spectrometry (MS) has become possible with the advent of tandem MS methods. The most widely used chemical method due to Edman (Edman & Begg, 1967) has shortcomings with regard to N- terminal blocked peptides, cyclic peptides and posttranslational modifications, for example phosphorylation (Metzger, 1994). However, mass spectrometric sequencing methods are increasingly becoming applicable for a variety of peptides and proteins, including N- and C- termini modified peptides and cyclic peptides (Jegorov et al., 2003; Sabareesh & Balaram, 2006; Sabareesh et al., 2007). Further, conventional and tandem mass spectrometry have proven useful in the detection of post-translational modifications (Hansson et al., 2004; Nair et al., 2006; Mandal et al., 2007). This thesis details mass spectrometric sequencing of acyclic and cyclic peptides, involving tandem MS methods carried out using both electrospray ionization (ESI) ion trap (Esquire 3000 plus, Bruker Daltonics) and matrix assisted laser desorption and ionization time-of-flight/time-of-flight (MALDI TOF/TOF) (Ultraflex TOF/TOF, Bruker Daltonics) instruments. The peptides are either chemically synthesized or isolated from diverse natural sources. Synthetically designed peptides possessing modified N- and C- termini and peptaibols from the soil fungus Trichoderma constitute the acyclic peptides. The cyclic peptides include backbone cyclized depsipeptides from the fungus Isaria and disulfide bonded peptides from the venom of marine cone snails. Chapter 1 gives an account of various concepts of mass spectrometry, tandem mass spectrometry and peptide fragmentation chemistry, providing necessary background information for the following chapters. Chapter 2 describes the fragmentation studies of [M + H]+ and [M + Na]+ adducts of six neutral peptides with blocked N- and C- termini investigated using an electrospray ion trap mass spectrometer. The N- terminus of these synthetically designed peptides is blocked with a tertiarybutyloxycarbonyl (Boc) group and the C- terminus is esterified. These peptides do not possess sidechains that are capable of complexation and hence the backbone amide units are the sole sites of protonation and metallation. The cleavage pattern of protonated adducts is strikingly different from that of sodium adducts. While the loss of the N- terminal blocking group happens quite readily in the case of MS/MS of [M + Na]+, the cleavage of C- terminal methoxy group seems to be a facile process in the case of MS/MS of [M + H]+. Fragmentation of the protonated adducts yields only bn ions, while yn and an type ions are predominantly formed from the fragmentation of sodium adducts. The an ions arising from the fragmentation of [M + Na]+ lack the N-terminal Boc group (termed as an*). MS/MS of [M + Na]+ species also yields bn ions of substantial lower intensities, that lack the N- terminal Boc group (bn*). Comparison of the fragmentation of [M + H]+ with [M + Na]+ of the peptides chosen in this study reveal that the combined use of both protonated and sodium adducts should prove useful in de novo sequencing of peptides that possess modified N- and C- termini, particularly naturally occurring neutral peptides, for example, peptaibols. Chapter 3 describes about the ESI-MS/MS investigation of an HPLC fraction from the soil fungus Trichoderma, which aided in identification of microheterogeneous trichotoxin peptaibols in that fraction. Dramatic differences were noted between the fragmentation spectra of [M + H]+ and [M + Na]+ species. While b-type ions were noted from the former, the latter yielded a-, b-and y- type ions (the same feature was noted in the cases presented in the previous chapter). Inspection of the isotope pattern of b-ions yielded from the dissociation of H+ species, clearly revealed the presence of three microheterogeneous trichotoxin sequences; two isobars (1718 Da), each possessing one Glu residue and another completely neutral peptide (1717 Da). The microheterogeneity is due to Gly ↔ Ala, Iva ↔ Aib and Gln ↔ Glu replacements and exchanges (Iva: DIva: R-Isovaline; Aib: α-aminoisobutyric acid). The MS/MS of [M + Na]+ adduct predominantly yielded product ions from the neutral peptaibol. Further, the fragmentation patterns of H+ and Na+ adducts of two N-acetyl peptide esters were found to be very similar to that of the neutral peptaibol component. The results presented in this chapter establish that under the electrospray ion trap conditions, the fragmentation patterns of the H+ and Na+ adducts of model peptides that possess modified N- (Boc and acetyl) and C- termini are indeed very similar to that of the neutral trichotoxin. Chapter 4 delineates the applicability of liquid chromatography coupled to conventional and tandem electrospray ionization mass spectrometry (LC-ESI-MS, LC-ESI-MS/MS, LC-ESI-MS3) for the screening of novel cyclic hexadepsipeptide metabolites directly from the crude hyphal extract of the fungus Isaria. The fungal strain was grown on a solid medium (potato carrot agar), which yields aerial hyphae growing erect from the basal mycelial colony (Ravindra et al., 2004). A total of ten microheterogeneous components were identified to belong to the isariin class of cyclodepsipeptides from the LC-ESI-MS and LC-ESI-MS/MS analysis of the crude hyphal extract. Out of ten, six are determined to be new and the remaining four are previously reported isariins A-D. The primary structures of isariins A-D were from the fungi Isaria cretacea and Isaria felina (Vining & Taber 1962; Deffieux et al., 1981) and the fungal strain used in this study resembles Isaria felina (Sabareesh et al., 2007). Isariins are backbone cyclized hexadepsipeptides composed of a D-β-hydroxy acid possessing a hydrocarbon sidechain and five α-amino acids; one of the α-amino acids is a D-amino acid (Vining & Taber 1962; Deffieux et al., 1981). The detection of fragment ions due to loss of CO concomitant with the loss of H2O from the protonated precursor ion ([M + H]+) ascertained the cyclic depsipeptide nature of both the known and the new components. The fragmentation behavior of the [M + H]+ of known isariins facilitated sequence determination of the new components. Therefore, the configuration of the amino acids and the β-hydroxy acid of the new components is assumed to be same as that of the reported peptides. The microheterogeneity of the ten sequences is due to changes in the D-β-hydroxy acid (residue 1) and the adjoining α-amino acid (residue 6), whose carbonyl is linked to the hydroxyl function by an ester linkage. The number of methylene units ((-CH2)n) in the hydrocarbon sidechain of the residue 1 differs between 2 and 8 and the variability of the residue 6 is limited to Ala/Val. The ester oxygen atom was chosen as the preferable site of protonation causing ring-opening, based on the observed distribution of the fragment ions. Chapter 5 demonstrates the utility of the LC-ESI-MS and LC-ESI-MS/MS methods in the identification and characterization of six microheterogeneous backbone cyclized hexadepsipeptides, isaridins, directly from the crude hyphal extract of the fungus Isaria. Among the six components, four were found to be novel. The other two peptides, isaridins A and B were identified earlier from this laboratory (Ravindra et al., 2004). The isaridins are characterized by the presence of unusual amino acids such as N-methylated residues, β-methylproline (β-MePro) and hydroxyleucine (HyLeu) (Ravindra et al., 2004). The cyclic nature of both the known and the new peptides were confirmed from the observation of peaks due to loss of CO and H2O from the protonated precursor ion ([M + H]+). However, unlike isariins (Chapter 4), the intensity of the peak corresponding to [M + H - H2O]+ was noted to be of very low intensity, in the case of isaridins. Detection of product ion peak due to [M + H - CO2]+ suggests an additional dissociation pathway involving cleavage at the depsipeptide linkage and is supportive of the cyclic depsipeptide nature (Eckart, 1994). The sequencing of the newly detected components was enabled by understanding the fragmentation mechanism of the known isaridins. The tertiary amide nitrogens of the N-methylated residues were regarded as the preferable sites of protonation leading to ring-opening, as noted from the fragmentation spectra. The microheterogeneity in the sequences was identified using the diagnostic product ions obtained from the protonated precursor of the known isaridins. The microheterogeneity can be attributed to the variations of two residues; Pro ↔ β-MePro and N-MePhe ↔ N-MeLxx (Lxx: Leu, Ile, alloIle). The recently reported ‘isarfelins’ from the fungus Isaria felina (Guo et al., 2005) were reassigned as ‘isaridins’. The reassignment was based on very similar fragmentation profiles observed for the [M + Na]+ adduct of isaridins and isarfelins; further, the fungal strain used in this study resembles Isaria felina (Sabareesh et al., 2007). Chapter 6 presents mass spectrometric sequencing of disulfide bonded peptides from marine cone snails (conopeptides), using the MALDI LIFT MS/MS method. Lo959, a single disulfide bonded octapeptide isolated from Conus loroisii, was identified to belong to the class of contryphans (Sabareesh et al., 2006). Contryphans are small single disulfide bonded conopeptides, whose length is in the range of 7-11 residues and are rich in tryptophan. A significant feature of the contryphans is the presence of conserved DTrp (DW) at the 3rd residue within the disulfide loop (Sabareesh et al., 2006). Lo959 displays an unusual behavior under reverse phase chromatographic conditions, typical of the DW containing contryphans (Jacobsen et al., 1998). It undergoes slow conformational interconversion on the chromatographic time scale exhibiting two distinct peaks. The presence of DW at the 4th position in Lo959 was established by comparing the chromatographic profiles of natural peptide with that of two chemically synthesized peptides, one containing LW (4) and another possessing DW (4). De novo sequencing of the two peptides Ar1446 and Ar1430 from Conus araneosus established that they belonged to M-superfamily of conotoxins, in particular m-2 branch. M-superfamily conotoxins are three-disulfide bonded peptides characterized by the consensus cysteine framework, CC…C…C…CC (Corpuz et al., 2005). Ar1446 and Ar1430 are fourteen residue long peptides, each possessing three disulfide bonds. The peptides have the cysteine scaffold typical of the M-superfamily, as shown above. Specifically, the peptides belong to m-2 branch of M-superfamily, where the fourth and fifth cysteines are separated by two residues (Corpuz et al., 2005). The sequences of the peptides were derived following chemical and enzymatic modifications. The carboxamidomethylation reaction established the presence of three disulfide bonds. Indeed, the sequences were deduced from the MALDI LIFT MS/MS of [M + H]+ of the tryptic peptides. The sequences of the two peptides are almost identical and they differ only at residue 12; hydroxyproline in Ar1446, proline in Ar1430.

Gegenstand vorliegender Arbeit ist die Untersuchung unterschiedlicher Modellansätze zur Beschreibung der Extraktion organischer Schadstoffe aus Böden unter Verwendung von überkritischem Wasser. Dazu wurden in der Literatur vorhandene Stofftransportmodelle herangezogen und eigene Modellansätze entwickelt. Das Modell berücksichtigt die Geschwindigkeits- und Temperaturverteilung im Reaktor und berechnet daraus, in Abhängigkeit der desorptiven, diffusiven und konvektiven Stofftransportvorgänge eine Schadstoffverteilung. Zur Lösung der Modellgleichungen wurde FEMLAB 3.1 verwendet. Zur Parameterbestimmung und Modellüberprüfung wurden Extraktionsversuche an real kontaminierten Böden und an künstlich kontaminierten Modellböden durchgeführt. Einfache und komplexe chemische Gleichgewichte der organischen Schadstoffe wurden auf Basis der Gibbs Energetik mit FACTSAGE 5.2 ermittelt und dienten als weitere Inputparameter für die Modellberechnungen.

The main objective of this dissertation is to quantify petrophysical properties of conventional and unconventional reservoirs using a mechanistic approach. Unconventional transport mechanisms are described from the pore to the reservoir scale to examine their effects on macroscopic petrophysical properties in hydrocarbon-bearing organic shale. Petrophysical properties at the pore level are quantified with a new finite-difference method. A geometrical approximation is invoked to describe the interstitial space of grid-based images of porous media. Subsequently, a generalized Laplace equation is derived and solved numerically to calculate fluid pressure and velocity distributions in the interstitial space. The resulting macroscopic permeability values are within 6% of results obtained with the Lattice-Boltzmann method after performing grid refinements. The finite-difference method is on average six times faster than the Lattice-Boltzmann method. In the next step, slip flow and Knudsen diffusion are added to the pore-scale method to take into account unconventional flow mechanisms in hydrocarbon-bearing shale. The effect of these mechanisms is appraised with a pore-scale image of Eagle Ford shale as well as with several grain packs. It is shown that neglecting slip flow in samples with pore-throat sizes in the nanometer range could result in errors as high as 2000% when estimating permeability in unconventional reservoirs. A new fluid percolation model is proposed for hydrocarbon-bearing shale. Electrical conductivity is quantified in the presence of kerogen, clay, hydrocarbon, water, and the Stern-diffuse layer in grain packs as well as in the Eagle Ford shale pore-scale image. The pore-scale model enables a critical study of the [delta]LogR evaluation method commonly used with gas-bearing shale to assess kerogen concentration. A parallel conductor model is introduced based on Archie's equation for water conductivity in pores and a parallel conductive path for the Stern-diffuse layer. Additionally, a non-destructive core analysis method is proposed for estimating input parameters of the parallel conductor model in shale formations. A modified reservoir model of single-phase, compressible fluid is also developed to take into account the following unconventional transport mechanisms: (a) slip flow and Knudsen diffusion enhancement in apparent permeability, (b) Langmuir desorption as a source of gas generation at kerogen surfaces, and (c) the diffusion mechanism in kerogen as a gas supply to adsorbed layers. The model includes an iterative verification method of surface mass balance to ensure real-time desorption-adsorption equilibrium with gas production. Gas desorption from kerogen surfaces and gas diffusion in kerogen are the main mechanisms responsible for higher-than-expected production velocities commonly observed in shale-gas reservoirs. Slip flow and Knudsen diffusion marginally enhance production rates by increasing permeability during production. / text

Sowohl in der Klinischen Labormedizin, der Klinischen Mikrobiologie als auch in der Pathologie ist die Massenspektrometrie (MS) ein bedeutender Bestandteil der Diagnostik geworden. Der Fortschritt in der Gerätetechnik ermöglicht in kurzer Zeit viele, hochaufgelöste Spektren zu generieren. Diese Informationsvielfalt macht die manuelle Auswertung durch den Anwender sehr kompliziert bis unmöglich. Aus diesem Grund ist die Unterstützung durch bioinformatische Programme notwendig. Für die Reproduzierbarkeit der Ergebnisse und die Qualitätskontrolle ist es essentiell, dass die verwendeten Algorithmen transparent und die Programme als Open Source Software (OSS) frei verfügbar sind (Aebersold and Mann, 2003). Das Ziel dieser Arbeit war die Entwicklung von MALDIquant, einer unter der GNU General Public License (GPL) stehenden, flexiblen OSS, die für die o.g. Anwendungsbereiche modernste Algorithmen für die komplette Analyse bietet und in der freien Programmiersprache R (R Core Team, 2014) geschrieben ist. Im Zusammenspiel mit dem dazugehörigen Paket MALDIquantForeign ist MALDIquant in der Lage die üblichen Dateiformate der verschiedenen MS-Geräte zu verarbeiten. Dadurch ist MALDIquant hersteller- und geräteunabhängig und eignet sich nicht nur für MALDI/TOF, sondern für alle zweidimensionalen MS-Daten. Angefangen vom Datenimport über die Prozessierung bis hin zur Analyse der Spektren bietet MALDIquant eine komplette Analyse-Pipeline und implementiert state-of-the-art Methoden. Neben weit verbreiteten Verfahren zur Baseline Correction und Peak Detection zeichnet sich MALDIquant besonders durch ein hervorragendes Peak Alignment aus. Dieses ist sehr genau und aufgrund des Fokus auf die Peaks schneller als die meisten anderen Verfahren und weitestgehend unabhängig von der Qualität der Intensitätenkalibrierung. Eine weitere Stärke von MALDIquant ist die Möglichkeit, eigene Algorithmen zu integrieren, sowie den Ablauf der Analyse den individuellen Bedürfnissen anzupassen. In der beispielhaften Analyse der Daten von Fiedler et al. (2009) konnten durch MALDIquant Peaks gefunden werden, die Patienten mit Pankreaskarzinom von nicht erkrankten Probanden unterscheiden. Einige dieser Peaks wurden bereits in anderen Publikationen beschrieben. Neben diesem Beispiel hat MALDIquant seine Nützlichkeit bereits in verschiedenen Anwendungsbereichen und Publikationen bewiesen, wie etwa in Ouedraogo et al. (2013) oder Jung et al. (2014).

This dissertation has investigated the adsorption, thermal behavior, and radiation (both photon and electron) processing of prebiotically-relevant ices and surfaces. A custom ultra-high vacuum (UHV) chamber has been built that is coupled with a Fourier Transform-Infrared (FT IR) spectrometer and a Temperature Programmed Desorption (TPD) system that utilizes Quadrupole Mass Spectrometry (QMS) to study selected organic:surface systems. Formamide (HCONH₂) has been studied in two related but distinct studies relevant to primitive Earth and interstellar chemistry. First, in collaboration with a theory group, formamide’s interaction with kaolinite (Al6Si6O36H30), a clay mineral relevant to early Earth chemistry, has been studied experimentally and theoretically. Experimental infrared results are compared with calculated infrared frequencies obtained by our collaborators. TPD analysis is compared with the calculated values of adsorption energy, and the optimal kaolinite termination site for adsorption is reported. Second, the first thermal and radiation damage study of pure formamide and HCONH₂:H₂O mixed ices on an interstellar icy grain analog (SiO₂) is reported. A discussion of the pure formamide ice phases identified with FT-IR upon warm-up, as well as the TPD binding energies of HCONH₂ on SiO₂, is presented. The observed Lyman-alpha photochemical products and proposed formation mechanisms from pure formamide ice is reported and discussed. In addition, results of Lyman alpha processing of mixed HCONH₂:H₂O ices are provided. Low-energy electron irradiation of pure HCONH₂ and HCONH₂:H₂O mixed ices has also been reported for the first time. A third investigation has studied acetylene (C₂D₂) and acetonitrile (CH₃CN) interactions and radiation stability in mixed low-temperature ices to simulate possible prebiotic reactions that may occur on Saturn’s moon, Titan. This investigation contributes to understanding the possible consumption, trapping, and degradation of these species on the surface of Titan.