Physical Sciences and Mathematics Commons^™

High Resolution Mass Spectrometry As A Platform For The Analysis Of Polyoxometalates, Their Solution Phase Dynamics, And Their Biological Interactions., Daniel T. Favre

Doctoral Dissertations

Polyoxometalates (POMs) are a class of inorganic molecule of increasing interest to the inorganic, bioinorganic and catalytic communities among many others. While their prevalence in research has increased, tools and methodologies for the analysis of their fundamental characteristics still need further development. Decavanadate (V10) specifically has been postulated to have several unique properties that have not been confirmed independently. Mass spectrometry (MS) and its ability to determine the composition of solution phase species by both mass and charge is uniquely well suited to the analysis of POMs. In this work we utilized high-resolution mass spectrometry to characterize V10 in aqueous …

Protein Stability In Solution And In The Gas Phase., Yousef Haidar

Electronic Thesis and Dissertation Repository

Electrospray Ionization mass spectrometry (ESI-MS) is widely used for probing proteins, yet many aspects of this technique remain elusive. Using MS, ion mobility spectrometry (IMS), and circular dichroism (CD) spectroscopy, this thesis sheds light on the stability differences of proteins in the gas phase and solution. After a general introduction (Chapter 1), Chapter 2 scrutinizes some aspects of native ESI. Our data highlight the significance of cone voltage in maintaining a native-like fold and show the advantage of using NH₄Ac in protein experiments. Chapter 3 focuses on hydrogen/deuterium exchange (HDX)-MS. Several studies have reported that D₂O …

Analytical Techniques For The Analysis Of Uranium Bearing Materials, Nathaniel D. Fletcher

Doctoral Dissertations

The interest in the use of nuclear power has increased drastically in recent years. This is due to significantly increased efficiency at producing energy when compared to fossil fuels. With the increased use of nuclear power comes an increased need to for monitor for uranium bearing materials outside of regulatory control. This dissertation covers four projects aimed at improving the analysis of these materials. The first projects aims to develop a method that allows for the analysis of elements that exist in nature as anions by triple quadrupole ICP – MS. This would allow for the ability to measure more …

Collision-Induced Dissociation And Ion Mobility Mass Spectrometry Of Au30(S-Tbu)18 Nanoclusters, Christopher Hood

Honors Theses

Collision Induced Dissociation (CID) and Ion Mobility Mass Spectrometry (IM-MS) are methods used to understand the structural arrangement and stability of large molecules. In this study, the gold nanocluster Au₃₀(S-tBu)₁₈ was dissociated at varying Trap collision energies, and drift time vs mass spectrometry data was plotted to determine the order of cluster fragmentation. Comparing Au₃₀(S-tBu)₁₈ data to that of Au₂₅(SCH₂CH₂Ph)₁₈, the only current nanocluster published with IM-MS data, two distinctly different dissociation patterns were seen. Unlike the linear CID fragmentation of Au …

Studies Toward Provenance Determination For Indigo Dyes, Erin Kibby

Undergraduate Honors Thesis Projects

Species of indigo-producing plants have been used to color textiles for thousands of years all over the globe. Natural indigo-producing species have historically been harvested in regions of Asia, North Africa, and North and South America. This study is an exploration of methods that can be used to determine the provenance (origin) of the indigo dye in a textile through the extraction and isolation of indigoids, flavonoids, and other compounds from the natural dyestuff. There is no accepted method of extracting flavonoids from indigo-dyed textiles specifically, and there is little investigation of the regionally different species. If a method is …

Deciphering Protein Higher-Order Structure And Interactions Via Diethylpyrocarbonate Labeling-Mass Spectrometry, Xiao Pan

Doctoral Dissertations

The study of protein higher-order structures is vital because it is closely related to the investigation of protein folding, aggregation, interaction and protein therapeutics. Consequently, numerous biochemical and biophysical tools have been developed to study protein higher-order structures in many different situations. The combination of covalent labeling (CL) and mass spectrometry (MS) has emerged as a powerful tool for studying protein structures and offers many advantages over other traditional techniques, such as better structural coverage, high throughput, high sensitivity, and the ability to study proteins in mixtures. This dissertation focuses on diethylpyrocarbonate (DEPC) as an effective CL reagent that can …

Mass Spectrometric Analysis Of Lignin Model Compounds: Fundamental Investigations Of Ionization And Supramolecular Interactions For Lignocellulosic Biomass Applications, Kimberly Dean

Theses and Dissertations--Chemistry

Lignocellulosic biomass is pivotal for the development of renewable energy sources and materials essential to mitigate the exploitation of fossil fuels causing climate change and environmental pollution issues. The conversion of biomass into fuel requires the hydrolysis of cellulose and a biproduct of this process is the isolation of millions of tons of lignin as biorefinery waste. Lignin is a complex high molecular weight polymer whose structure remains undefined and critically limits potential industrial applications of lignocellulosic biomass. The advancement of analytical methods for structural elucidation of lignin and its ensemble of phenolic compounds is therefore essential to advance this …

Application Of Mass Spectrometry For Characterization Of Plant-Based Phenolics And Alkaloids, Masoumeh Dorrani

Theses and Dissertations--Chemistry

Plant-derived compounds have the potential to produce value-added compounds with a variety of applications. For example, the lignin part of the lignocellulosic biomass, produced in large quantities as waste from the paper and pulp industries, is a rich source of phenolics with potential applications in the renewable energy sector, pharmaceutical, and chemical industries. On the other hand, plant alkaloids are the primary source for developing plant-derived therapeutics. Unfortunately, the recalcitrant nature of plant cell walls, low extraction yields of small secondary metabolites, and the lack of effective analytical methods for a rapid and accurate identification of plant-based compounds and plant’s …

Computational Approaches For The Multimodal Imaging Of Nanomaterials And Their Biochemical Effects, Laura J. Castellanos

Doctoral Dissertations

Nanomaterial delivery systems constitute a group of drug delivery vehicles that have been used extensively in biodelivery. The proper characterization of the therapeutic function of these nanomaterials requires analytical methods to track the presence of the cargo and its biochemical effects. In some cases, the detection of the cargo and biochemical changes are not attainable in the same experiment, and more than one technique might be needed for the proper analysis of the drug delivery system. In this case, separate analysis of adjacent tissue sections is performed by techniques that offer complementary information such as MALDI-MS and LA-ICP-MS. However, the …

Amyloidogenesis Of Β-2-Microglobulin Studied By Mass Spectrometry And Covalent Labeling, Blaise G. Arden

Doctoral Dissertations

Amyloid-forming proteins are implicated in a number of debilitating diseases. While many amyloid-forming proteins are well studied, the early stages of amyloidosis are still not well understood on a molecular level. Covalent labeling, combined with mass spectrometry (CL-MS), is uniquely well suited to provide molecular-level insight into the factors governing the early stages of amyloidosis. This dissertation leverages CL-MS techniques to examine the early stages of β-2-microglobulin (β2m) amyloidosis. β2m is the protein that forms amyloids in the condition known as dialysis-related amyloidosis. An automated CL-MS technique that uses dimethyl(2-hydroxy-5-nitrobenzyl) sulfonium bromide as a labeling reagent was developed and used …

Comparison Of Supported Liquid Extraction And Solid Phase Extraction Of Methamphetamine From Urine And Method Validation By Gas Chromatography-Mass Spectrometry, Taylor Hood

Master's Theses

Applications of SLE (supported liquid extraction) is a relatively new extraction technique that is not widely used in forensic toxicology. SLE is also easier and less time consuming than traditional LLE (liquid-liquid extraction) and SPE (Solid phase extraction). This work will compare the extraction efficiencies between SLE and SPE for methamphetamine from urine with detection and quantitation using GC-MS (gas chromatography- mass spectrometry). The SLE cartridges provide better analyte recoveries, eliminate emulsion formation, and allow for shorter processing time than other extraction techniques. The SPE cartridges used have a mixed-mode non-polar/strong cation exchange retention mechanism to extract basic analytes like …

Development Of Vibrating Sharp-Edge Spray Ionization (Vssi) Methods For Mass Spectrometry Analysis And Imaging, Nandhini Ranganathan

Graduate Theses, Dissertations, and Problem Reports

Mass Spectrometry (MS) is one of the widely used tools for chemical detection down to attomole concentrations for certain proteins. Ionization sources are a critical component for MS analysis. One of the major ionization methods is electrospray ionization (ESI), which remains a gold standard for proteins and peptides. ESI uses voltages up to ~4 kV to produce ions from solubilized molecules. Recently, a novel ionization method termed vibrating sharp-edge spray ionization (VSSI) that nebulizes liquids efficiently at the edge of a vibrating glass slide has been reported. The work in this thesis leverages the capabilities of VSSI for continuous flow-based …

Determination Of Molecular Markers Of Vaccinium Berry Standard Reference Materials Through Differential Analysis With Ultrahigh Resolution Lc/Ms, Abby Mikolitis

Dissertations, Master's Theses and Master's Reports

Blueberries and cranberries have vastly different flavor profiles despite both being a part of the Vaccinium genus. Their high content of phenolics makes them subjects of interest in preventative medicine, especially research in illnesses such as heart disease and cancer. Analysis has primarily focused on the identification and characterization of polyphenols, primarily anthocyanins which are a subclass of polyphenols, with ultra-high performance liquid chromatography coupled with electrospray ionization high resolution mass spectrometry (UHPLC-ES/HRMS). This study aims to develop a novel method of non-targeted UHPLC-ES/MS analysis with post processing and formula assignment performed with MZmine 2.53 and MFAssignR software tools. Pairing …

Mass Spectrometry Method Development For The Discovery And Characterization Of Secondary Metabolites, Zachary Kelley

Theses and Dissertations--Chemistry

Secondary metabolites are organic compounds produced by an organism for reasons other than growth and development. In plants, secondary metabolites generally act as defense agents produced to deter predators and inhibit other competitive species. For humans, these compounds can often have a beneficial effect and are pursued and utilized as natural pharmaceuticals. The development of sensitive, high-throughput analytical screening methods for plant derived metabolites is crucial for natural pharmaceutical product discovery and plant metabolomic profiling. Here, metabolomic profiling methods were developed using a microfluidic capillary zone electrophoresis device and evaluated against traditional separation approaches. An alkaloid screening assay was constructed …

Lcms-Based Analysis Explains The Basis Of Oxidative Resistance In Selenium-Containing Thioredoxin Reductase, Daniel Haupt

Graduate College Dissertations and Theses

Selenocysteine (Sec) is referred to as the 21st proteogenic amino acid and is found in place of the redox-sensitive amino acid cysteine (Cys) in a small number of proteins. Sec and Cys carry out similar chemistry and are structural isomers save for a single atom difference; the former contains selenium (Se), while the latter contains sulfur (S) in the identical position. Sec poses a high bioenergetic cost for its synthesis and subsequent incorporation into protein not shared by Cys. Since Sec’s discovery in 1976, scientists have debated why certain proteins express Sec while others express Cys. In recent years, it …

Functionalized Materials From Atom Transfer Radical Processes, Sean Fischer

Electronic Theses and Dissertations

This work is focused on the synthesis, characterization, and application of functionalized materials prepared from atom transfer radical processes. Atom transfer radical processes encompass both atom transfer radical addition (ATRA) and polymerization (ATRP) reactions, both of which are catalyzed by ppm amounts of copper complexes. The synthetic efforts of ATRA include increasing adduct selectivity through optimization of reaction conditions to generate small molecules in high to moderate yields. ATRA provides retention of the halogen moiety, which is an attractive functional group that can be further modified with other transformations. Specifically, the copper-catalyzed azide-alkyne [3+2] cycloaddition (CuAAC) allows for the realization …

Development And Application Of Mass Spectrometry-Based Approaches For Protein Higher Order Structure Analysis And Protein-Protein Interaction Characterization, Mengru Zhang

Arts & Sciences Electronic Theses and Dissertations

Proteins, one of the most fundamental biomolecules, adopt unique higher order structures (HOS) to enable diverse biological functions. Deciphering protein HOS is crucial to gain deeper insights of their working mechanisms and to develop biotherapeutics. Mass spectrometry (MS)-based approaches evolved rapidly in the past 30 years and are now playing critical roles in protein HOS characterization. One of those approaches is MS-based footprinting whose principle is to map the solvent accessible surface area (SASA) to deliver structural information. Protein footprinting can be achieved by reversible labeling, e.g., hydrogen-deuterium exchange (HDX), and by irreversible labeling using radical-based reagents or other targeted …

Structural Analysis Of Protein Therapeutics Using Covalent Labeling – Mass Spectrometry, Patanachai Limpikirati

Doctoral Dissertations

Using mass spectrometry (MS) to obtain information about a higher order structure of protein requires that a protein’s structural properties are encoded into the mass of that protein. Covalent labeling (CL) with reagents that can irreversibly modify solvent accessible amino acid side chains is an effective way to encode structural information into the mass of a protein, as this information can be read-out in a straightforward manner using standard MS-based proteomics techniques. The differential reactivity of proteins under two or more conditions can be used to distinguish protein topologies, conformations, and/or binding sites. CL-MS methods have been effectively used for …

Intrinsic Buffer Hydroxyl Radical Dosimetry For Hydroxyl Radical Protein Footprinting, Addison Roush

Honors Theses

Hydroxyl radical protein footprinting (HRPF) coupled to mass spectrometry is a powerful technique for the analysis of protein topography as it generates covalent mass labels that can survive downstream sample handling, and it is sensitive to the solvent accessibility of amino acid sidechains. Of the multiple platforms for HRPF, fast photochemical oxidation of proteins (FPOP) utilizes a pulsed 248 nm KrF excimer laser to label proteins by photolyzing hydrogen peroxide. FPOP is the most widely used HRPF platform because it labels proteins faster than unfolding can occur. Variations in FPOP sample conditions make it difficult to compare results between experiments …

Analysis Of Oxidatively Damaged Proteins By Mass Spectrometry, Vincent Saullo

Electronic Thesis and Dissertation Repository

As humans age, exposure to oxidative stress may induce protein degradation or aggregation; both resulting in loss of protein function. Protein oxidative damage remains a dominant pathology in many common ailments. To combat these pathologies, scientists must understand the nature of oxidative modifications and their effects on protein structure and dynamics. This work employs a range of mass spectrometry (MS) methods to characterize and analyze the effects of oxidative damage on the model protein myoglobin (Mb). Mb was oxidized using tert-butyl hydroperoxide, and the resulting modifications were characterized by top-down and bottom-up MS workflows. Hydrogen/deuterium exchange MS indicated elevated structural …

Covalent Labeling-Mass Spectrometry For Characterizing Protein-Ligand Complexes, Tianying Liu

Doctoral Dissertations

This dissertation focuses on applying covalent labeling (CL) and mass spectrometry (MS) for characterizing protein-ligand complexes. Understanding protein-ligand interactions has both fundamental and applied significance. Covalent labeling is a protein surface modification technique that selectively modifies solvent-exposed amino acid side chains of proteins. A covalent bond is formed between the functional groups of labeling reagent and protein’s side chain. One of the key factors that affects CL reactivity is a side chain’s solvent accessibility. Ligand binding protects residues on the protein surface from being labeled, and residues involved in ligand binding can be indicated via decreases in labeling extents. The …

Development Of Methods For The Removal Of Selected Pollutants From Several Matrices And Identification Of Unknown Pollutants Adsorbed Onto Plastics Collected From Freshwater, Kathryn Marie Renyer

Dissertations

Plastic pollution represents one of greatest anthropogenic threats to the environment. Five to ten billion tons of plastic are manufactured every year. Currently, Earth's ecosystem is contaminated with billions of tons of plastic debris, much of which cannot be recycled. Over time, this plastic debris decomposes into small particles. Small plastic particles are known to adsorb toxic compounds in marine environments. My research is concerned with creating novel methods for the detection and quantification of selected persistent organic pollutants from several media. Specifically, I developed methods for the detection and quantification of endosulfan sulfate (ESS) from Lumbricus terrestris tissue and …

Bottom-Up Lignomics: Towards The Development Of Adduct Electrospray Ionization Mass Spectrometric Methods To Characterize And Sequence Lignin Oligomers, Shardrack O. Asare

Theses and Dissertations--Chemistry

Lignin, the second most abundant naturally occurring polymer found in plant cell wall has the potential of becoming an alternative source for the production of chemical synthons for the pharmaceuticals and other chemical industries. While much gain has been made towards the development of degradation methods to break down lignin, effective analytical methods are still required to rapidly and accurately identify the products of lignin breakdown experiments. The goal of this work was to develop mass spectrometric methods for the characterization of lignin oligomers based on the study of model lignin compounds.

Unlike peptides and oligosaccharides, lignin model compounds that …

Extreme Molecular Diversity In Biomass Burning Atmospheric Organic Aerosol Observed Through Ultrahigh Resolution Mass Spectrometry, Matthew Brege

Dissertations, Master's Theses and Master's Reports

Ambient atmospheric aerosol is ubiquitous in the atmosphere, originating from a variety of natural and man-made sources. These microscopic particles have profound impacts on the global climate system as well as human health. The organic fraction of atmospheric aerosol is an extremely complex mixture which is not yet fully characterized. These unknown organic aerosol species contribute to the uncertainty in the effect of aerosol on climate and uncertainty in overall ambient aerosol toxicity. Light absorbing organic aerosol can interact with incoming solar radiation and contribute to atmospheric heating; however, the source apportionment and overall fate of these absorbing organic aerosol …

Multidimensional Mass Spectrometry Of Chemonic™ Ccg-6 Nonionic Surfactant With Separation By Polarity And Shape, Charles Johnson

Williams Honors College, Honors Research Projects

Chemonic™ CCG-6 surfactant is a water-soluble poly(ethylene glycol) (PEG) conjugated alkyl glyceride emollient. This surfactant exists as a complex mixture of a glycerol cores conjugated with poly(ethylene glycol) branches (PEGylation) that were partially esterified with caprylic (C8) and capric (C10) acids. These may be esterified on one, two, or all three arms of the glyceride. The architecture of the structures in this mixture was studied using multidimensional mass spectrometry (MS). Mass spectrometry was interfaced with ultra-performance liquid chromatography (UPLC) and ion mobility (IM) separation. The mixture was separated by reversed-phase LC, oligomers of the star-branched polymer were separated according to …

Novel Mass Spectrometric Approaches For Deciphering The Epitranscriptomic Code, William D. Mcintyre

Legacy Theses & Dissertations (2009 - 2024)

According to the results of the Human Genome Project, less than 5% of our genome consists of sequences that code for actual proteins. At the same time, however, ~90% of these non-coding sequences are transcribed into a myriad of classes of ribonucleic acids collectively known as ncRNAs, which have been recognized as essential regulatory factors. It has been recently shown that the activity of ncRNAs can be in turn modulated by post-transcriptional modifications (PTMs), covalent marks that can be established/removed by tightly regulated enzymatic pathways. Now, the race is on to understand the new set of controls of cellular functions …

Roaming Transition States And Highly Accurate Thermochemistry: A Pepico Study Of Two Small Combustion Systems, Kyle John Covert

University of the Pacific Theses and Dissertations

Two small combustion systems, methyl hydroperoxide (CH₃OOH) and 2-propanol ((CH₃)₂CHOH), were studied using imaging photoelectron photoion coincidence spectroscopy (iPEPICO), which combines photoelectron spectroscopy and photoionization mass spectrometry to detect coincident photoelectron-photoion pairs. In the photon energy range of 11.4–14.0 eV, energy selected CH₃OOH⁺ ions dissociate into CH₂OOH⁺, HCO⁺, CH₃⁺, and H₃O⁺ ions. The lowest-energy dissociation channel is the formation of the cation of the smallest “QOOH” radical, CH₂OOH⁺. A statistical rate model fitted to the …

Investigation Of Thiol-Containing Biomarkers And Their Role In The Exposome, Tracy Gastineau-Stevens

Theses and Dissertations--Chemistry

Exposomics is an emerging area of study that looks at how the environment around a person or persons affects their overall health. Biomarkers have emerged as useful tools to better understand how the exposome affects a person. In this work, we investigate two potential endogenous biomarkers, homocysteine and glutathione that have been previously implicated in a number of diseases that have been linked to environmental causes. We also investigated an environmental exposure, the fungicide Ziram, which epidemiologically has been linked to diseases. In our investigation, we utilized capillary electrophoresis and capillary electrophoresis-mass spectrometry to develop a method for homocysteine and …

Investigating Non-Targeted Screening And Accurate Quantitation Of Trace Surface Water Contaminants Using High-Resolution Mass Spectrometry, Lucas M. Morrison

Electronic Thesis and Dissertation Repository

The human impact on surface water is a growing concern and the chemical surveying of contaminants including pharmaceuticals and pesticides is currently lacking. Neonicotinoids in particular, are among the most widely used insecticides that have prompted environmental concern and require monitoring. Chemical contaminants in environmental water samples are commonly analyzed by targeted tandem mass spectrometry. However, this requires a prior knowledge of the contaminants in the area of interest. Here, surface water samples were screened by utilizing optimized data-independent acquisition (DIA) methods and the spectra were databased for future retrospective analysis. This circumvents the requirement for target analytes prior to …

Novel Mass Spectrometry Methods For The Analysis Of Covalent And Non-Covalent Protein Structures And Their Influence On The Functions Of Therapeutic Proteins, Jake Pawlowski

Doctoral Dissertations

Biotherapeutics consist of biopolymers (proteins, polysaccharides, DNA, and RNA) that are used to treat a wide range of conditions from cancer to autoimmune disease to enzyme replacement. In recent years biotherapeutics have experience tremendous growth due to advances in technology and our understanding of human biology. They are very important to modern medicine due to their ability to treat diseases which are unable to be treated with small molecule-based drugs. Unlike small molecule drugs which are synthetically produced, biotherapeutics are expressed inside cells. Produced biotherapeutics are not made up of a single homogenous population but instead a population of highly …