Physical Sciences and Mathematics Commons^™

Development And Application Of Mass Spectrometry-Based Protein Footprinting In Structural Proteomics, Ming Cheng

Arts & Sciences Electronic Theses and Dissertations

Integral mass spectrometry (MS) has emerged as an important tool for protein structural characterization. It readouts are a broad range of structural information, including stoichiometry, interactions, conformations and conformation change, and dynamics. Protein footprinting is a pivotal component in the intergral MS toolkit.My dissertation centers around the development and application of protein footprinting to characterize protein structure. It is divided into seven chapters.Chapter 1 serves as the introduction for integral mass spectrometry in structural proteomic.In Chapter 2, we extended the fast-photochemical oxidation of proteins (FPOP) platform by adding the trifluoromethyl radical (•CF3) as a new reagent. We discovered that •CF3 …

Design, Synthesis, And Self-Assembly Of Supramolecular Fractals Based On Terpyridine With Different Transition Metal Ions, Lei Wang

USF Tampa Graduate Theses and Dissertations

Fractals have existed in a variety of natural forms, and the concept of "fractal geometry" has been developed in many areas by humankind, including art, economics, mathematics, physics, chemistry, material science, and etc. In the field of chemistry, researchers have endeavored great efforts to express the concept using molecules either by theoretical prediction or using synthetic methods in the past few decades, and one successful example is the “Sierpiński triangle”. Challenge still remains to achieve other fractal geometries as well as high generation of fractals with precisely controlled shape and size. Coordination-driven self-assembly has witnessed a wide array of well-defined …

Comprehensive Analysis Of Synthetic Cannabinoids And Metabolites In Oral Fluid By Liquid Chromatography Triple Quadrupole Mass Spectrometry, Carmen T. Mulet

FIU Electronic Theses and Dissertations

According to NIDA, synthetic cannabinoids (SC) include man-made, mind-altering chemicals. Their typically rapid metabolism and instability in biological matrices requires fast analytical methods for detection and confirmation; therefore, the use of oral fluid (OF) matrix is advantageous because collection is fast and non-invasive. The use of liquid chromatography triple quadrupole mass spectrometry (LC-QqQ-MS) and online solid phase extraction (SPE) for sample pretreatment minimizes bias and facilitates low level detection.

This study demonstrates the first use of online SPE for sample pretreatment in the comprehensive analysis of 100 SC and metabolites in OF by LC-QqQ-MS. The method was validated according the …

Investigating The Rotary Mechanism Of Atp Synthase Using Molecular Dynamics Simulations, Angela Marcela Murcia Rios

Electronic Thesis and Dissertation Repository

F₁-ATPase is a motor protein that can use ATP hydrolysis to drive rotation of the central subunit. The γ C-terminal helix constitutes of the rotor tip that is seated in an apical bearing formed by the α₃β₃ head. It remains uncertain to what extent the γ conformation during rotation differs from that seen in rigid crystal structures. Existing models assume that the entire γ subunit participates in every rotation. Here we develop a molecular dynamics (MD) strategy to model the off-axis forces acting on γ in F₁-ATPase. MD runs showed stalling of the …

Interrogation Of Ion-Neutral Complexes By Trapped Ion Mobility-Mass Spectrometry And Theoretical Calculations, Alan A. Mckenzie Coe

FIU Electronic Theses and Dissertations

In the present study, the fundamentals of molecular ion trapping and the application of trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) to the separation and identification of molecular components in complex mixtures are shown. In particular, ion-neutral complexes lifetimes, relative stability, binding energies and candidate structures are described for common explosives during TIMS-MS, as well as the effect of the micro-environment, during complex sample analysis. A novel TIMS-MS workflow was developed for the detection of both inorganic residues (IGSR; inorganic gunshot residues) and organic residues (OGSR) of firearm discharge residue from skin swabs, capable of high specificity 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 …

I3: Isomerization Of Isomer Ions, Krisztián Gabor Torma

University of the Pacific Theses and Dissertations

Photoelectron Photoion Coincidence (PEPICO) spectroscopy is a robust tool for elucidating complex unimolecular dissociation mechanisms and for determining thermochemical and kinetic data of gas-phase ion dissociations with high accuracy. In this work, the dissociative photoionization of two sets of isomeric systems were analyzed with PEPICO: 1) C7H7+ ions of toluene (Tol) and 1,3,5-cycloheptatriene (CHT), and 2) two butyl alcohol isomers, 1-butanol and isobutanol. Threshold dissociative photoionization data on these four molecules of interest were collected on the imaging PEPICO apparatus at the VUV beamline of the Swiss Light Source. Data analysis was aided by ab initio calculations and Rice-Ramsperger-Kassel-Marcus (RRKM) …

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 …