Physical Sciences and Mathematics Commons^™

Novel Applications Of Mass Spectrometry For Quantitation And Reaction Mechanism Elucidation, Pengyi Zhao

Dissertations

Mass spectrometry (MS) has been growing as one of the most widely used tools in the field of analytical chemistry. Various applications have been developed to harness the high sensitivity and specificity of mass spectrometric analysis. In this dissertation, two major challenges are addressed. By developing mass spectrometric-based methods, absolute quantitation of proteins/peptides have been achieved. Elucidation of various reaction mechanisms are also enabled. These are the focuses of this dissertation.

In Chapters 2 to 4, a novel quantitation method is developed, titled as coulometric mass spectrometry (CMS). The strength of this method is that no reference standard or isotope-labeled …

Instrumentation And Application Of Image-Charge Detection Of Electrospray-Charged Microparticles And Microdroplets, Jiuzhi Gao

Theses and Dissertations

Image-charge detection is emerging as an important tool to analyze heavy and heterogeneous samples because of its unique advantages in measuring highly charged microparticles. Conventional image-charge detection instruments include at least three fundamental components: an ionization source, an aerodynamic particle delivery system, and an image-charge detector. Here I report research efforts that investigated the mechanisms of image-charge detection and proposed some instrumental developments of these components to suit specific research purposes. In Chapter 2, I report an investigation of the electrospray ionization (ESI) mechanism based on an observation that a certain portion of charged particles generated with an ESI source …

Effects Of Oxidative Modifications On The Structure And Non-Canonical Functions Of Cytochrome C Studied By Mass Spectrometry, Victor Yin

Electronic Thesis and Dissertation Repository

The peroxidase activity of the mitochondrial protein cytochrome c (cyt c) plays a critical role in triggering programmed cell death, or apoptosis. However, the native structure of cyt c should render this activity impossible due to the lack of open iron coordination sites at its heme cofactor. Despite its key biological importance, the molecular mechanisms underlying this structure-function mismatch remain enigmatic. The work detailed in this dissertation fills this knowledge gap by using mass spectrometry (MS) to decipher the central role that protein oxidative modifications and their associated structural changes play in activating the peroxidase function of cyt c …

Analysis Of Secondary Metabolites Biosynthesized By Pathogenic And Symbiotic Fungi Using High-Resolution Tandem Lc-Ms And Spectral Molecular Networking, Natasha Desrochers

Electronic Thesis and Dissertation Repository

Fungi from Canadian crops affect many aspects of agriculture. For example, ginseng root rot caused by Ilyonectria spp. is a major issue for farmers. Ilyonectria spp. make few reported natural products and it is not known if those products are unique to virulent species. PCA and molecular networking were applied to HRMS data to establish a distinct metabolomic profile of root rot pathogens, characterized by antifungal resorcyclic acid lactones (RALs). These likely protect Ilyonectria from other soil pathogens, which gives it the opportunity to infect ginseng root.

Molecular networking was also applied to fungal endophytes from fruit crops to identify …

Structural Characterization Of Biomolecules Using Tandem Non- Linear And Linear Ion Mobility, Action Spectroscopy, Mass Spectrometry And Molecular Dynamics, Jacob Edward Porter

FIU Electronic Theses and Dissertations

The following thesis comprises the use of novel gas-phase spectroscopic and spectrometric techniques complemented with molecular dynamics for the structural characterization of biomolecules: from small model systems to large proteins. In particular, complementary linear and non-linear ion mobility, mass spectrometry and action spectroscopy has been applied to the separation and characterization of native and kinetic intermediate states of biomolecular ions. This suite of tools, comprising ion mobility in tandem with non-ergodic fragmentation and action spectroscopy, provided unique information on the conformational space, folding and binding dynamics of single stranded DNA, peptides, peptide-cofactor and protein systems. Theoretical modeling provided candidate structures …

A Critical Review Of The 15N2 Tracer Method To Measure Diazotrophic Production In Pelagic Ecosystems, Angelicque E. White, Julie Granger, Corday Seldon, Mary R. Gradoville, Lindsey Potts, Annie Bourbonnais, Robinson W. Fulweiler, Angela N. Knapp, Wiebke Mohr, Pia H. Moisander, Craig R. Tobias, Mathieu Caffin, Samuel T. Wilson, Mar Benavides, Sophie Bonnet, Margaret R. Mulholland, Bonnie X. Chang

OES Faculty Publications

Dinitrogen (N₂) fixation is an important source of biologically reactive nitrogen (N) to the global ocean. The magnitude of this flux, however, remains uncertain, in part because N₂ fixation rates have been estimated following divergent protocols and because associated levels of uncertainty are seldom reported—confounding comparison and extrapolation of rate measurements. A growing number of reports of relatively low but potentially significant rates of N₂ fixation in regions such as oxygen minimum zones, the mesopelagic water column of the tropical and subtropical oceans, and polar waters further highlights the need for standardized methodological protocols for measurements …

From Neutral Aniline To Aniline Trication: A Computational And Experimental Study, G. L. Gutsev, H. A. López Peña, S. L. Mcpherson, Derrick Ampadu Boateng, B. R. Ramachandran, L. G. Gutsev, Katharine M. Tibbetts

Chemistry Publications

We report density functional theory computations and photoionization mass spectrometry measurements of aniline and its positively charged ions. The geometrical structures and properties of the neutral, singly, doubly, and triply positively charged aniline are computed using density functional theory with the generalized gradient approximation. At each charge, there are multiple isomers closely spaced in total energy. Whereas the lowest energy states of both neutral and cation have the same topology C₆H₅–NH₂, the dication and trication have the C₅NH₅–CH₂ topology with the nitrogen atom in the meta and para positions, …

Dissociation Of Singly And Multiply Charged Nitromethane Cations: Femtosecond Laser Mass Spectrometry And Theoretical Modeling, G. L. Gutsev, S. L. Mcpherson, Hugo A. López Peña, Derrick Ampadu Boateng, L. G. Gutsev, B. R. Ramachandran, Katharine M. Tibbetts

Chemistry Publications

Dissociation pathways of singly- and multiply charged gas-phase nitromethane cations were investigated with strong-field laser photoionization mass spectrometry and density functional theory computations. There are multiple isomers of the singly charged nitromethane radical cation, several of which can be accessed by rearrangement of the parent CH3–NO2 structure with low energy barriers. While direct cleavage of the C–N bond from the parent nitromethane cation produces NO2+ and CH3+, rearrangement prior to dissociation accounts for fragmentation products including NO+, CH2OH+, and CH2NO+. Extensive Coulomb explosion in fragment ions observed at high laser intensity indicates that rapid dissociation of multiply charged nitromethane cations …

Investigation Of The Chemical Composition Of Plasma-Treated Water By Midiplexc And Its Antimicrobial Effect On L. Monocytogenes And Pseudomonas Fluorescens Monospecies Suspension Cultures, Oliver Handorf, Harald Below, Uta Schnabel, Katharina Riedel

Articles

Plasma -generated compounds conceived by microwave -induced plasma (MidiPLexc) were physicochemically investigated in their molecular compositions. Therefore, plasma -treated water (PTW) was generated by treatment with the MidiPLexc within a 1 l glass bottle for a pre -treatment time of 100 s, 300 s and 900 s. The PTW was further investigated in its composition of reactive oxygen/nitrogen species. For this purpose, the hydrogen peroxide (H2O2) concentration of the PTW was determined electrochemically using chronoamperometry, and the anionic components were determined using ion chromatography. As a result, H2O2 concentrations of up to 720 mg l−1 , nitrite concentrations of 1600 …

Abiotic Formation Of Dissolved Organic Sulfur In Anoxic Sediments Of Santa Barbara Basin, Hussain A. Abdulla, David J. Burdige, Tomoko Komada

OES Faculty Publications

Sulfurization has been found to enhance organic matter preservation and petroleum formation in marine sediments. However, we do not yet have a comprehensive understanding of sulfurization mechanisms. In this study, we investigated several possible mechanisms of dissolved organic sulfur (DOS) formation in the top 4.5 m of anoxic sediments of Santa Barbara Basin (SBB), California Borderland. Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS), we identified chemical formulas of potential dissolved organic matter (DOM) precursors to these DOS compounds. We also examined how the formulas of abiotically formed DOS changed as a function of depth across a major redox …

Genetic And Biochemical Characterization Of Ergot Alkaloid Synthesizing Fungi And Their Symbionts, Matthew Duane Maust

Graduate Theses, Dissertations, and Problem Reports

Ergot alkaloids are fungal tryptophan derived toxins which affect mammalian circulation and neurotransmission. These compounds are biosynthesized by a conserved genetic pathway, known as the ergot alkaloid synthesis (EAS) pathway by fungi belonging to the ascomycete families Trichocomaceae and Clavicipitaceae. Several Ipomoea species and related plants in the morning glory family harbor vertically transmitted symbiotic fungi in the genus Periglandula, also members of Clavicipitaceae, that produce ergot alkaloids. Metabolomic analysis of seeds identified a previously uncharacterized glycoside form of the pharmaceutically important ergot alkaloid, ergonovine. Several species belonging to the fungal genus Metarhizium have recently been shown to have the …

Protein/Peptide Characterization Using Mass Spectrometry And Molecular Dynamics Simulations, Ahmad Kiani Karanji

Graduate Theses, Dissertations, and Problem Reports

Mass spectrometry (MS) based-techniques and molecular dynamics (MD) simulations have been used to characterize protein/peptide structure as well as their interactions with lipid vesicles and detergents. Chapter 1 introduces an introduction to the concepts and tools that were used in this work. In Chapter 2, the dominant gas-phase conformer of [M+3H]3+ ions of the model peptide Acetyl-PSSSSKSSSSKSSSSKSSSSK are examined with ion mobility spectrometry (IMS), gas-phase hydrogen deuterium exchange (HDX), and mass spectrometry (MS) techniques. This section furthers the development of a protein structural prediction tool by providing information about gas-phase ion conformers of two model peptides having different solution conformational …

“Notame”: Workflow For Non-Targeted Lc-Ms Metabolic Profiling, Anton Klåvus, Marietta Kokla, Stefania Noerman, Ville M. Koistinen, Marjo Tuomainen, Iman Zarei, Topi Meuronen, Merja R. Häkkinen, Soile Rummukainen, Ambrin Farizah Babu, Taisa Sallinen, Olli Karkkainen, Jussi Paananen, David Broadhurst, Carl Brunius, Kati Hanhineva, Hanhineva

Research outputs 2014 to 2021

Metabolomics analysis generates vast arrays of data, necessitating comprehensive workflows involving expertise in analytics, biochemistry and bioinformatics in order to provide coherent and high-quality data that enable discovery of robust and biologically significant metabolic findings. In this protocol article, we introduce notame, an analytical workflow for non-targeted metabolic profiling approaches, utilizing liquid chromatography-mass spectrometry analysis. We provide an overview of lab protocols and statistical methods that we commonly practice for the analysis of nutritional metabolomics data. The paper is divided into three main sections: the first and second sections introducing the background and the study designs available for metabolomics research …

Development And Implementation Of A Novel Voltage-Free Interface For Capillary Electrophoresis-Mass Spectrometry Separations Of Proteins, Courtney J. Kristoff

Graduate Theses, Dissertations, and Problem Reports

Capillary electrophoresis-mass spectrometry is a powerful technique for high-throughput and high efficiency separations combined with structural identification. Electrospray ionization is the primary interface used to couple capillary electrophoresis to mass analyzers; however, improved designs continue to be reported. A new interfacing method based on vibrating sharp-edge spray ionization is presented in this work to overcome the challenges of decoupling applied voltages and to enhance the compatibility with separations performed at near-neutral pH. The versatility and ease of use of this ionization source is demonstrated using β-blockers, peptides, and proteins. The cationic β-blocker pindolol was injected electrokinetically and detected at concentrations …