Chemistry Commons^™

Characterization Of Noncovalent Complexes Of Polyelectrolytes By Mass Spectrometry, Anthony J. Marino

Williams Honors College, Honors Research Projects

Various ions of poly-L-lysine and polystyrene sulfonic acid were successfully observed first within a matrix-assisted laser desorption/ionization mass spectrometer and subsequently in an electrospray ionization mass spectrometer. The successful ionization of these polymers allowed for studies to be performed on the noncovalent interactions between the two. Noncovalent interactions were effectively studied on both instruments, but further quantified using tandem mass spectrometry found within the MALDI system and ion-mobility mass spectrometry found within the electrospray ionization system. As a result of employing the use of ion-mobility, various different stoichiometries and charges of polyelectrolyte complexes could be distinguished.

Enzyme, Cosolvent, And Substrate Interactions In Ple Hydrolysis Reactions And Evaluation Of The Stability Of An Unnatural Glutathione Analogue, Maureen Elizabeth Smith

Dissertations

Prochiral diester malonates have been hydrolyzed in the presence of Pig Liver Esterase (PLE). Several of the diesters produced the respective half-ester in moderate to high enantioselectivity. A series of cosolvent assays were performed to evaluate the ability of the cosolvent to influence the enantioselective outcome of the hydrolysis reactions. Ethanol produced the largest changes in enantioselectivity of all solvents evaluated. The isoenzymes of PLE were also evaluated and provided very different enantioselective outcomes than that of crude PLE. A series of NMR titrations was performed to explore the interactions between the substrates and ethanol cosolvents.

Improvements to our previously …

Biomarker Discovery Of Liver Diseases Using Mass Spectrometry-Based Metabolomics., Xue Shi

Electronic Theses and Dissertations

Metabolomics has emerged as one of the latest of the "-omics" disciplines that can detect metabolite biomarkers in biological samples. The diverse characteristics of metabolites make the analytical platform challenging in metabolomics. Two bioanalytical platforms were developed in this study to investigate metabolite abundance changes under different biological conditions. We first developed a bioanalytical platform that coupled linear trap quadruple - Fourier transform ion cyclotron mass spectrometer (LTQ-FTICR MS) with direct infusion chip-based nano-electrospray ionization (DI-nESI) and applied it to study polychlorinated biphenyls (PCB) effects on non-alcoholic fatty liver disease (NAFLD). We also employed this platform in conjunction with in …

Development And Applications Of Mass Spectrometric Methods For Phosphorylation Analysis, Hsin-Pin Ho

Dissertations, Theses, and Capstone Projects

Protein phosphorylation modification regulates numerous cellular functions by a reversible and selective control of kinases and phosphatases. To understand the entire dynamic network of phosphorylation requires sensitive and reliable quantification of phosphorylation, measurements that can be achieved by mass spectrometry. In this research, we established efficient MALDI-mass spectrometric methods as strategies for single- or multi-site phosphorylation quantification without the use of isotopes, chromatography and calibration curves. The methods were assessed by analyzing peptide standards with different single-multiple phosphorylation sites, showing a wide dynamic range, good accuracy and reproducibility. This is the first label-free MALDI method without using a calibration methodology …

Bioinformatic Solutions To Complex Problems In Mass Spectrometry Based Analysis Of Biomolecules, Ryan M. Taylor

Theses and Dissertations

Biological research has benefitted greatly from the advent of omic methods. For many biomolecules, mass spectrometry (MS) methods are most widely employed due to the sensitivity which allows low quantities of sample and the speed which allows analysis of complex samples. Improvements in instrument and sample preparation techniques create opportunities for large scale experimentation. The complexity and volume of data produced by modern MS-omic instrumentation challenges biological interpretation, while the complexity of the instrumentation, sample noise, and complexity of data analysis present difficulties in maintaining and ensuring data quality, validity, and relevance. We present a corpus of tools which improves …

Fundamental Studies Of Protein Ionization For Improved Analysis By Electrospray Ionization Mass Spectrometry And Related Methods, Kevin A. Douglass

Dissertations

Mass spectrometry (MS) is an analytical technique in which a sample is converted to gas-phase ions that are subsequently separated and detected. It offers great speed, selectivity, and sensitivity during analysis, characteristics which have enabled it to become a leading method for the study of proteins. The applications of MS for these biologically significant macromolecules range from accurately determining identity and sequence to shedding light on post-translational modifications and protein-molecule interactions. As a first step towards analysis by MS, gas-phase protein ions must be formed. A common method for ionization is electrospray ionization (ESI), where a liquid sample including the …

Ambient Ionization Sources For Mass Spectrometry, Paul Farnsworth

Journal of Undergraduate Research

MEG funding directly supported the efforts of three students in my laboratory during the calendar year 2011. A graduate student, Manan Dhunna, received partial support (approximately one-third of his annual stipend) during the year. His role, in addition to carrying out his own research on ambient ionization sources, was to provide continuity and consistent in-lab supervision for the undergraduates during the times that I could not be present in the lab. Two undergraduates were supported by the grant, Jonathan Wright and Kellie Woodfield. These three students were part of a larger group effort to develop advanced ambient ionization sources for …

An Ethnobotanical, Ecological And Lc-Ms-Based Chemometric Investigation Of Phaleria Nisidai, A Traditional Adaptogen Containing Diterpene Esters From Palau, Micronesia, Daniel Kulakowski

Dissertations, Theses, and Capstone Projects

An ethnobotanical, ecological and LC-MS-based chemometric investigation of Phaleria nisidai, a traditional adaptogen containing diterpene esters from Palau, Micronesia

Palau is a country with a rich heritage of traditional medicine still being practiced. One of the most popular and respected remedies in Palau is a tea made from fresh leaves of Phaleria nisidai Kaneh. (Thymelaeaceae). Interviews conducted to determine the use of this plant revealed that it is employed non-specifically to treat a variety of general health concerns. Its use as a prophylactic to keep away sickness, as a 'system cleaner', as well as for strength and energy indicate …

Investigation Into The Cellular Actions Of Carnosine And C-Peptide, Emma H. Gardner

Theses, Dissertations and Capstones

Carnosine is a dipeptide composed of beta-alanine and histidine found exclusively in long-lived animal tissues. The cellular action of carnosine is still under extensive investigation; however, it has been proposed to have a role as an anti-oxidant and oxygen free radical scavenger, a physiological buffer, a heavy metal chelator, and has been implicated as an anti-aging agent.^2,4 Our lab has been studying the interaction between carnosine and heme by analyzing both the effect carnosine has on the glycation of the heme containing protein cytochrome c and the interaction of carnosine with free hemin. We have observed that the addition …

Exploring The Asymmetric Environment Of Various Chiral Catalysts Using A Modified Ion-Trap Mass Spectrometer: Towards The Development Of A Rapid Chiral Catalyst Screening Method, Cary M. Davis

Theses and Dissertations

Since the tragedy of the drug Thalidomide® in the late 1950 to early 1960’s, chirality has been recognized as an important aspect that must be controlled in the drug development process in the pharmaceutical industry. Since then, there has been a considerable movement towards single enantiomer drugs. This demand has presented many challenges for the synthetic organic chemist. Chiral catalysts offer one solution to this problem, as they afford the unique ability to preferentially synthesize one enantiomer. Unfortunately, the design of new chiral catalysts is often empirical, with luck and trial and error necessary due to factors that govern enantioselectivity. …

Monitoring Ligand-Induced Nucleic Acid Conformational Changes Using Ion Mobility Spectrometry-Mass Spectrometry, Bill Kenneth Redick

Legacy Theses & Dissertations (2009 - 2024)

Three-dimensional structures of biopolymers frequently dictate the biological role those molecules play. As such, investigation into structure of nucleic acids can provide important information pertaining to how those nucleic acids work. Many nucleic acid species, especially single-stranded RNA, fold into unique structures that allow them to function properly. Metals, and other cationic species, are often bound to the nucleic acid to make folding into the proper structure more favorable by neutralizing the negative charge on the nucleic acid imparted by the phosphate group. This investigation explores tertiary structure of nucleic acids that have been folded in the presence of ligands …

Estimating Hydroxyl Radical Photochemical Formation Rates In Natural Waters During Long-Term Laboratory Irradiation Experiments, Luni Sun, Hongmei Chen, Hussain A. Abdulla, Kenneth Mopper

Chemistry & Biochemistry Faculty Publications

In this study it was observed that, during long-term irradiations (>1 day) of natural waters, the methods for measuring hydroxyl radical (˙OH) formation rates based upon sequentially determined cumulative concentrations of photoproducts from probes significantly underestimate actual ˙OH formation rates. Performing a correction using the photodegradation rates of the probe products improves the ˙OH estimation for short term irradiations (<1 day), but not long term irradiations. Only the ‘instantaneous’ formation rates, which were obtained by adding probes to aliquots at each time point and irradiating these sub-samples for a short time (≤2 h), were found appropriate for accurately estimating ˙OH photochemical formation rates during long-term laboratory irradiation experiments. Our results also showed that in iron- and dissolved organic matter (DOM)-rich water samples, ˙OH appears to be mainly produced from the Fenton reaction initially, but subsequently from other sources possibly from DOM photoreactions. Pathways of ˙OH formation in long-term irradiations in relation to H2O2 and iron concentrations are discussed.

Methods Development In Biological Mass Spectrometry: Application In Glycoproteomics, Sanja Trajkovic

Theses and Dissertations--Chemistry

Proteomics refers to global characterization of the full set of proteins present in a biological sample. Various analytical disciplines contribute to proteomics but mass spectrometry became method of choice for analysis of complex protein samples.

Mass spectrometry allows for high throughput analysis of the proteome but, moreover, it has the ability to acquire higher-order information such as post-translational modifications (PTM). Glycosylation is the most abundant PTM on eukaryotic proteins.

This dissertation will focus on method development for structural proteomics that will be utilized to explain the glycoproteome of obligate intracellular protozoan parasite Toxoplasma gondii as a model system.

Optimization of …

Particle Formation In Ambient Mass Spectrometry, Thabiso Musapelo

LSU Doctoral Dissertations

A particle sizing system was developed that couples a light scattering particle sizer with a differential mobility analyzer for particle detection and elucidation with the capability for measuring particle sizes in the range of 10 nm to 20 μm. The particle sizing system was used to investigate particle formation that is associated with several methods of atmospheric pressure ion formation used in mass spectrometry: atmospheric pressure matrix-assisted laser desorption ionization (MALDI) and inlet ionization. The methods for particle formation were 1) ultraviolet (UV) laser ablation, 2) infrared (IR) laser ablation, and 3) shock-generated particle formation. Particles formed by UV laser …

Development Of A Field-Portable Miniature Mass Spectrometer Designed For In-Situ Analysis And Ion Trap Miniaturization, Paul Isaac Hendricks

Open Access Dissertations

Chemical analysis by mass spectrometry has become the gold standard due to the sensitivity, selectivity, and short analysis times that are afforded by the method. Advances in miniaturized vacuum systems, mass analyzers, electronics, and ionization sources have allowed for the development of field-portable mass spectrometers. The performance of portable instruments has received much attention for their utility in the detection of illicit drugs, explosives, environmental contaminants, therapeutic drugs, and more recently, biological tissues. Furthermore, detection of the aforementioned compounds can be completed at atmospheric pressures and in the presence of complex matrices and sample surfaces when used in conjunction with …

Instrumentation, Applications And Fundamentals Of Plasma Ionization Of Organic Molecules From Surfaces, Joshua Scott Wiley

Open Access Dissertations

Various aspects of the interaction of low-temperature plasma (LTP) ambient ionization with organic molecules and surfaces are discussed. As an application, LTP-MS has been used for the analysis of pesticides directly from fruits and vegetables revealing low parts per billion limits of detection (LODs). Due to low power and gas requirements, a battery-operated and handheld LTP probe was developed for the point-and-shoot MS analyses. Handheld LTP was compared with large-scale LTP on a benchtop and miniature MS revealing similar LODs for both. Long-distance ion transport up to one meter was also demonstrated with flexible tubing for non-proximate sample interrogation. Fundamentals …

Gas-Phase Covalent And Non-Covalent Ion/Ion Chemistry Of Biological Macromolecules, John Robert Stutzman

Open Access Dissertations

Gas-phase ion/ion chemistry involves the interaction of oppositely charged ions inside of the mass spectrometer. During this gas-phase chemistry, particle transfer (i.e., proton and electron) or synthesis can occur at rapid reaction rates. Particle transfer represents a mature area of ion/ion chemistry, while selective covalent modification represents a fairly new area of gas-phase chemistry. Gas-phase covalent chemistry is based on traditional solution phase organic chemistry.

The work demonstrated in this dissertation greatly involves gas-phase covalent and non-covalent Schiff base chemistry on peptide and protein ions. The reagent dianion, 4-formyl 1,3-benzene disulfonic acid, has been used to covalently modify unprotonated primary …

Top-Down Interrogation And Characterization Of Biological Macromolecules, Yang Gao

Open Access Dissertations

Analytical mass spectrometry has been widely applied in the field of biomolecule identification and characterization. It provides fast, accurate and robust information relevant to the molecular mass, composition and structure of the target analytes.

This thesis is focused on the top-down analysis of various macrobiomolecules, nucleic acids and proteins, in the context of ion/ion reaction and gas-phase unimolecular dissociation. The first part of the thesis deals with gas phase fragmentation behavior of chemically modified oligonucleotides. Factors, such as the observation time-scale, the ion type and the energy deposition method, are explored using a quadrupole/time-of-flight mass spectrometer. Novel fragmentation pathway associated …

Structural Analysis Of Carbohydrates By Mass Spectrometry, Chiharu Konda

Open Access Dissertations

Protein glycosylation is a highly frequent post-translational modification. Glycosylation is actively involved in intermolecular and intercellular binding events that are important to a wide range of biological functions such as immunity and fertility. The unique functions of glycans are directly related to their structures. In order to fully characterize the structure of an unknown glycan, 5 levels of structural information is needed: sugar unit identity, anomeric configuration, linkage types, sequence, and branching location. One of the grand challenges limiting the advance of glycosciences is the lack of sensitive tools for detailed glycan structural analysis. Tandem mass spectrometry (MS/MS) is a …

Mass Spectrometric Studies On The Primary Products Of Fast Pyrolysis Of Carbohydrates And The Molecular Structures Of Asphaltenes, And The Development Of A Rastering Probe For Laser-Induced Acoustic Desorption Into An Atmospheric Pressure Chemical Ionization Source, Matthew Robert Hurt

Open Access Dissertations

Mass spectrometry (MS) has proven invaluable in the field of mixture analysis and structural elucidation. Tandem mass spectrometry (MS/MS) utilizing collision-activated dissociation (CAD) has become the technique of choice for structural elucidation of unknown analytes in mixtures. When coupled with gas chromatography (GC) or high performance liquid chromatography (HPLC), it allows for trace level analysis of mixture components. In spite of the utility of mass spectrometry in complex mixture analysis, it does have limitations. Traditional GC/MS methods used for the analysis of fast pyrolysis products cannot be used to analyze the primary products, thus limiting the knowledge that can be …

The Planar Ion Trap, Ivan Miller, Dr. Daniel Austin

Journal of Undergraduate Research

Mass spectrometry has been a common analytical procedure for over fifty years. Today it is most commonly used to characterize and quantify unknown solutions, solids, and vapors in chemical and biochemical environments by determining the specific masses of atoms and molecules. Ion traps have become standard methods in analysis as they have dramatically improved the selectivity and resolution of mass spectrometers. Ion traps use applied voltages to create electrical fields in a small trapping volume. These fields interact with the molecules in the mass analyzer by trapping ionized molecules over a broad mass range. The trapped ions are eventually ejected …

Structural And Functional Study Of The Diheme Cytochrome C Subunit Of The Cytochrome Bc Complex In Heliobacterium Modesticaldum, Hair Yue

Arts & Sciences Graduate Student Theses and Dissertations

This dissertation is focused on the structural and functional study of the unique diheme cytochrome c subunit of the cytochrome bc complex in H. modesticaldum, and its application in determining the stoichiometry between H. modesticaldum's cytochrome bc complex and its reaction center. Heliobacterium modesticaldum is a gram positive, anaerobic, anoxygenic photoheterotrophic bacterium. Its cytochrome bc complex (Rieske/cyt b complex) has some similarities to cytochrome b6f complexes from cyanobacteria and chloroplasts, and also shares some characteristics of typical bacterial cytochrome bc1 complexes. One of the unique features of the heliobacterial cytochrome bc complex is the presence of a diheme cytochrome c …

Analyses Of Multivitamins In Nutraceuticals By Reverse Phase Hplc With Dad, Elsd And Ms, Hsiang-Chi Huang

All Theses

ABSTRACT
Vitamins are essential to human beings and support long-term healthy lifestyle. They exist widely in food, but in small amount. Hence, dietary supplements and fortified food products are more and more popular in the nutritional markets. According to the Infant Formula Act of 1980, the range of each of the nutrients should fall within a specific range or above the required minimum, so there is an increasing interest of accurate measurement of vitamins, particularly the B-group vitamins. However, traditional methods for vitamin B analyses are time-consuming and often in poor accuracy. As a result, rapid and reliable analytical methods …

Optimization Of Sample Preparation In Matrix-Assisted Laser Desorption/Ionization (Maldi) Mass Spectrometry Of Macromolecules, Evgenia Akhmetova

Graduate Theses and Dissertations

New method for the matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) and Fourier transform mass spectrometry (MALDI-FTMS) analysis of low molecular weight polyvinyl acetate (PVAc) was developed and then applied to the characterization of commercially available chewing gum. The optimization of MALDI analysis of PVAc was achieved by investigating the influence of sample preparation variables such as the choice of solvent and choice of matrix-analyte ratio. It was demonstrated that the use of ethyl acetate as a solvent and 2,5-Dihydroxybenzoic acid as a matrix yielded the highest signal intensity for the pure polymer sample. The application of TOF technique did not …

Bacterial Spores Remain Viable After Electrospray Charging And Desolvation, Sara Nielson Pratt

Theses and Dissertations

The electrospray survivability of B. subtilis spores and E. coli was tested in atmospheric mobility experiments. E. coli did not survive electrospray charging and desolvation, but B. subtilis did. Experimental conditions ensured that any surviving bacteria were charged, desolvated, and de-agglomerated. B. subtilis was also found to survive both positive and negative electrospray and subsequent introduction into vacuum conditions. Attempts were made to measure the charge distribution of viable B. subtilis spores using electrostatic deflection. From those experiments, it was found that either the spores do not become highly charged under the electrospray conditions used or only spores in a …

Photoionization Mass Spectrometry And Photoelectron-Photoion Coincidence (Pepico) Spectroscopy Studies Of Select Biofuel Molecules, Joseph G. Czekner

Master's Theses

This thesis is the culmination of numerous experiments, performed on two different continents, investigating the spectroscopic and thermodynamic properties of several biofuels and fuel additives. It will start with an introduction about the motivation behind these experiments. The second chapter will outline the experimental details of the apparatus at the Advanced Light Source (ALS) in Berkeley, CA, followed by the Swiss Light Source (SLS) in Villigen, Switzerland. Third, the theoretical concepts and data analysis methods will be discussed in detail.

Chapter 4 will be the start of the newly obtained data. It presents some photoionization mass spectrometry studies on γ-valerolactone …

Binding Energies And Solvation Of Organic Molecular Ions, Reactions Of Transition Metal Ions With, And Plasma Discharge Ionization Of Molecular Clusters, Isaac Kwame Attah

Theses and Dissertations

In this dissertation, different approaches have been employed to address the quest of understanding the formation and growth mechanisms of carbon-containing molecular ions with relevance to astrochemistry. Ion mobility mass spectrometry and DFT computations were used to investigate how a second nitrogen in the pyrimidine ring will affect the formation of a covalent bond between the benzene radical cation and the neutral pyrimidine molecule, after it was shown that a stable covalent adduct can be formed between benzene radical cation and the neutral pyridine. Evidence for the formation of a more stable covalent adduct between the benzene radical cation and …

A Novel Algorithm For Validating Peptide Identification From A Shotgun Proteomics Search Engine, Ling Jian, Xinnan Niu, Zhonghang Xia, Parimal Samir, Chiranthani Sumanasekera, Zheng Mu, Jennifer L. Jennings, Kristen L. Hoek, Tara Allos, Leigh M. Howard, Kathryn M. Edwards, P. Anthony Weil, Andrew J. Link

Chemistry Faculty Research

Liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) has revolutionized the proteomics analysis of complexes, cells, and tissues. In a typical proteomic analysis, the tandem mass spectra from a LC–MS/MS experiment are assigned to a peptide by a search engine that compares the experimental MS/MS peptide data to theoretical peptide sequences in a protein database. The peptide spectra matches are then used to infer a list of identified proteins in the original sample. However, the search engines often fail to distinguish between correct and incorrect peptides assignments. In this study, we designed and implemented a novel algorithm called De-Noise to …

Monitoring The Health Of Glen Helen Nature Preserve: Fall 2012 Sediment And Water, Audrey E. Mcgowin Ph.D., Triet Minh Truong

Chemistry Student Publications

This poster presents the results for environmental testing in Glen Helen by the Special Topics in Analytical Chemistry course at Wright State University under the direction of Professor Audrey McGowin in Spring 2012. Water quality data are presented for the Yellow Spring in Yellow Springs, Ohio for April and May of 2012. Other test sites range from locations along Yellow Springs Creek to the covered bridge near Little Miami River.

This poster was created by Triet M. Truong.

Development Of Quantitative Bioanalytical Methods For The Pharmacological Studies Of Anti-Cancer Drugs, Ye Feng

ETD Archive

In the anticancer drug discovery and therapy development, it is essential to understand the pharmacological properties of the drugs. Today, pharmaceutical analysis is employed throughout the whole drug discovery and development process. Pharmacokinetic-pharmacodynamic relationships are playing an increasingly important role in decisions on the rational development and use of new drugs and they can provide a detailed knowledge of the mechanism of the drug and a better understanding of the molecular targets on which they act. Due to the significance of pharmacological analysis, sensitive analytical methods are critically needed for pharmacological studies. Therefore, our long-term goal is to provide guidelines …