Physical Sciences and Mathematics Commons^™

Analytical Methods To Support Design And Optimization Of Protein Drug Conjugate: Focusing On Haptoglobin-Hemoglobin Complex As A Drug Carrier, Shengsheng Xu

Doctoral Dissertations

Acquired immunodeficiency syndrome (AIDS) remains one of the most serious public health challenges and a significant cause of mortality for certain populations. Despite the large number of antiretrovirals (mostly nucleotide and nucleoside analogs) developed in the past two decades, the inability of small molecule therapeutics to target HIV reservoirs directly creates a significant obstacle to their effective utilization. Indeed, achieving the desired therapeutic effect in the absence of the effective targeted delivery must rely on dosage escalation, which frequently causes severe toxicity. This problem may be solved by conjugation of antiretroviral agents to endogenous proteins (e.g., hemoglobin haptoglobin complex) that …

Fundamental Studies And Applications Of Ambient Plasma Ionization Sources For Mass Spectrometry, Wade C. Ellis

Theses and Dissertations

The field of ambient desorption/ionization mass spectrometry (ADI-MS) has existed for over a decade. ADI-MS is a technique that offers benefits including fast analysis time, simple ionization sources that are easily constructed, and little to no required sample preparation. The research presented here describes efforts to better understand plasma-based ADI-MS sources and to explore the use of hydrogen-doped plasma gases with these sources. The use of hydrogen-doped argon (H₂/Ar) and hydrogen-doped helium (H₂/He) as plasma gases for a dielectric barrier discharge (DBD) and an AC glow discharge is presented first. When using the DBD, the intensity …

Mapping Analyte-Signal Relations In Lc-Ms Based Untargeted Metabolomics, Nathaniel Guy Mahieu

Arts & Sciences Electronic Theses and Dissertations

The goal of untargeted metabolomics is to profile metabolism by measuring as many metabolites as possible. A major advantage of the untargeted approach is the detection of unexpected or unknown metabolites. These metabolites have chemical structures, metabolic pathways, or cellular functions that have not been previously described. Hence, they represent exciting opportunities to advance our understanding of biology. This beneficial approach, however, also adds considerable complexity to the analysis of metabolomics data - an individual signal cannot be readily identified as a unique metabolite. As such, a major challenge faced by the untargeted metabolomic workflow is extracting the analyte content …

Desorption Electrospray Ionization (Desi) Mass Spectrometric Imaging Of Spatially Regulated In Vivo Metabolic Rates, Charlotte Reininger Lewis

Theses and Dissertations

Desorption electrospray ionization (DESI) is an ambient ionization technique used for mass spectrometric imaging of biological samples. When coupled with isotopic ratio measurements of deuterium-labeled tissues, DESI provides a means of measuring metabolic rates on a spatially resolved basis. In vivo metabolic rates are desired to better understand diseases such as Alzheimer's, Parkinson's, Huntington's, and various forms of cancer that negatively impact metabolic rates within different organs of the human body. Although DESI has been used to image lipids and metabolites of a variety of tissues and other imaging techniques, such as NIMS, have been used to study kinetic turnover …

New Mass Spectrometric Methods For Studying Proteins In Solution And In The Gas Phase, Zhe Zhang

Doctoral Dissertations

This dissertation focuses on the mass spectrometric based methods for studying protein structures in solution phase and in gas phase. Protein structure is important to study because it is related to many disease mechanism and related therapies. The relationship between protein structures in solution phase and in gas phase has been investigated. Especially, the electrostatic interaction is characterized by mass spectrometry (MS). A HDX method has been developed to study protein oligomer kinetics and applied to study β-2-microglobulin (β2m) oligomerization. This dissertation firstly focuses on the relationship between protein gas phase structure and solution phase structure. We studied the structures …

Analysis Of Gold Nanoparticles And Their Use With Laser Desorption/Ionization Mass Spectrometry, Alyssa Marsico

Doctoral Dissertations

Gold nanoparticles (AuNPs) have many unique properties that make them attractive for use in various biological applications. Laser desorption/ionization mass spectrometry (LDI-MS) has been used to monitor AuNPs in complex biological samples but there are still many ways in which AuNPs can be used with MS. In this dissertation, the use of AuNPs to assist in analyte ionization has been investigated. Their ability to enhance signal from biomolecules based on their surface chemistry, size, aggregation and method of deposition has been studied. The first use of an inkjet printer to create surfaces from which analytes can be sampled is discussed …

Influence Of Magnetic Nanoparticles And Magnetic Stress On An Ionic Liquid Electrospray Source, Kurt Joseph Terhune

Dissertations, Master's Theses and Master's Reports

Two electrospray sources were developed to operate on an ionic liquid ferrofluid; one source was a pressure‑fed capillary electrospray source and the other was a novel electrospray source which used a magnetically‑induced instability to produce a peak from which an electric field could extract electrospray. Multiple characteristics of electrospray operation were examined for both sources using faraday plates/cups, a quartz crystal microbalance, a retarding potential analyzer, and a time-of-flight mass spectrometer. The ILFF electrosprays for a capillary source were shown to operate in a mixed ion/droplet regime. The mass flow of the electrospray beam was primarily transported by larger particles …

Further Development Of Raman Spectroscopy For Body Fluid Investigation : Forensic Identification, Limit Of Detection, And Donor Characterization, Claire K. Muro

Legacy Theses & Dissertations (2009 - 2024)

The challenges to forensic body fluid analysis have placed limitations on the type of information that investigators can acquire and how that information can be collected. In recent years, Raman spectroscopy has proven itself useful for characterizing body fluids. In 2008, a large-scale investigation was undertaken to explore the use of Raman spectroscopy as a means of identifying body fluids. This work resulted in multidimensional Raman spectroscopic signatures for the five main body fluids: semen, peripheral blood, saliva, vaginal fluid, and sweat. These studies were incredibly successful and created the foundation for years of continued research. Accordingly, the studies included …

Ambient Ionization - Mass Spectrometry: Advances Toward Intrasurgical Cancer Detection, Alan Keith Jarmusch

Open Access Dissertations

My dissertation research has focused on the development of ambient ionization – mass spectrometry (MS) for clinical measurements, specifically intrasurgical cancer detection. The molecular differences between normal and cancerous tissue were detected via direct tissue analysis in vitro by touch spray ionization (TS) or by analyzing sectioned or smeared tissue using desorption electrospray ionization (DESI). The physical form of the tissue, e.g. in vitro sampling, sectioned, or smeared, was inconsequential in differentiating normal from cancerous tissue; however, the spectra acquired by TS and DESI differed due to differences in ionization processes. We envision that TS-MS and DESI-MS could impact diagnostic …

Preparative Mass Spectrometry Applications In Nanomaterials And Organic Synthesis, Michael Wleklinski

Open Access Dissertations

Preparative mass spectrometry was traditionally a vacuum based experiment where mass selected ion beams were deposited onto surfaces; however, recently ions have been manipulated in the open air to perform accelerated synthesis. The work of this dissertation focuses on the generation of charged ions from microdroplets and their use in organic synthesis and the preparation of atomically precise metal nanoclusters. First the mechanism for charging in the zero volt paper spray will be presented. This works builds a computational model based on the statistical fluctuation of positive and negative charges based on the theory of Dodd. It is found through …

Investigation Of Dynamic Biological Systems Using Direct Injection And Liquid Chromatography Mass Spectrometry, Adam Clayton Swensen

Theses and Dissertations

In biological systems, small changes can have significant impacts. It is, therefore, very important to be able to identify these changes in order to understand what is occurring in the organism. In many cases, this is not an easy task. Mass spectrometry has proven to be a very useful tool in elucidating biological changes even at a very small scale. Several different mass spectrometry based techniques have been developed to discover and investigate complex biological changes. Some of these techniques, such as proteomics, have been through years of development and have advanced to the point that anyone can complete complex …

Mass Spectrometric Characterization Of Remotely Charged Amino Acids And Peptides, Damodar Koirala

Open Access Dissertations

Ion–molecule reactions in a flowing afterglow are used to examine the electronic structure of 3- and 4-pyridinylnitrene-n-oxide radical anions. Reactions with nitric oxide are generally similar to those reported previously for other aromatic nitrene radical anions. In particular, phenoxide formation by nitrogen–oxygen exchange is observed with both isomers. Oxygen atom abstraction by NO is also observed with both isomers. Very significant differences in the reactivity are observed in the reactions of the two isomers with carbon disulfide. The reactivity of the 3-noxide isomer with CS2 is similar to that observed previously for nitrene radical anions, and reactions of the n-oxide …

Novel Analytical Methods Combining Non-Denaturing Chromatography And Mass Spectrometry To Study Biopolymer Structure And Interactions, Khaja Muneeruddin

Doctoral Dissertations

Biotherapeutics, an emerging class of medicines containing biopolymers (e.g., proteins, peptide, and polysaccharides) have been developed for a variety of indications including cancer, autoimmune, genetic, and blood diseases. Among these biopolymers protein therapeutics have been the rapidly growing segment in the pharmaceutical industry. This trend combined with the complexity of proteins has necessitated the development of powerful and robust analytical methods to study their structure and interactions with physiological partners. Mass spectrometry (MS) has become an indispensable tool to analyze various attributes of protein drugs such as profiling of intact mass, amino acid sequencing, and post translational modifications (PTMs). In …

Possible Sources And Impacts Of Biochar Water Extractable Organic Compounds On Aquatic Microorganisms, Cameron Russell Smith

Chemistry & Biochemistry Theses & Dissertations

Smokeless biomass pyrolysis with application of biochar as a soil amendment could be a significant approach for carbon sequestration to possibly control climate change for energy and environmental sustainability. If biochar were to be utilized as a soil amendment and a carbon sequestration agent at Gt C scales, the release of potentially toxic compounds into soils and associated hydrological systems, through soil rainwater runoff and leaching, might have negative consequences, in both agro-ecosystems and aquatic environmental systems. Therefore, the main focus of this dissertation was to study the sources and chemical composition of biochar water extractable (soluble) organic compounds and …

Application Of Electrospray Ionization Mass Spectrometry For Ionic Liquids And Their Biodegradation Products, Sepideh Rahbarirad

Masters Theses

Ionic liquids (ILs) are organic salts with unique physico-chemical properties and are used as green alternatives to volatile organic solvents. ESI-MS is a sensitive technique to detect these stable, permanent ions. My research focused on (1) Identification of biodegradation products of ionic liquids and (2) Multiplexed tandem MS by modulation of ionization efficiency.

Studies, have demonstrated that ILs are toxic to the environment, which makes their biodegradability an important consideration. In this work, metabolites generated during the biodegradation of 1-butyl-3-methylimidazolium chloride (BMIM), a degradation resistant and commonly used ionic liquid, are identified using high performance liquid chromatography-mass spectrometry (LC-MS).

Multiplexed …

Environmental Applications Of Chromatography-Mass Spectrometry, Wisam Abdulabbas Flayyih Al Isawi

Masters Theses

Gas chromatography-mass spectrometry (GC-MS) and liquid chromatographymass spectrometry (LC-MS) are powerful analytical techniques that combine the separation power in a stationary phase with the detection power of mass spectrometry. GCMS and LC-MS have gained dominant positions in identifying and quantifying different analyte species due to their high selectivity, high sensitivity, and high reproducibility.

My research utilizes the analytical power of LC-MS and GC-MS to address two environmental issues: 1) Identification of biodegradation products of the ionic liquid 1- butyl-3-methylimidazolium chloride (BMIMCl) by an activated sludge microbial community using LC-MS and 2) identification and quantification of polycyclic aromatic hydrocarbons (PAHs) in …

Discovery Of Low-Molecular Weight Novel Serum Biomarkers For Diagnosing Preeclampsia And Alzheimer's Disease, Swati Anand

Theses and Dissertations

Preeclampsia (PE), a life threatening pregnancy-related disorder, is characterized mainly by new onset of hypertension and proteinuria after 20 weeks of gestation. Currently, PE cannot be predicted prior to onset of symptoms and there is no cure for the disease. There is a clear value in having biomarkers able, early in a pregnancy, to identify women at risk for PE so that proper treatment therapies could be developed. Although a number of serum candidate markers have been proposed to be altered in PE patients, their use is limited due to poor sensitivity and specificity. Therefore, there is ongoing need for …

The Development Of Peptide Ligands To Target H69 Rrna, Danielle Nicole Dremann

Wayne State University Dissertations

ABSTRACT

THE DEVELOPMENT OF PEPTIDE LIGANDS TO TARGET H69

by

DANIELLE NICOLE DREMANN

December 2015

Advisor: Prof. Christine S. Chow

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

In the development of peptide ligands to target H69, SPPS and ESI MS was used to determine if 1) peptides could bind to modified H69 and 2) if increased affinity for the target RNA could be enhanced with modification. An alanine and arginine scan was synthesized and tested for this determination. Selected peptides were then tested using biophysical techniques such as circular dichroism and isothermal titration calorimetry. An assay was also designed to …

Development Of Direct Analysis In Real Time-High Resolution Mass Spectrometry (Dart-Hrms) And Statistical Analysis Tools For The Identification And Classification Of Psychoactive Plant Drugs, Ashton Danielle Lesiak

Legacy Theses & Dissertations (2009 - 2024)

In current forensic testing, a new pattern is emerging where the drugs that are submitted to crime labs for analysis are no longer restricted to well-characterized substances such as cocaine, heroin and tetrahydrocannabinol (THC). The appearance of new psychoactive substances (NPS) in forensic laboratories, including synthetic alternatives to scheduled substances and plant-based psychotropics, has highlighted issues that traditional analytical methods such as gas chromatography- and liquid chromatography-mass spectrometry impose in the characterization of these samples. These can include lengthy extractions, derivatization steps, pH adjustments and/or a host of other procedures. Since the creation of legislation to address the use of …

Mass Spectrometry Based Proteomics And Lipidomics Studies, Huan Kang

Theses and Dissertations

Mass spectrometry has emerged as having a vital role in various applications to biochemical fields. In this thesis, we have utilized a variety of mass spectrometry techniques for both bacteriophage proteomics and colostrum and milk lipidomics studies. Our first study was the proteome characterization of Great Salt Lake bacteriophage NS01 with SDS-PAGE GEL to separate the viral proteins and high performance liquid chromatography (HPLC) coupled with an LTQ Orbitrap to identify the proteins after in-gel digestion. In this project, we have successfully identified 11 proteins with high confidence, p-values < 0.01, including coat protein gp88 with a coverage of 91% and tail protein gp86 with a coverage of 40.96%, which facilitated the classification of NS01 as a T7-like phage. Our second study was the discovery of colostrum and milk biomarkers that can be used to predict the likelihood of development of production-related metabolic diseases (PRMDs) in dairy cows through a lipidomics approach. In this study, an electrospray ionization, time-of-flight mass spectrometer was applied to lipid profiling, quantification and significant biomolecule selection. A Q-Star quadrupole, orthogonal time-of-flight mass spectrometer and an Agilent 6530 accurate-mass quadrupole/time-of flight mass spectrometer were both used for lipid biomarker fragmentation and identification. According to linear discriminative statistical modeling, three panels of biomarkers were defined. A combination of 2 milk lipid predictors, including DG18:0/18:0 and TG 18:0/18:0/18:1, provided PRMD predictions with 75.0% sensitivity at 90.0% specificity. A combination of 3 colostrum lipid predictors, including TG16:0/18:1/18:3, DG16:0/16:0 and C₄₀H₆₀NO, provided PRMD prediction with 90.0% sensitivity at …

Image-Charge Detection €“ Novel Instrumentation And Applications, Brandon Lee Barney

Theses and Dissertations

Image-charge detection is an analytical technique in which a highly-charged particle is detected by the magnitude of the image current that it generates in a detecting electrode. This current is represented as a voltage between the charged particle and the sensing electrode. It is a single particle detection method, ideal for the analysis of large, variable mass particles such as biological cells. Some of the physical properties of Bacillus subtilis spores were explored using different applications of image-charge detection. B. subtilis is a gram-negative spore-forming bacteria that has been shown to exhibit extremophile behavior. The particular extremophile behavior that was …

Mass Spectrometric Analyses Of Surface Proteins From Candida Albicans After Treatment With Histatin 5, Shirley Fan

Electronic Thesis and Dissertation Repository

Current drug therapies have lost their effectiveness in controlling the fungal species known as C. albicans; therefore, the need for newer drugs becomes crucial. Histatin 5 (Hst 5), a naturally occurring peptide found in the oral cavity, has demonstrated strong effects on controlling candidiasis. Here, we have proposed that the adhesion of cells through surface proteins is an important process. To allow the analysis of surface proteins, the concept of on-whole cell tryptic digestions were developed. This on-target approach allows for isolation of the peptides of interest, while greatly reducing digestion times.

To study the effects of Histatin 5 …

Transferrin-Based Therapeutics And Analytical Methods To Characterize Them, Son N. Nguyen

Doctoral Dissertations

Modern development of medicine requires detailed characterization by state-of-the art analytical techniques that can be used to analyze covalent structure, conformations and protein-receptor interaction to quantitatively measure biodistribution of protein therapeutics. Mass spectrometry has already become an indispensable tool facilitating all stages of protein drug development. Particularly, this work has demonstrated the tremendous potential of electrospray ionization (ESI) mass spectrometry (MS) in this arena by providing invaluable information beyond mass measurement that can be used to optimize protein drug conjugate structures during early stages of development, and to further catalyze drug design efforts. Additionally, a new sensitive and selective method …

Ribosome Component Turnover Kinetics Describes A Two-Pool Kinetic Model In Dietary Restriction That Suggests Rpl10 Is Exchanged During Ribosome Lifespan, Andrew David Mathis

Theses and Dissertations

The eukaryotic ribosome is a large molecular machine consisting of ~80 ribosomal proteins and 4 rRNAs. The 40S and 60S ribosomal subunits are assembled in the nucleolus by ~200 helper proteins then shipped into the cytoplasm or to the endoplasmic reticulum where protein translation takes place. Eventually ribosomes are removed from the cytoplasm and recycled through ribophagy, however, very is little is known about ribosomal protein exchange after assembly but before ribophagy. Using kinetic turnover measurements of ribosomal proteins and rRNA in vivo we determined ribosomal protein replacement rates are diverse suggesting ribosomal components may be replaced without destruction of …

Hydrogen Exchange Mass Spectrometry For Studying Protein-Ligand Interactions, Modupeola A. Sowole

Electronic Thesis and Dissertation Repository

Hydrogen deuterium exchange (HDX) coupled with mass spectrometry is widely used for probing protein structure and dynamics. Protein-ligand interactions usually induce a reduction in the measured HDX rates an effect that may be ascribed to stabilization of the protein structure. This work aims to improve the general understanding of the changes in HDX patterns associated with ligand binding.

We initially applied HDX for studying differences between oxy-hemoglobin (Oxy-Hb) and aquomet-hemoglobin (Chapter 2). The results show that the α and β subunits respond differently to the oxy to aquomet transition with the heme binding pocket being destabilized in both cases. The …

Using Ion Mobility Spectrometry To Study Protein Conformations In The Gas Phase, Yu Sun

Electronic Thesis and Dissertation Repository

The question whether electrosprayed protein ions retain solution-like conformations remains a matter of debate. One way to address this issue involves comparisons of collision cross sections measured by travelling wave ion mobility spectrometry (TWIMS) with the values calculated for model structures. It is often implied that nanoESI is more conducive for the retention of solution structure than regular ESI. Focusing on four different proteins we demonstrated that collision cross section values and collisional unfolding profiles are virtually indistinguishable under both conditions. Calibration can be challenging because differences in the extent of collisional activation for TWIMS and drift tube calibrant data …

Mass Spectrometry-Based Strategies For Biomolecular Structure Analysis: Steroid Metabolites Structures And Protein-Protein Interactions, Yuetian Yan

Arts & Sciences Electronic Theses and Dissertations

Mass spectrometry is an important method for studying the structure of both small molecules and large biomolecules (e.g., proteins). The majority of the applications prior to 1970 were focused on small molecules, owing to the limited ionization methods which posed difficulties in producing gas-phase ions for large biomolecules then. Beginning in the 1980's, with the introduction of new ionization methods (ESI and MALDI), the applications have gradually switched to biological science measuring large bioorganic molecules. Today, with the developing interest in metabolomics and proteomics, and ongoing improvement in MS-based techniques, mass spectrometry is extensively applied in the study of both …

Analysis Of Anacardic Acid On The Surface Of Pelargonium × Hortorum Using Matrix Assisted Laser Desorptoin Ionization Mass Spectrometry Imaging., Bryan Edward Wessel 1989-

Electronic Theses and Dissertations

The biosynthetic pathway leading to the production of anacardic acids (AnAcs) in glandular trichomes on the surface of geranium plants remains unclear. Anacardic acids are salicylic acid derivatives known to possess various medicinal benefits. Gene silencing techniques, such as RNA interference, could be useful in determining specific enzymes involved in the synthesis of AnAcs. However, it is first necessary to develop methodologies to image AnAcs. In this project, both fluorescence (FL) and mass spectral imaging (MSI) were tested. Our results indicate that cellular imaging of AnAcs, via FL, is not suitable because the spectral ranges of absorption and emission of …

Distinguishing Macrophage Activation States By Mass Spectrometry, Matthias Manfred Knust

Graduate Theses and Dissertations

Macrophages are versatile and highly adaptive cells that are involved in a wide range of physiological processes including host defense, homeostasis or regeneration, as well as pathogenesis. They react to their microenvironment, assuming various roles based on chemical and/or physical cues, and can reversibly shift between these so-called activation states. Concurrently, the technique of immunohistochemistry is used to gain spatial information on activated macrophages on tissue sections. The aim of this work was to find mass spectral biomarkers that allow the differentiation of activation states, and establish conditions that can be used in imaging mass spectrometry (IMS) experiments to investigate …

Investigation Of The Chemical Protection Capacity Of Common Shoe Materials In Undergraduate Laboratories, Sarah E. Lawson

Undergraduate Honors Theses

The objective of this study was to evaluate the chemical resistance of common shoe materials regularly worn in undergraduate chemistry laboratories by subjecting the materials to hydrochloric acid and sodium hydroxide. The materials tested were leather, canvas cotton, and polyester. Due to the lack of restriction on undergraduate laboratory footwear, the research discussed in this thesis is important to undergraduate universities. Currently, many universities across the nation only require undergraduate students to wear close-toed, close-heeled shoes in chemistry laboratories, and often the resistance of the shoe material to acids and bases may not be taken into careful consideration. Overall, the …