Physical Sciences and Mathematics Commons^™

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 …

A Framework For The Statistical Analysis Of Mass Spectrometry Imaging Experiments, Kyle Bemis

Open Access Dissertations

Mass spectrometry (MS) imaging is a powerful investigation technique for a wide range of biological applications such as molecular histology of tissue, whole body sections, and bacterial films , and biomedical applications such as cancer diagnosis. MS imaging visualizes the spatial distribution of molecular ions in a sample by repeatedly collecting mass spectra across its surface, resulting in complex, high-dimensional imaging datasets. Two of the primary goals of statistical analysis of MS imaging experiments are classification (for supervised experiments), i.e. assigning pixels to pre-defined classes based on their spectral profiles, and segmentation (for unsupervised experiments), i.e. assigning pixels to newly …

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 …

Rapid High-Throughput Species Identification Of Botanical Material Using Direct Analysis In Real Time High Resolution Mass Spectrometry, Rabi A. Musah, Ashton D. Lesiak

Chemistry Department Faculty Scholarship

We demonstrate that direct analysis in real time-high resolution mass spectrometry can be used to produce mass spectral profiles of botanical material, and that these chemical fingerprints can be used for plant species identification. The mass spectral data can be acquired rapidly and in a high throughput manner without the need for sample extraction, derivatization or pH adjustment steps. The use of this technique bypasses challenges presented by more conventional techniques including lengthy chromatography analysis times and resource intensive methods. The high throughput capabilities of the direct analysis in real time-high resolution mass spectrometry protocol, coupled with multivariate statistical analysis …

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 …

Comparative Analysis Of In Situ Fibronectin Using Tof-Sims, Spi-Ms, And Dropdesi-Ms In A Microfluidic Reactor, Shannon Fasing, Xiao-Ying Yu, Juan Yao, Jiachao Yu

STAR Program Research Presentations

Fibronectin is an important biomolecule due to its role in cell differentiation, growth, kinesis, and adhesion. Such biological responses are mediated through membrane recognition and signaling; where fibronectin is found. Studying the outer molecular surface of fibronectin allows deeper insight into the microbiological reactions that occur during these processes. In situ mass spectrometry analysis in aqueous solution accurately represents fibronectin’s chemical components, made possible by a vacuum compatible microfluidic reactor, SALVI (System for Analysis at the Liquid Vacuum Interface). SALVI was paired with the analytical tools: time-of-flight secondary ion mass spectrometer (ToF-SIMS), single photon ionization mass spectrometer (SPI-MS) and drop …

Advancing Algorithms For Mass Spectrometry Data Analysis, Rob Smith

University Grant Program Reports

Our objective with this award was to conduct the preliminary experiments necessary to assess the state of the art of existing mass spectrometry signal segmentation algorithms. Although unforeseeable complications prevented the completion of all proposed research goals, completed research aims resulted in:

• A cross-platform mass spectrometry data viewer with the ability to pan, zoom, and scroll.
• Motivation for experimental ground truth data through exposing breakdown cases of the leading mass spectrometry simulator.
• A completed code framework for running and testing existing isotopic trace segmentation algorithms.

Since the receipt of this award, we have submitted three related external research proposals. One …

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 …

Analysis Of Improvised Explosives By Electrospray Ionization - Mass Spectrometry And Microfluidic Techniques, Inge Corbin

FIU Electronic Theses and Dissertations

Improvised explosives may be based on smokeless gunpowder, fertilizers, or inorganic oxidizers such as nitrate (NO3-), chlorate (ClO3-), and perchlorate (ClO4-) salts.

Identification is a priority for the military and law enforcement but due to their varying physical properties and complexity, identification can be challenging. Consequently, three methods have been developed to aid in presumptive and confirmatory detection.

Smokeless powder contains plasticizers, stabilizers, dyes, opacifiers, flash suppressants, and other compounds. Identification of these additives can narrow down or identify the brands of smokeless powder used in a device. Fourteen organic smokeless powder components were identified by capillary electrochromatography (CEC) using …

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 …

Glycine N-Acyltransferase-Like 3 Is Responsible For Long-Chain N-Acylglycine Formation In N18Tg2 Cells, Kristen A Jeffries, Daniel R Dempsey, Emma K Farrell, Ryan L Anderson, Gabrielle J Garbade, Tatyana S Gurina, Imran Gruhonjic, Carly A Gunderson, David J Merkler

Chemistry Faculty Publications

Long-chain fatty acid amides are signaling lipids found in mammals and other organisms; however, details of the metabolic pathways for the N-acylglycines and primary fatty acid amides (PFAMs) have remained elusive. Heavy-labeled precursor and subtraction lipidomic experiments in mouse neuroblastoma N18TG2 cells, a model cell line for the study of fatty acid amide metabolism, establish the biosynthetic pathways for the N-acylglycines and the PFAMs. We provide evidence that the N-acylglycines are formed by a long-chain specific glycine-conjugating enzyme, glycine N-acyltransferase-like 3 (GLYATL3). siRNA knockdown of GLYATL3 in the N18TG2 cells resulted in a decrease in the levels of the N-acylglycines …

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 …

The Role Of Microbial Exopolymers In Determining The Fate Of Oil And Chemical Dispersants In The Ocean, Antonietta Quigg, Uta Passow, Wei-Chun Chin, Chen Xu, Shawn Doyle, Laura Bretherton, Manoj Kamalanathan, Alicia K. Williams, Jason B. Sylvan, Zoe V. Finkel, Anthony H. Knap, Kathleen A. Schwehr, Saijin Zhang, Luni Sun, Terry L. Wade, Wassim Obeid, Patrick G. Hatcher, Peter H. Santschi

Chemistry & Biochemistry Faculty Publications

The production of extracellular polymeric substances (EPS) by planktonic microbes can influence the fate of oil and chemical dispersants in the ocean through emulsification, degradation, dispersion, aggregation, and/or sedimentation. In turn, microbial community structure and function, including the production and character of EPS, is influenced by the concentration and chemical composition of oil and chemical dispersants. For example, the production of marine oil snow and its sedimentation and flocculent accumulation to the seafloor were observed on an expansive scale after the Deepwater Horizon oil spill in the Northern Gulf of Mexico in 2010, but little is known about the underlying …

An Alignment-Free "Metapeptide" Strategy For Metaproteomic Characterization Of Microbiome Samples Using Shotgun Metagenomic Sequencing, Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, H. Rodger Harvey, Elhanan Borenstein, Brook L. Nunn, William S. Noble

OES Faculty Publications

In principle, tandem mass spectrometry can be used to detect and quantify the peptides present in a microbiome sample, enabling functional and taxonomic insight into microbiome metabolic activity. However, the phylogenetic diversity constituting a particular microbiome is often unknown, and many of the organisms present may not have assembled genomes. In ocean microbiome samples, with particularly diverse and uncultured bacterial communities, it is difficult to construct protein databases that contain the bulk of the peptides in the sample without losing detection sensitivity due to the overwhelming number of candidate peptides for each tandem mass spectrum. We describe a method for …

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 …

Electrochemistry-Coupled To Mass Spectrometry In Simulation Of Metabolic Oxidation Of Methimazole: Identification And Characterization Of Metabolites, Kudzanai Chipiso, Reuben H. Simoyi

Chemistry Faculty Publications and Presentations

Methimazole (MMI), an antithyroid drug, is associated with idiosyncratic toxicity. Reactive metabolites resulting from bioactivation of the drug have been implicated in these adverse drug reactions. Mimicry of enzymatic oxidation of MMI was carried out by electrochemically oxidizing MMI using a coulometric flow-through cell equipped with a porous graphite working electrode. The cell was coupled on-line to electrospray ionization mass spectrometry (EC/ESI-MS). ESI spectra were acquired in both negative and positive modes. In acidic medium, ESI spectral analysis showed that the dimer was the main product, while in neutral and basic media, methimazole sulfenic acid, methimazole sulfinic acid and methimazole …