Development Of Ultrafast Protein Digestion And Standards Free Quantitation Methods For Mass Spectrometric Analysis, Praneeth Ivan Joel Fnu

Dissertations

A wide variety of biologically important molecules, such as enzymes, antibodies, hormones, transporters and receptors are proteins by composition and they play key roles in biological functions such as cellular regulation, communication, metabolism and physiological function. Protein dysfunctions and abnormalities are associated with numerous diseases, making proteins critical targets for understanding disease mechanisms and developing therapeutic interventions. Protein-based therapeutics such as monoclonal antibodies, hormones and vaccines gained popularity due to their high specificity, efficacy, and ability to treat complex diseases that are often difficult to address with small-molecule drugs.

Given the important role of proteins in a variety of biological …

On The Operation Of A Proteomics Core Facility: Selected Mass Spectrometric Studies And Methods, Rachel E. Muriph

Graduate Doctoral Dissertations

Mass spectrometry has become an indispensable analytical platform for investigating complex biological systems owing to its sensitivity, selectivity, and molecular specificity. This Dissertation demonstrates the versatility of liquid chromatography-tandem mass spectrometry (LC-MS/MS) through three studies focused on nanoparticle characterization, protein structural analysis, and plasma proteomics. In Chapter 2, LC-MS methods were developed to characterize novel lipidoid incorporated into lipid nanoparticles (LNPs) and to evaluate their in vivo biodistribution following systematic administration. Comparative proteomic analysis of the resulting protein coronas revealed distinct differences between liver and lung targeting LNP formulations, providing insight into the potential role of adsorbed blood proteins in …

The Study Of Hydrophobic Biomolecules With Matrix Assisted Laser Desorption Ionization Mass Spectrometry And Atomic Force Microscopy, Brandy L. Perkins

LSU Doctoral Dissertations

Abstract

Matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS) can be used to obtain localization and chemical information of hydrophobic biomolecules on tissue samples.  A technique has been developed to modify a standard MALDI matrix that improves the selectivity for hydrophobic biomolecules on the tissue sample. The modification involves the use of a Group of Uniform Materials Based on Organic Salts (GUMBOS). GUMBOS are ionic liquids (IL) that are bulky organic ions with a counter ion that can be changed for tuning.  They are more stable than traditional matrices under vacuum.  Unlike traditional IL’s, the GUMBOS melting point ranges …

Research Instrumentation Center (Ric), Ryan Hilger, Purdue University Office Of Research

University Research Core Facility Boilerplate Descriptions

No abstract provided.

Separating And Identifying Delta-8-Thc And Delta-9-Thc On Gc/Ms, Ann Schmidt

Honors Projects

Delta-8-THC and delta-9-THC are two psychoactive compounds found in marijuana products which are only distinguishable from each other by alternating the location of a single double bond.  This makes them a challenge to separate and identify as different compounds using the GC/MS.  These isomers are legally recognized as the different compounds, so being able to identify delta-8 and delta-9 THC separately is crucial to forensic analysis. The goal of this research project is to optimize an Intuvo 9000 GC connected to a standard MS to be able to separately and prominently identify delta-8-THC and delta-9-THC in a sample.  This was …

Early Detection Of Infectious Diseases: A Review Of Recent Advances In Pathogen Identification, Molecular Tools, And Metabolomics-Driven Biomarker Discovery, Patrica Ivy Agorsor, Michael O. Eze

Chemistry Faculty Research & Creative Works

The recent COVID-19 pandemic has heightened public interest in noninvasive methods for early diagnosis of infectious diseases. In addition, various government agencies have implemented "infectious disease preparedness" to mitigate future outbreaks. This review highlights conventional and advanced methods for infectious disease diagnosis with an emphasis on emerging mass spectrometry methods. Conventional methods for pathogen identification, such as culture-based techniques and molecular methods, have limitations with respect to sensitivity, specificity, and turnaround time. Recent advances in high-resolution mass spectrometry have revolutionized the field of infectious disease biomarker discovery. These techniques enable the comprehensive profiling of metabolites in various biological samples, identification …

Lc-Ms/Ms Method Development For The Analysis Of Cannabinoids In Wastewater, Abigail M. Castellanos, Ava La Lande

The Kean Review: Journal in Student Research

The goal of this research was to establish a reliable method to detect the presence of cannabinoids in wastewater and increase the sensitivity of detection. Since the legalization of cannabis in many states, toxicology research has expanded on methods of detection in hopes of identifying usage patterns. At the Joint Meeting of Essex and Union Counties, it was established that cannabinoids are not thoroughly accounted for in the process of filtering wastewater in addition to our limited understanding of consumption trends. This stands true for many wastewater facilities, especially as the intake of cannabis remains prevalent for various populations across …

Identification Of Modified Polymer End Groups For Correlations To Physical Properties, Tj Sacco

Williams Honors College, Honors Research Projects

Plastic has become the primary material for containers in both industrial and commercial fields. Plastics are the optimal choice since they have many physical properties that make them ideal candidates: durability, heat resistance, chemical stability, as well as their inexpensive production cost. Nowadays, the desire for more versatile plastics with strength, flexibility, hydrophobicity, and biodegradability has grown; however, concerns for plastic use have started to rise as well. The overuse of plastics poses a threat to the environment and people’s health: plastics are hard to break down completely which results in the formation of micro(nano)plastics (MNPs). In attempts to circumvent …

Rapid Classification And Quality Assessment Of Citrus Essential Oils Via Machine-Learning-Assisted Raman Spectroscopy, Yong Xuan Hong, Jia Wei Tang, Jie Chen, Yun Yun Xie, Zhang Wen Ma, Qing Hua Liu, Liang Wang

Research outputs 2022 to 2026

Citrus essential oils (EOs) require accurate identification and assessment to ensure authenticity and consistency. However, conventional techniques such as gas chromatography (GC) and mass spectrometry (MS) are time-consuming and expensive, highlighting the need for novel analytical methods. This study proposes an approach for EOs detection using Raman spectroscopy (RS) combined with machine learning (ML) algorithms. Six citrus EOs underwent an evaporation experiment, with Raman spectra collected at five time points and GC-MS was used to analyze compositional changes at the starting and ending points of evaporation as a standard reference. Five ML algorithms were developed to identify differences among EOs …

Development And Implementation Of Novel Mass Spectrometric Methods For Metabolism Studies In Drug Discoveries, Huifang Yao

Dissertations

The field of drug discovery has evolved significantly over the past few decades, with a growing emphasis on understanding the metabolic pathways and biotransformation processes that influence the pharmacokinetics and pharmacodynamics of drug candidates. Novel mass spectrometric methods have emerged as powerful tools in this domain, facilitating the comprehensive analysis of metabolic profiles and enabling the identification of metabolites with implications for safety, efficacy, and overall drug development. However, challenges remain in quantifying metabolic flux—an essential aspect of understanding drug action—particularly due to the limitations of traditional isotope kinetic assays, which often involve lengthy sample preparation and the use of …

Infrared Laser Ablation Of Biomolecules From Formalin-Fixed Tissue, Blessing Chisom Egbejiogu

LSU Doctoral Dissertations

In the research described in this dissertation, a high-precision infrared laser ablation microsampling method was utilized for spatially resolved proteomic and lipidomic analyses of formalin fixed paraffin embedded (FFPE) tissue, a widely used archival sample in biomedical research. Despite its extensive use, FFPE tissue presents challenges for proteomic analysis due to protein cross-linking and modifications introduced during fixation, which can hinder extraction and identification. Developing a streamlined high-resolution method to recover biomolecules from FFPE samples is critical for advancing biomarker discovery, retrospective studies, and multi-omics research. To address these challenges, this study employs an infrared (IR) laser ablation microdissection system …

Investigating Dna Damage Caused By Reactive Oxygen And Nitrogen Species Via Guided-Ion-Beam Scattering And Computational Techniques, Jonathan Benny

Dissertations, Theses, and Capstone Projects

Among DNA nucleobases, guanine (G) is the primary target for one-electron ionization and oxidation, generating G●+ through various processes, including photooxidation, electrocatalytic oxidation, DNA-binding transition metals, ionizing radiation, and photolysis. This is due to the low adiabatic ionization potential and oxidation potential of guanine. Electron holes from other nucleobases can move to guanine, proving that G●+ production traps oxidative DNA damage. G●+ formation can exacerbate DNA damages and cause secondary reactions from reactive oxygen species (ROS) and reactive nitrogen species (RNS) during pathological processes. The following three projects were conducted using a customized electrospray ionization (ESI) guided-ion-beam tandem mass spectrometer, …

High Throughput, Solid Sample Analysis With Cone-Based Mass Spectrometric Ionization Sources, Emily J. Wiggins

Theses and Dissertations

The widespread presence of environmental and consumer-product contaminants (e.g. trace metals, opium alkaloids) has underscored the need for rapid, reliable, and high-throughput analytical techniques that are capable of handling complex solid samples. While traditional mass spectrometric (MS) methods tend to have high sensitivity and accuracy, they often require labor-intensive and time-consuming sample preparation steps that limit throughput and field applicability. This thesis investigates the use of 3D-Printed Cone Spray Ionization-Mass Spectrometry (3D-PCSI-MS) as an ambient ionization technique for the direct screening of contaminants from solid matrices, eliminating the need for traditional sample preparation and allowing for real-time analysis.

In …

Challenges Associated With Pfas Detection Method In Africa, Abdullahi Tunde Aborode, Ridwan Olamilekan Adesola, Ibrahim Idris, Waheed Sakariyau Adio, Segun Olapade, Gladys Oluwafisayo, Israel Ayobami Onifade, Sodiq Fakorede, Taiwo Bakare-Abidola, Jelil Olaoye, Adedeji Daniel Ogunyemi, Oluwaseun Adeolu Ogundijo, Olamilekan Gabriel Banwo, Adetolase Azizat Bakre, Peter Oladoye, Grace Adegoye, Noimat Abeni Jinadu

Chemistry & Biochemistry Faculty Publications

Per- and polyfluoroalkyl substances (PFAS) are a group of man-made chemicals that are widely present in many industries. Monitoring and analyzing PFAS in Africa is challenging due to the limited availability of mass spectrometry (MS), which is an essential technique for detecting PFAS. This review assesses the scope and impact of the shortage of mass spectrometry instruments in Africa, emphasizing the resulting limitations in monitoring environmental and public health threats. The review analyzes the existing PFAS monitoring, the accessibility of MS instruments, and the technical capabilities within the continent. This study suggests that fewer African countries have sufficient MS instruments, …

Moderate Heating Renders 7.8-Million-Year-Old Sedimentary Organic Matter Bioavailable, Shuchai Gan, Verena B. Heuer, Frauke Schmidt, Lars Wormer, Faming Wang, Rishi R. Adhikari, Patrick Hatcher, Ann Pearson, Kai-Uwe Hinrichs

Chemistry & Biochemistry Faculty Publications

Marine sediments are a large reservoir of recalcitrant organic matter and host microbes at subsurface depths exceeding 2.4 kilometers and temperatures up to 120°C, yet the mechanisms supplying bioavailable substrates remain unclear. Here, we investigated 7.8-million-year-old sediment from IODP Site C0012 off the Nankai Trough, Japan, through incubations at 20°, 35°, 55°, and 85°C to simulate burial temperatures. Using 3D fluorescence spectroscopy and ultrahigh-resolution mass spectrometry, we tracked changes in dissolved organic matter (DOM). At 35°C, humic-like DOM was released alongside metal ions, exhibiting low bioavailability. At 55°C, abiotic decomposition of humic compounds generated smaller, more bioavailable DOM, promoting fermentation. …

Extended Inter-Laboratory Characterization Of The New Coastal Seawater Dissolved Organic Matter Reference Material Trm-0522, Alexander J. Craig, Lydia Babcock-Adams, Maxime C. Bridoux, Charlotte Brun, Juliana D'Andrilli, Aleksandar I. Goranov, Patrick G. Hatcher, Oliver Lechtenfeld, Hang Li, Rebecca Matos, Garrett Mckay, Amy M. Mckenna, Madelyn Miller, Sasha Wagner, Margot E. White, Alexander Zherebker, Jeffrey A. Hawkes

Chemistry & Biochemistry Faculty Publications

Dissolved organic matter (DOM) reference materials are critical to ensuring reliable comparability of measurements across experiments and between labs. TRM-0522, isolated in 2022 from 45 m deep seawater off of Sweden’s west coast, fills the niche of a previously unavailable coastal marine DOM reference material. After its isolation, we detailed a limited number of metrics for TRM-0522, initially disclosing Orbitrap high-resolution mass spectrometry, nuclear magnetic resonance, carbon proportion, absorbance, and fluorescence data. With TRM-0522 becoming more widely used, a variety of labs have generated different metrics that help to characterize and define the chemical properties of this coastal reference material. …

Unraveling The Reactivity Of Nitrate Ester Explosives: Insights From Femtosecond Time-Resolved Mass Spectrometry And Computational Chemistry, Erica Britt

Theses and Dissertations

This dissertation uncovers the ultrafast molecular mechanisms underlying the decomposition of nitrate ester explosives—nitroglycerin (NG), ethylene glycol dinitrate (EGDN), and amyl nitrate—through the integration of femtosecond time-resolved mass spectrometry and advanced computational chemistry. Although these compounds play fundamental roles in both military and civilian contexts, the precise molecular dynamics governing their pronounced reactivity and impact sensitivity have remained inadequately characterized. Our research establishes that low O–NO2 bond dissociation energies are the primary driver of ultrafast fragmentation and high reactivity in all three esters. The distinctive molecular architectures of these esters dictate their explosive properties: NG’s tri-nitrate configuration leads to exceptional …

Intrinsic Gas-Phase Behavior Of Uranium Species: A Comprehensive Reactivity Study Of [O=U≡Ch]+ And [Uh]+, Justin Terhorst

Electronic Theses and Dissertations

The intrinsic chemistry of actinide elements, particularly uranium, remains a key challenge in understanding f-block reactivity due to the complexity introduced by solvent interactions, counter-ions, and complex equilibria in the condensed phase. In this dissertation, a systematic gas-phase study utilizing preparative tandem ion-trap mass spectrometry (PTMSⁿ) is presented, focusing on the reactivity of uranium-centered species, specifically [OUCH]⁺, an oxy uranium methylidyne species, and [UH]⁺ ions. By stripping away solvent effects and isolating the ions, PTMSⁿ provides a powerful platform to probe the fundamental chemical behavior of uranium species in their intrinsic state.

The …

Developing A Method To Identify Tyre Particles By Detecting Benzothiazole Via Gc-Ms, Emma Paull

The Plymouth Student Scientist

Tyre particles are a dominant source of microplastic pollution in our environment. However, their chemical and physical properties are poorly understood and no standardised methods for identifying and quantifying them exist. This study looked to develop a method to identify tyre particles using two tyre samples of differing particle sizes, fine (62 - 125 µm) and coarse (250 – 500 µm). Both samples underwent ultrasound-assisted extraction before being analysed via gas chromatography-mass spectrometry (GC-MS) in both full scan and SIM mode, using benzothiazole as a marker. Both samples were also analysed via particle size analysis, scanning electron microscopy (SEM) and …

Assessing Reproducibility Challenges In Clinical Metabolics, Darcy Lin Cochran

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Current metabolomics research is expanding to be multiplatform and interdisciplinary. Metabolomic analysis has the potential to provide detailed insight into any biological system of interest to analyze the underlying molecular mechanisms of variables like environment, disease, and genetics. Human clinical metabolomics is a major research area that is often focused on finding biomarkers or panels of biomarkers for different diseases. However, results are difficult to compare across different laboratories since the field of metabolomics has yet to widely adopt best practices for sample preparation, data acquisition and data processing, results are difficult to compare across different laboratories.

This thesis focuses …

Liquid Chromatography-Mass Spectrometry Based Metabolomics, Lipidomics And Epitranscriptomics., Raobo Xu

Electronic Theses and Dissertations

Metabolomics and lipidomics are the comprehensive studies of metabolites and lipids in cells, biological fluids, tissues, or organisms. These distinct chemical fingerprints are left behind by cellular processes. Epitranscriptomics is the field that focuses on examining chemical modifications on RNA molecules at the transcriptome level. Liquid chromatography-mass spectrometry (LC-MS) has been widely used in those omics studies. In this dissertation, I developed and applied both untargeted and targeted approaches using LC-MS based various analytical platforms to conduct omics studies. Firstly, I investigated caffeine metabolites in human urine and discovered three potential functional biomarkers to differentiate the stages of alcohol-associated liver …

Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Applications For Metabolomics, Darcy Cochran, Robert Powers

Robert Powers Publications

Metabolomics is an interdisciplinary field that aims to study all metabolites < 1500 Da that are ubiquitously found within all organisms. Metabolomics is experiencing exponential growth and commonly relies on high-resolution mass spectrometry (HRMS). Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is a form of HRMS that is particularly well suited for metabolomics research due to its exceptionally high resolution (10⁵–10⁶) and sensitivity with a mass accuracy in parts per billion (ppb). In this regard, FT-ICR-MS can provide valuable insights into the metabolomics analysis of complex biological systems due to unique capabilities such as the easy separation of isobaric and isomeric species, isotopic fine structure analysis, spatial resolution of metabolites in cells and tissues, and a high confidence (error) in metabolite identification. Alternatively, the large and complex data sets, long acquisition times, high cost, and limited access mainly through national mass spectrometry facilities may impede the …

High-Resolution Ion Mobility Analysis Of Isomeric Bile Acids Using Structures For Lossless Ion Manipulations (Slim) Im-Ms, Emmaleigh D. Efird

All Theses

Bile acids are an essential part of the human digestion system and play an important role in lipid absorption, bacteria movement in the small intestine, and regulation of the farnesoid X receptor (FXR) and G protein-coupled bile acid receptors (GPBAR) responsible for homeostasis. They are synthesized in the liver, stored in the gallbladder and the excess is carried on to the small intestine. Many liver and intestinal diseases are diagnosed based on bile acid metabolism pathways and the structures of those bile acids. Therefore, the bile acid structure determines the function of the molecule. Many bile acids are similar in …

Using Ion Mobility Mass Spectrometry In Conjuction With Derivatization Methods To Enhance The Separation Of Different Steroid Isomers, Shadrack Lucas

All Theses

One of the major problems facing analytical chemistry challenge is the isomers separation, due to their closely related molecular structures and physicochemical properties. Therefore, in this thesis, we have performed the separation of steroid isomers through the use of ion mobility mass spectrometry, using various chemical approaches. Ion mobility is an effective high-resolution separation techniques that utilizes the mobility of ions in the gas-phase environment. A useful tool for isomeric analysis due to the ability to separate different isomeric classes of steroids according to their varied collision cross-sections, which is achieved by taking advantage of differences in ion mobility.

Moreover, …

Cyanide Abundance Of Highly Aqueously Altered Cm Chondrites: Insight For Asteroid Bennu, Rachel A. Reichow

Boise State University Theses and Dissertations

Asteroids, and the meteorites that come from them, retained the composition of the early Solar System and can give us insight to the processes that lead to the origin of life. The current NASA mission, OSIRIS-REx, has returned asteroid samples from the near-Earth asteroid Bennu. This asteroid is thought to be similar in composition to highly aqueously altered meteorites including CM1 and CM1/2 meteorites. Cyanide is thought to be an important molecule for prebiotic chemistry. Simple cyanide salts would have been the most accessible form of cyanide for reactions to occur; however, they may have recombined to form different metal-cyanide …

Chemical Composition, Fate, And Toxicity Of Dissolved Hydrocarbon Oxidation Products In High Latitude Aquatic Environments, Maxwell Louis Harsha

LSU New Orleans Theses and Dissertations

Oil spilled in aquatic environments undergoes abiotic and biotic oxidation processes that produce hydrocarbon oxidation products (HOPs). HOPs rapidly diffuse in the water column, persisting and readily bioavailable to aquatic organisms. Characterizing HOPs is challenging because most of the mixture resides in the unresolved complex mixture (UCM). Understanding of the formation, fate, and toxicity of HOPs in high latitude environments remains limited. This research addresses these gaps through a comprehensive experimental approach, utilizing various analytical techniques including nonvolatile dissolved organic carbon (NVDOC) analysis, ultrahigh-resolution mass spectrometry, tandem mass spectrometry, inductively coupled plasma mass spectrometry, and fluorescence excitation-emission matrix spectroscopy. Additionally, …

A Multi-Omics Investigation Into The Mechanism Of Action Of An Anti-Tubercular Fatty Acid Analog, Isin T. Sakallioglu, Amith S. Maroli, Aline De Lima Leite, Darrell D. Marshall, Boone W. Evans, Denise K. Zinniel, Patrick H. Dussault, Raul G. Barletta, Robert Powers

Patrick Dussault Publications

The mechanism of action (MoA) of a clickable fatty acid analogue 8-(2-Cyclobuten-1-yl)octanoic acid (DA-CB) has been investigated for the first time. Proteomics, metabolomics, and lipidomics were combined with a network analysis to investigate the MoA of DA-CB against Mycobacterium smegmatis (Msm). The metabolomics results showed that DA-CB has a general MoA related to that of ethionamide, a mycolic acid inhibitor that targets enoyl-ACP reductase (InhA), but DA-CB likely inhibits a step downstream from InhA. Our combined multi-omics approach showed that DA-CB appears to disrupt the pathway leading to the biosynthesis of mycolic acids, an essential mycobacterial fatty acid …

Development Of Mass Spectrometric Glycan Characterization Tags Using Acid-Base Chemistry And/Or Free Radical Chemistry, Rayan Murtada, Shane Finn, Jinshan Gao

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

Despite recent advances in glycomics, glycan characterization still remains an analytical challenge. Accordingly, numerous glycan-tagging reagents with different chemistries were developed, including those involving acid-base chemistry and/or free radical chemistry. Acid-base chemistry excels at dissociating glycans into their constituent components in a systematic and predictable manner to generate cleavages at glycosidic bonds. Glycans are also highly susceptible to depolymerization by free radical processes, which is supported by results observed from electron-activated dissociation techniques. Therefore, the free radical activated glycan sequencing (FRAGS) reagent was developed so as to possess the characteristics of both acid-base and free radical chemistry, thus generating information-rich …

Development Of Vacuum-Assisted Headspace High-Capacity Solid-Phase Microextraction For The Determination Of Semi-Volatile Compounds From Samples At Lower Temperatures, Shannon L. Thomas, Kevin A. Schug, Colton Myers, Jason S. Herrington, Reagan L. Miller, Anush Pabley, Frank W. Foss

Chemistry & Biochemistry Dissertations - Archive

Vacuum-assisted headspace solid-phase microextraction (Vac-HS-SPME) is a method used to increase solid-phase microextraction sampling of semi-volatile organic compounds. Three studies were conducted using Vac-HS-SPME via gas chromatography - mass spectrometry (GC-MS) methods for analysis of various sample types. First, a study was performed using Vac- HS-SPME combined with a high-capacity (HC) SPME Arrow to determine the operational fundamentals and workflow necessary to achieve optimal extraction of semi-volatile compounds from a model solid matrix (Ottawa sand). The fundamentals investigated included the seals necessary to create a leak-free sampling vial under vacuum conditions; the magnitude of the vacuum exerted, and the time …

Development Of Novel Protein Digestion And Quantitation Methods For Mass Spectrometic Analysis, Yongling Ai

Dissertations

Proteins are the workhorses of biology, playing multifaceted roles in maintaining cellular function, signaling, and response to environmental cues. Understanding their abundance and dynamics is pivotal for unraveling the complexities of biological processes, which underpins the foundations of molecular and cellular biology. Accurate measurement of protein quantities provides insights into cellular homeostasis, facilitates the discovery of biomarkers, and sheds light on the molecular mechanisms of diseases, bridging the gap between the molecular intricacies of proteins and their functional consequences in health and disease. The evolution of protein quantitation methodologies, from classical colorimetric assays to sophisticated mass spectrometry-based approaches, has expanded …