Physical Sciences and Mathematics Commons^™

Protein Detection And Structural Characterization By Mass Spectrometry Using Supramolecular Assemblies And Small Molecules, Bo Zhao

Doctoral Dissertations

Mass spectrometry (MS) has played an increasingly prominent role in proteomics and structure biology because it shows superior capabilities in identification, quantification and structural characterization of proteins. To realize its full potential in protein analysis, significant progress has been made in developing innovative techniques and reagents that can couple to MS detection. This dissertation demonstrates the use of polymeric supramolecular assemblies for enhanced protein detection in complex biological mixtures by MS. An amphiphilic random co-polymer scaffold is developed to form functional supramolecular assemblies for protein/ peptide enrichment. The influences of charge density and functional group pK_a on host-guest interactions …

Development Of A Screening Method For Drugs Of Abuse By Direct Analysis Of Dried Urine Spots Coupled To Mass Spectrometry, Melanie Goldstein

Student Theses

Fast and easy screening procedures are essential in any forensic toxicology laboratory to differentiate negative samples from presumptive positive cases. Immunoassay techniques, such as enzyme multiplied immunoassay technique (EMIT), are routinely employed as screening procedures. However, these techniques lack specificity (only differentiate group of drugs and not individual compounds) and it is difficult to add new compounds to the panel. Direct analysis of dried urine spots (DUS) by mass spectrometry (MS) offers a novel strategy to overcome these issues. DUS offer an improved storage alternative for biological samples, reducing costs and space requirements. In this work, an original method to …

Lipid Biomarkers Of Bering And Chukchi Sea Euphausiids And Their Application To Diet History, Rachel L. Pleuthner

OES Theses and Dissertations

In the eastern Bering Sea, Thysanoessa raschii are the most abundant krill species and a keystone trophic member that serve as both an important grazer and link to upper level consumers. In this system krill experience large annual variation in food resources, especially during ice advance and retreat; multiple lipid classes are used to temper the effects of those fluctuations, as well as to fuel reproduction and growth. Two shipboard feeding experiments that occurred during late spring and early summer of 2010, respectively, monitored the lipid retention in adult T. raschii and examined the fluctuation of specific lipid biomarkers under …

Improving Protein Analysis By Desorption Electrospray Ionization (Desi-Ms), Elahe Honarvar

Dissertations

Electrospray ionization mass spectrometry (ESI-MS) is one of the most well-known and versatile techniques for analyzing a broad range of molecules and it has become one of the leading techniques to study biomolecules, such as proteins. ESI-MS can accurately determine the molecular weight of proteins and provide information about their peptide sequence, post-translational modifications as well as their interaction with other molecules.

During ESI-MS analysis, by spraying a sample of proteins, prepared in form of a solution, charged droplets are produced using an electric field. As the solvent molecules gradually evaporate from these droplets, freely hovering bare protein ions remain. …

Enhanced Mass Spectrometric Analysis Of Peptides And Proteins Using Polymeric Reverse Micelles, Mahalia Adelina Corazon Paningbatan Serrano

Doctoral Dissertations

Mass spectrometry (MS) has become a key and indispensable tool in the identification, characterization, and quantitative analysis of proteins owing to its universality, sensitivity, specificity, and its capability for multiplexed detection. Because biological samples containing these protein analytes are almost always complex systems, various techniques are employed in conjunction with MS to fully harness its analytical potential and enhance its detection capabilities. This dissertation explores the use of amphiphilic polymeric reverse micelles in enriching proteins and peptides from complex biological mixtures and in enhancing their mass spectrometric analysis. Fundamental studies that elucidate the molecular basis for the observed MS signal …

Xflow: An Algorithm For Extracting Ion Chromatograms, Mathew M. Gutierrez, Rob Smith

Graduate Student Theses, Dissertations, & Professional Papers

Abstract: Mass spectrometry is a fundamental tool for modern proteomics. The increasing availability of mass spectrometry data paired with the increasing sensitivity and fidelity of the instruments necessitates new and more potent analytical methods. To that end, we have created and present XFlow, a feature detection algorithm for extracting ion chromatograms from MS1 LC-MS data. XFlow is a parameter-free procedurally agnostic feature detection algorithm that utilizes the latent properties of ion chromatograms to resolve them from the surrounding noise present in MS1 data. XFlow is designed to function on either profile or centroided data across different resolutions and instruments. This …

Evaluating Methods Of Obtaining Male Pheromone From Hymenochirus Sp. Using Analytical Chemistry, Vincent Wing-Kun Leung

University of the Pacific Theses and Dissertations

Male Hymenochirus sp. frogs are known to release pheromone that attracts females of the same species. Four methods for collecting secretions containing pheromone in Hymenochirus sp. were tested: norepinephrine injection, gonadotropin-releasing hormone injection, homogenization of gland tissue, and electrostimulation of the skin over the breeding gland area. The samples collected were analyzed using high-performance liquid chromatography (HPLC) and mass spectrometry. The HPLC chromatograph for the male norepinephrine sample contained a peak at 6.4 min that was not in the female norepinephrine sample HPLC chromatograph. The male norepinephrine sample mass spectrum had a peak of m/z 292.0 not in the female …

Non-Target Analyses Of Novel Psychoactive Substances; Inherent Variation In Gcms Relative Abundances And Gas Phase Hydrogen Deuterium Exchange Isomer Discrimination, Kristin Michelle Kelly

Graduate Theses, Dissertations, and Problem Reports

Novel psychoactive substances (NPSs) are synthetically derived compounds designed to mimic the effects of other illicit drugs. An endless cycle of NPSs continually reach the drug market due to limitations in drug legislation creating two problems: (1) non-availability of standards and (2) multiple isobars indistinguishable even to high resolution mass spectrometry. Gas chromatography-mass spectrometry (GCMS) is the most common instrument used for compound identification in non-targeted seized drug analysis. Compound identification using this technique relies on mass spectra where the percent relative abundances (%RAs) of all m/z values are compared manually or searched against a library database. Lacking standards, laboratories …

Development Of Laser Ablation Direct Analysis In Real Time Imaging-Mass Spectrometry (Ladi-Ms)-Applications To Questions Of Relevance To Forensic Science And Plant Biochemistry, Kristen Leigh Fowble

Legacy Theses & Dissertations (2009 - 2024)

Methods for the accomplishment of small molecule imaging by mass spectrometry are challenged by the need for sample pre-treatment steps such as cryo-sectioning, dehydration, chemical fixation, or application of a matrix or solvent, that must be performed to obtain interpretable spatial distribution data. Furthermore, these steps along with requirements of the mass analyzer such as high vacuum, can severely limit the range of sample types that can be analyzed by this powerful method. Here, we report the development of a laser ablation-direct analysis in real time imaging-mass spectrometry (LADI-MS) approach which couples a 213 nm Nd:YAG solid state UV laser …

Novel Mass Spectrometric Approaches For Deciphering The Epitranscriptomic Code, William D. Mcintyre

Legacy Theses & Dissertations (2009 - 2024)

According to the results of the Human Genome Project, less than 5% of our genome consists of sequences that code for actual proteins. At the same time, however, ~90% of these non-coding sequences are transcribed into a myriad of classes of ribonucleic acids collectively known as ncRNAs, which have been recognized as essential regulatory factors. It has been recently shown that the activity of ncRNAs can be in turn modulated by post-transcriptional modifications (PTMs), covalent marks that can be established/removed by tightly regulated enzymatic pathways. Now, the race is on to understand the new set of controls of cellular functions …