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A Review And Evaluation Of Techniques For Improved Feature Detection In Mass Spectrometry Data, Annika R. Tostengard, Rob Smith

Graduate Student Theses, Dissertations, & Professional Papers

Mass spectrometry (MS) is used in analysis of chemical samples to identify the molecules present and their quantities. This analytical technique has applications in many fields, from pharmacology to space exploration. Its impacts on medicine are particularly significant, since MS aids in the identification of molecules associated with disease; for instance, in proteomics, MS allows researchers to identify proteins that are associated with autoimmune disorders, cancers, and other conditions. Since the applications are so wide-ranging and the tool is ubiquitous across so many fields, it is critical that the analytical methods used to collect data are sound.

Data analysis in …

Characterization Of Nucleocapsid-Rna Interactions In Rift Valley Fever Virus Infection, Miyuki Hayashi

Graduate Student Theses, Dissertations, & Professional Papers

Rift Valley fever virus (RVFV) is a mosquito-borne virus that infects humans and livestock and exhibits potential for global spread. No vaccine or treatment is currently available for human use. The nucleocapsid protein (N) in RVFV is a multifunctional RNA-binding protein that is necessary for viral replication and dissemination. Because of its essential roles, N is a promising candidate to be targeted for anti-RVFV therapy. The goal of this dissertation is to characterize N-RNA interactions in RVFV infected cells. To achieve this goal, two methods, strand-specific reverse transcription and quantitative PCR (RT-qPCR) as well as multiple reaction monitoring mass spectrometry …

Zero-Knowledge De Novo Algorithms For Analyzing Small Molecules Using Mass Spectrometry, Patrick Anthony Kreitzberg

Graduate Student Theses, Dissertations, & Professional Papers

In the analysis of mass spectra, if a superset of the molecules thought to be in a sample is known a priori, then there are well established techniques for the identification of the molecules such as database search and spectral libraries. Linear molecules are chains of subunits. For example, a peptide is a linear molecule with an “alphabet” of 20 possible amino acid subunits. A peptide of length six will have 20⁶ = 64, 000, 000 different possible outcomes. Small molecules, such as sugars and metabolites, are not constrained to linear structures and may branch. These molecules are …

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 …