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Full-Text Articles in Physical Sciences and Mathematics
Zero-Knowledge De Novo Algorithms For Analyzing Small Molecules Using Mass Spectrometry, Patrick Anthony Kreitzberg
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 …
Bayesian Analytical Approaches For Metabolomics : A Novel Method For Molecular Structure-Informed Metabolite Interaction Modeling, A Novel Diagnostic Model For Differentiating Myocardial Infarction Type, And Approaches For Compound Identification Given Mass Spectrometry Data., Patrick J. Trainor
Electronic Theses and Dissertations
Metabolomics, the study of small molecules in biological systems, has enjoyed great success in enabling researchers to examine disease-associated metabolic dysregulation and has been utilized for the discovery biomarkers of disease and phenotypic states. In spite of recent technological advances in the analytical platforms utilized in metabolomics and the proliferation of tools for the analysis of metabolomics data, significant challenges in metabolomics data analyses remain. In this dissertation, we present three of these challenges and Bayesian methodological solutions for each. In the first part we develop a new methodology to serve a basis for making higher order inferences in metabolomics, …
A Framework For The Statistical Analysis Of Mass Spectrometry Imaging Experiments, Kyle Bemis
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 …
Elucidation And Improvement Of Algorithms For Mass Spectrometry Isotope Trace Detection, Robert Anthony Smith
Elucidation And Improvement Of Algorithms For Mass Spectrometry Isotope Trace Detection, Robert Anthony Smith
Theses and Dissertations
Mass spectrometry facilitates cutting edge advancements in many fields. Although instrumentation has advanced dramatically in the last 100 years, data processing algorithms have not kept pace. Without sensitive and accurate signal segmentation algorithms, the utility of mass spectrometry is limited. In this dissertation, we provide an overview and analysis of mass spectrometry data processing. A tutorial to ease the learning curve for those outside the field is provided. We draw attention to the lack of critical evaluation in the field and describe the resulting effects, including a glut of algorithm contributions of questionable novel contribution. To facilitate increased critical evaluation, …
A Dynamic State Metabolic Journey: From Mass Spectrometry To Network Analysis Via Estimation Of Kinetic Parameters, Arockia Ranjitha Dhanasekaran
A Dynamic State Metabolic Journey: From Mass Spectrometry To Network Analysis Via Estimation Of Kinetic Parameters, Arockia Ranjitha Dhanasekaran
All Graduate Theses and Dissertations, Spring 1920 to Summer 2023
The term "metabolism" refers to the chemical processes occurring in a living organism to convert the food consumed into the energy needed to maintain a living state. Metabolism consists of two states, namely, a dynamic state and a steady state. In the dynamic state, the rate of chemical conversion of a substance is proportional to the amount of substance available, whereas in the steady state this rate is constant and independent of the amount of substance present (Chapter 4 Figure 1). Like all other fields of engineering, metabolic engineering involves the analysis and synthesis of metabolism. Molecular biological tools for …