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And Ion Mobility – Mass Spectrometry As Platforms for X-Omic Analyses ABSTRACT Fueling Advances in Ultra Performance Liquid Chromatography – and Ion Mobility – Mass Spectrometry as Platforms for X-omic Analyses Sharon Michelle Munisamy, Ph.D. Mentor: C. Kevin Chambliss, Ph.D. Analysis of x-omics samples presents a significant challenge to analytical chemists. The complexity and diversity of x-omics samples make it difficult to determine or develop the right analytical approach. This dissertation presents novel applications of ultra performance liquid chromatography – high-resolution mass spectrometry (UPLC- HRMS) and ion mobility – high-resolution mass spectrometry (IM-HRMS) in two emerging x-omics areas: lignocellulomics and petroleomics. Compared to traditional methods of x-omics analyses, these techniques offer higher chromatographic efficiency with UPLC, which can equate to faster analysis times and greater separation, an additional degree of separation with ion mobility spectrometry (IMS), and high peak resolution and mass accuracy with HRMS, which allow for identification of known and unknown analytes. Direct infusion electrospray ionization – ion mobility – high-resolution mass spectrometry (DIESI-IM-HRMS) has been evaluated as a rapid technique for the determination of total molecular composition in “whole-sample” biomass hydrolysates and extracts. IM-HRMS data reveal a high molecular weight range of biomass components (up to 1100 m/z) and provide trendline isolation of feedstock components from those introduced “in process”. Carbohydrates and other lignocellulosic degradation products were identified via HRMS exact mass measurements (with typical mass errors less than 5 ppm). Analyte assignments were supported via IM-MS collision-cross-section (CCS) measurements and trendline analysis. An automated “omics” approach utilizing UPLC-HR-TOF-MS was developed for the identification of previously unknown lignocellulosic degradation products. The approach combines traditional HRMS techniques with a “metabolomics” method for novel compound identification. Evaluation of the method for a small subset (16) of the identified peaks enabled unambiguous molecular formula assignment for 69% of the peaks. Ion mobility – mass spectrometry and several model compounds were employed to better understand asphaltene molecules in terms of their structural types and degree of structural diversity. CCS analysis demonstrates that both monomeric and dimeric archipelago- and island-type structures might be present in asphaltenes. Comparison of arrival time peak widths for asphaltenes and model compounds indicates structural or conformational diversity for asphaltene compounds within a given nominal m/z. Fueling Advances in Ultra Performance Liquid Chromatography – and Ion Mobility – Mass Spectrometry as Platforms for X-omic Analyses by Sharon Michelle Munisamy, B.S. A Dissertation Approved by the Department of Chemistry and Biochemistry ___________________________________ Patrick J. Farmer, Ph.D., Chairperson Submitted to the Graduate Faculty of Baylor University in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Approved by the Dissertation Committee ___________________________________ C. Kevin Chambliss, Ph.D., Chairperson ___________________________________ Stephen L. Gipson, Ph.D. ___________________________________ Touradj Solouki, Ph.D. ___________________________________ Charles M. Garner, Ph.D. ___________________________________ William C. Hockaday, Ph.D. Accepted by the Graduate School May 2012 ___________________________________ J. Larry Lyon, Ph.D., Dean Page bearing signatures is kept on file in the Graduate School. Copyright © 2012 by Sharon Michelle Munisamy All rights reserved TABLE OF CONTENTS LIST OF FIGURES .......................................................................................................... vii LIST OF TABLES ............................................................................................................ xii ACKNOWLEDGMENTS ............................................................................................... xiv CHAPTER ONE-Introduction to X-omics Areas and Analyses .........................................1 Introduction to X-omes and X-omics: A Brief History ...........................................1 Traditional and Contemporary Techniques for X-omics Analyses .........................2 Established X-omics: Genomics and Proteomics ........................................3 Emerging X-omics: Petroleomics and Lignocellulomics ............................6 Common Limitations in X-omics Analyses ...........................................................10 UPLC-IM-HRMS as an Emerging Tool for X-omics Analyses ............................11 Ultra Performance Liquid Chromatography ..............................................11 Ion Mobility Spectrometry .........................................................................12 High-Resolution Time-of-Flight Mass Spectrometry ................................16 Scope of the Dissertation .......................................................................................19 CHAPTER TWO- Direct Infusion Electrospray Ionization – Ion Mobility – High- Resolution Mass Spectrometry (DIESI-IM-HRMS) for Rapid Characterization of Potential .................................................................................21 Introduction ............................................................................................................21 Experimental: Materials and Methods ...................................................................23 Chemicals and Reagents ............................................................................23 Preparation of Standards and Generation of Aqueous Extract and Hydrolysate Samples .........................................................................24 iii DIESI-IM-HRMS Analysis .......................................................................25 Collision-Cross-Section Measurements .....................................................26 Results and Discussion ..........................................................................................27 Analyte Identification via HRMS ..............................................................27 Characterization of IM-MS Spectra of Biomass Pretreatment Hydrolysates and Aqueous Extracts ..........................................................32 Evaluation of IM-HRMS Separation of Biomass Components .................42 Mass-Mobility Correlations of Carbohydrates in Biomass .......................48 Collision-Cross-Section Measurements of Biomass Analytes ..................50 Conclusions ............................................................................................................56 CHAPTER THREE- A “Metabolomics” Approach for Identification of Unknown Degradation Products in Lignocellulomic Samples using Ultra Performance Liquid Chromatography – High-Resolution Mass Spectrometry ..........................58 Introduction ............................................................................................................58 Experimental: Materials and Methods .......................................................60 Chemicals and Reagents ................................................................60 Generation of Extracted Hydrolysate Samples ..............................60 Preparation of Standards ................................................................61 Ultra Performance Liquid Chromatography ..................................61 High-Resolution Mass Spectrometry .............................................62 MetaboLynx Methodology ............................................................63 Results and Discussion ..........................................................................................66 UPLC Method Development .....................................................................66 Evaluation of HR-TOF-MS Mass Spectral Data .......................................68 A “Metabolomics” Approach to Unknown Component Identification .....71 iv Development of MetaboLynx Methodology .................................71 Automated Detection of Unknown Peaks in Hydrolysate .............73 Compositional Analysis from MetaboLynx-Generated Mass Spectral Data ....................................................................................75 Kendrick Mass Defect Analyses for Identification of Functional Groups ......................................................................................80 Comparison of Automated Compositional Analysis to Manual Data Inspection ...................................................................................................92 Visual identification of new peaks .................................................92 Manual MS/MS vs. automated MSe analyses ................................93 Conclusions ..........................................................................................................104 CHAPTER FOUR- Ion Mobility – Mass Spectrometry Analysis of Asphaltenes using Model Compounds to Understand Structure, Diversity, and Aggregation..........................................................................................................106 Introduction ..........................................................................................................106 Experimental: Materials and Methods .................................................................108 Chemicals and Reagents ..........................................................................108 Preparation
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