Kong Kam-chuen, Ebenezer. / Thesis submitted in: July 2003. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2004. / Includes bibliographical references (leaves 131-149). / Abstracts in English and Chinese. / Abstract in English --- p.i / Abstract in Chinese --- p.ii / Table of Content --- p.iii -vii / Acknowledgement --- p.viii / List of Abbreviations --- p.ix -x / List of Tables --- p.xi / List of Figures --- p.xii -xiii / List of Appendices --- p.xiv -xv / Chapter CHAPTER 1 --- Review of Literature / Chapter 1.1 --- Peptidomic Research / Chapter 1.1.1 --- Proteomics and Genomics --- p.1-2 / Chapter 1.1.2 --- Peptidomics and Quantitative Profiling --- p.2-5 / Chapter 1.1.3 --- Proteomics and Peptidomics in Medical Research --- p.5-6 / Chapter 1.1.4 --- Application of Quantitative Peptidomic Profiling in Cancer Research --- p.6-8 / Chapter 1.2 --- Technologies for Peptidomic Studies and Limitations --- p.9-11 / Chapter 1.2.1 --- High Performance Liquid Chromatograph (HPLC) --- p.12 / Chapter 1.2.1.1 --- Basic Principle --- p.13-15 / Chapter 1.2.1.2 --- Application in Peptidomic / Proteomic Research --- p.16-17 / Chapter 1.2.2 --- Peptide Gel Electrophoresis --- p.18 -19 / Chapter 1.2.2.1 --- Basic Principle --- p.19-21 / Chapter 1.2.2.2 --- Application in Peptidomic / Proteomic Research --- p.21 -22 / Chapter 1.2.3 --- Capillary Electrophoresis (CE) --- p.23 -24 / Chapter 1.2.3.1 --- Basic Principle --- p.24-29 / Chapter 1.2.4 --- Mass Spectrometry --- p.30 / Chapter 1.2.4.1 --- Electro spray Ionization (ESI) Mass Spectrometry --- p.31 / Chapter 1.2.4.1.1 --- Basic Principle --- p.31-34 / Chapter 1.2.4.2 --- Matrix-assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry --- p.35 / Chapter 1.2.4.2.1 --- Ionization of Sample --- p.35 -38 / Chapter 1.2.4.2.2 --- Time-of-Flight (TOF) Analyzer --- p.39-40 / Chapter 1.2.4.2.3 --- Application in Peptidomic / Proteomic Research --- p.40-42 / Chapter 1.2.4.2.4 --- Isotope-Coded Affinity Tags (ICAT®) --- p.42 -46 / Chapter 1.2.4.2.5 --- Limitations --- p.46 -48 / Chapter 1.2.4.3 --- Surface Enhanced Laser Desorption/Ionization (SELDI) Mass Spectrometry --- p.49 / Chapter 1.2.4.3.1 --- Basic Principle --- p.49 -51 / Chapter 1.2.4.3.2 --- Application in Peptidomic / Proteomic Research --- p.51-52 / Chapter 1.2.4.3.3 --- Retentate Chromatography (RC) --- p.53-54 / Chapter 1.2.4.4. --- Recent Advances in Application of MALDI Technologies --- p.55 -57 / Chapter CHAPTER 2 --- Objectives --- p.58 -59 / Chapter CHAPTER 3 --- Methodologies / Chapter 3.1 --- Method Development / Chapter 3.1.1 --- Nitrocellulose (NC) Preparation --- p.60 / Chapter 3.1.2 --- Matrix Chemicals Preparation --- p.60 / Chapter 3.1.3 --- Spotting Methods --- p.61 / Chapter 3.1.4 --- Standard Preparation --- p.61 -63 / Chapter 3.1.5 --- Data Collection and Analysis --- p.64 / Chapter 3.2 --- Identification of Distinguishing Features for HCC --- p.65 / Chapter 3.2.1 --- Classification Trees --- p.65 -66 / Chapter 3.2.2 --- Statistical Analysis --- p.66 / Chapter CHAPTER 4 --- Results / Chapter 4.1 --- Optimization of Spotting Methods in Protein Quantification --- p.67 -68 / Chapter 4.1.1 --- Detection of Low-Molecular Weight Proteins / Peptides --- p.68 -71 / Chapter 4.1.2 --- Detection of High-Molecular Weight Proteins --- p.71 -74 / Chapter 4.2 --- Assay Linearity of the Nitrocellulose-MALDI-TOF MS for Peptides with Different Masses --- p.75 -84 / Chapter 4.3 --- Accuracy of Mass Measurement --- p.84 -85 / Chapter 4.4 --- Applications in Quantitative Peptidomic Profiling of Serum --- p.86 -88 / Chapter 4.5 --- Application in Tumor Marker Discovery / Chapter 4.5.1 --- Identification of Peptidomic Features For Classification Between the HCC and CLD Patients by Classification Tree Analysis --- p.89 - 92 / Chapter 4.5.2 --- Serum Levels of the Diagnostic Peptides in the HCC and CLD Patient Groups --- p.93 / Chapter 4.5.3 --- Spearman's Rank Correlation Analysis of the Diagnostic Peptides and AFP --- p.93-101 / Chapter 4.5.4 --- Combined Use of the Diagnostic Peptides and AFP in the Diagnosis of HCC --- p.102-105 / Chapter CHAPTER 5 --- Discussion --- p.106-108 / Chapter 5.1 --- Evaluation of Different Matrix Chemical and Sample Spotting Techniques / Chapter 5.1.1 --- Effect of CHCA and SA --- p.109 / Chapter 5.1.2 --- Effect of Nitrocellulose in Peptide Ions Formation --- p.110-112 / Chapter 5.2 --- MS Automation and High-Throughput Sampling --- p.113 / Chapter 5.3 --- Reproducibility and Signal Quantitations --- p.114-115 / Chapter 5.4 --- Peptidomics: The Study of Entire Peptidome --- p.116 / Chapter 5.5 --- Serum Peptides --- p.117-118 / Chapter 5.6 --- Application of Peptidomics to Discover Markers for HCC / Chapter 5.6.1 --- Hepatocellular Carcinoma --- p.119 / Chapter 5.6.2 --- Causes of HCC --- p.119-120 / Chapter 5.6.3 --- HCC Tumor Markers --- p.120-122 / Chapter 5.6.4 --- HCC Tumor Markers Identified in the Current Studies --- p.122-124 / Chapter 5.7 --- "Role of MALDI-TOF MS, SELDI-TOF MS and 2-DE in Peptidomics" --- p.125-128 / Chapter CHAPTER 6 --- Conclusion --- p.129-130 / Chapter CHAPTER 7 --- References --- p.131-140 / Chapter CHAPTER 8 --- Original Data --- p.150 / Chapter CHAPTER 9 --- Appendices --- p.151-167

Choy, Man Fai. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (leaves 120-123). / Abstracts in English and Chinese. / Title Page --- p.1 / Abstract (English) --- p.2 / Abstract (Chinese) --- p.3 / Acknowledgement --- p.4 / Declaration --- p.5 / Table of Content --- p.6 / Lists of Figures --- p.9 / Lists of Tables --- p.12 / List of Schemes --- p.13 / Chapter Chapter One --- Introduction / Historical perspective and overview of tandem mass spectrometry for structural biochemistry --- p.14 / Electrospray ionization (ESI) --- p.15 / Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) --- p.18 / Chapter 1.3.1 --- History of FTICR --- p.18 / Chapter 1.3.2 --- Theory of FTICR --- p.21 / Chapter 1.4 --- Sequencing of DNA fragments --- p.26 / Chapter 1.4.1 --- Conventional and mass spectrometric sequencing techniques --- p.26 / Chapter 1.4.2 --- Fragment-ion nomenclature --- p.27 / Chapter 1.4.3 --- Tandem mass spectrometry of oligonucleotide ions --- p.29 / Chapter 1.4.4 --- Electron capture dissociation of oligonucleotide ions --- p.31 / Chapter 1.5 --- Outline of the present work --- p.32 / Chapter Chapter Two --- Instrument and Experimental / Chapter 2.1 --- Instrumentation --- p.35 / Chapter 2.1.1 --- Fourier-transform ion cyclotron resonance mass spectrometer --- p.35 / Chapter 2.1.2 --- Vacuum system --- p.35 / Chapter 2.1.3 --- Nanospray ion source --- p.39 / Chapter 2.1.4 --- Ion Transfer system --- p.41 / Chapter 2.1.5 --- Infinity cell --- p.43 / Chapter 2.1.6 --- Electron emission source --- p.44 / Chapter 2.2 --- Experimental section --- p.47 / Chapter 2.2.1 --- Simple acquisition pulse program --- p.47 / Chapter 2.2.2 --- ECD pulse program --- p.49 / Chapter Chapter Three --- Production of Doubly-prontonated Oligonucleotide ions using Nanospray Ionization / Chapter 3.1 --- Introduction --- p.52 / Chapter 3.2 --- Experimental and instrumental section --- p.53 / Chapter 3.2.1 --- Materials --- p.53 / Chapter 3.2.2 --- Sample preparation --- p.53 / Chapter 3.2.3 --- Instrumentation --- p.54 / Chapter 3.3 --- Results and discussion --- p.54 / Chapter 3.3.1 --- Effect of the concentration of ammonium formate --- p.54 / Chapter 3.3.2 --- Effects of the anionic pair of the ammonium salts --- p.57 / Chapter 3.3.3 --- Effects of solvent composition --- p.64 / Chapter 3.3.4 --- Effects of analyte concentration --- p.66 / Chapter 3.4 --- Conclusion --- p.68 / Chapter Chapter Four --- Electron Capture Dissociation of Model Oligonucleotides / Chapter 4.1 --- Introduction --- p.69 / Chapter 4.2 --- Experimental and instrumental section --- p.70 / Chapter 4.2.1 --- Materials --- p.70 / Chapter 4.2.2 --- Sample preparation --- p.70 / Chapter 4.2.3 --- Instrumentation --- p.71 / Chapter 4.2.4 --- Method of calculations --- p.71 / Chapter 4.3 --- Results and discussion --- p.72 / Chapter 4.3.1 --- "ECD of d(CCCCC), d(CCAAC), d(CCTTC) and d(CCGGC)" --- p.72 / Chapter 4.3.1.1 --- General features --- p.72 / Chapter 4.3.1.2 --- Protonated nucleobases and nucleoside-like fragments --- p.73 / Chapter 4.3.1.3 --- Doubly-charged fragment ions --- p.79 / Chapter 4.3.2 --- Theoretical calculation of electron capture affinities of common functionalities in oligonucleotides --- p.80 / Chapter 4.3.3 --- Electron capture dissociation of C/T binary-based oligonucleotides --- p.81 / Chapter 4.3.3.1 --- "ECD of d(CTCTC), d(TCCCT) and d(CTTTC)" --- p.84 / Chapter 4.3.3.2 --- ECD of d(CCCCT) and d(TCCCC) --- p.84 / Chapter 4.3.4 --- Mechanistic implications --- p.89 / Chapter 4.4 --- Conclusion --- p.99 / Chapter Chapter Five --- Electron Capture Dissociation of a Series of G/T Binary Base of Oligonucleotides / Chapter 5.1 --- Introduction --- p.100 / Chapter 5.2 --- Experimental and instrumental section --- p.100 / Chapter 5.2.1 --- Materials --- p.100 / Chapter 5.2.2 --- Sample preparation --- p.100 / Chapter 5.2.3 --- Instrumentation --- p.101 / Chapter 5.3 --- Results and discussion --- p.101 / Chapter 5.3.1 --- Electron capture dissociation of d(GGGGG) --- p.101 / Chapter 5.3.2 --- Electron capture dissociation of G/T binary-based oligonucleotides --- p.104 / Chapter 5.3.2.1 --- "ECD of d(GTGTG), d(GTTTG) and d(TGGGT)" --- p.104 / Chapter 5.3.2.2 --- ECD of d(GGGGT) and d(TGGGG) --- p.107 / Chapter 5.3.3 --- Mechanistic implications --- p.110 / Chapter 5.4 --- Conclusion --- p.117 / Chapter Chapter Six --- Conclusion Remarks --- p.118 / References --- p.120 / Appendix A --- p.124 / Appendix B --- p.127

Li, Gang. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (leaves 102-108). / Abstracts in English and Chinese. / TABLE OF CONTENTS --- p.v / LIST OF FIGURES --- p.viii / LIST OF TABLES --- p.xi / ABBREVIATIONS --- p.xii / Chapter Chapter One --- Introduction / Chapter 1.1 --- Matrix-assisted Laser Desorption/Ionization (MALDI) --- p.2 / Chapter 1.1.1 --- Laser Desorption --- p.2 / Chapter 1.1.2 --- Matrix-assisted Laser Desorption/Ionization --- p.2 / Chapter 1.2 --- Time-of-flight Mass Spectrometry --- p.6 / Chapter 1.2.1 --- Linear Time-of-flight Mass Spectrometer --- p.6 / Chapter 1.2.2 --- Reflectron Time-of-flight Mass Spectrometer --- p.7 / Chapter 1.2.2.1 --- Linear-field Reflectron --- p.9 / Chapter 1.2.2.2 --- Nonlinear-field Reflectron --- p.12 / Chapter 1.3 --- Structural Analysis Using Time-of-flight Mass Spectrometer --- p.13 / Chapter 1.4 --- Project Objectives --- p.17 / Chapter Chapter Two --- Instrumentation and Experimental / Chapter 2.1 --- Instrumentation --- p.20 / Chapter 2.1.1 --- Laser system --- p.20 / Chapter 2.1.2 --- Flight Tube and Vacuum System --- p.20 / Chapter 2.1.3 --- Ion source --- p.22 / Chapter 2.1.4 --- Deflector and Time Ion Selector --- p.24 / Chapter 2.1.5 --- Two-stage Gridless Reflectron --- p.28 / Chapter 2.1.6 --- "Detectors, Digitizer and Computer System" --- p.28 / Chapter 2.2 --- Experimental --- p.31 / Chapter 2.2.1 --- Sample preparation --- p.32 / Chapter 2.2.2 --- PSD calibration --- p.32 / Chapter Chapter Three --- "Simulation Studies of Time Ion Selector, Collision cells and Curved-field Reflectron" / Chapter 3.1 --- Introduction --- p.35 / Chapter 3.2 --- Time Ion selector --- p.37 / Chapter 3.3 --- Collision cell --- p.46 / Chapter 3.3.1 --- Simulation of Collision Induced Dissociation (CID) Conditions --- p.46 / Chapter 3.3.2 --- Design and Performance Evaluation of Different Collision Cells --- p.48 / Chapter 3.4 --- Curved-field reflectron (CFR) --- p.58 / Chapter 3.4.1 --- Introduction --- p.58 / Chapter 3.4.2 --- Derivation of Analytical Equations --- p.58 / Chapter 3.4.3 --- Effect of Floating Potential of the Collision Cell --- p.65 / Chapter 3.4.4 --- Effect of R and θ Parameters --- p.65 / Chapter 3.4.5 --- Effect of Length of the Reflectron --- p.70 / Chapter 3.5 --- Conclusions --- p.73 / Chapter Chapter Four --- Construction and Performance Evaluation of Modified Time-of-flight Mass Spectrometer / Chapter 4.1 --- Benchmark Results for the Origin Reflectron Time-of-flight Mass Spectrometer --- p.75 / Chapter 4.2 --- Hardware Modifications of Reflectron Time-of-flight Mass Spectrometer --- p.75 / Chapter 4.2.1 --- Collision Cell --- p.75 / Chapter 4.2.2 --- Curved-field Reflectron --- p.79 / Chapter 4.3 --- Evaluation of the Curved-field Reflectron --- p.81 / Chapter 4.4 --- Evaluation of the field-shaped cylindrical collision cell --- p.85 / Chapter 4.5 --- Conclusions --- p.95 / Chapter Chapter Five --- Concluding Remarks / Chapter 5.1 --- Concluding Remarks --- p.100 / References --- p.101 / Appendix / Appendix 1 User program for time ion selection --- p.108 / Appendix 2 User program for gas collision --- p.111 / Appendix 3 MATHEMATICA program used in calculation for curved-fleld reflectron --- p.114

Amphibians contain a rich chemical arsenal in their skin glands, vital for their defence against predators, both large and small. The peptides secreted by the frogs have a range of biological activities. These include both antibacterial and anticancer activity, others are neuropeptides, while some exhibit antifungal and antimalarial activity. Peptides are usually sequenced using positive ion mass spectrometry ( MS ). However, negative ion MS can also provide valuable sequencing information. Under negative ion MS conditions, the presence of a Cys residue is immediately identified by the facile side chain loss of H [subscript 2] S. The position of the Cys residue is determined by the formation of a side chain induced backbone cleavage ion. When a Cys residue is in the C - terminal position of a peptide, the spectrum is dominated by the loss of both H [subscript 2] S and CO [subscript 2]. Negative ion MS can also be used to identify and sequence intramolecular disulfide bridged peptides. The disulfide bridge is immediately identified by the facile loss of H [subscript 2] S [subscript 2] from the parent anion. Once the disulfide bridge is cleaved, further amide cleavages provide much of the sequence of the peptide, including the residues originally within the disulfide link. When one of the disulfide bridged Cys residues is in the C - terminal position, the major fragmentation is the loss of H [subscript 2] S [subscript 2] and CO [subscipt 2] from the parent ion. The negative ion mass spectra of citropin 1.1 and synthetically modified analogues show an unusual loss of an internal Val residue from the ( M - H ) - parent ion. This rearrangement requires the decomposing anion to have an α - helical structure. The skin secretions of Litoria peronii or Peron ' s Tree Frog contain five novel peptides which have been named peroneins. Four pro - peroneins are present in the summer secretions only. The biologically active peptides caerulein 1.1, caerin 1.1 and caerin 2.1 are also present in the glandular secretions. / Thesis (Ph.D.)--School of Chemistry and Physics, 2006.

<p>The work in this thesis has demonstrated the advantages and limitations of using MS based technologies in protein and peptide structural studies. </p><p>Tandem MS, specifically electron capture dissociation (ECD) have shown the ability to provide structural insights in molecules containing the slightest of all modifications (D-AA substitution). Additionally, it can be concluded that charge localization in molecular ions is best identified with ECD and to a lesser degree using CAD. </p><p>Fragment ion abundances are a quantifiable tool providing chiral recognition (R_Chiral). An analytical model demonstrating the detection and quantification of D-AAs within proteins and peptides has been achieved. ECD has demonstrated the ability to quantify stereoisomeric mixtures to as little as 1%. Chirality elucidation on a nano LC-MS/MS time scale has been shown. </p><p>The structures of various stereoisomers of the mini protein Trp Cage were explored, each providing unique ECD fragment ion abundances suggestive of gas phase structural differences. The uniqueness of these abundances combined with MDS data have been used in proposing a new mechanism in c and z fragment ion formation in ECD. This mechanism suggests initial electron capture on a backbone amide involved in (neutral) hydrogen bonding.</p><p>The wealth of solution phase (circular dichroism), transitition phase (charge state distribution, CSD) and gas phase (ECD) data for Trp Cage suggest that at low charge states (2+) the molecule has a high degree of structural similarity in solution- and gas- phases. Furthermore, quantitative information from CSD studies is garnered when using a “native” deuteriated form as part of the stereoisomeric mixture. It has also been shown that the stability of the reduced species after electron capture is indicative of the recombination energy release, which in turn is linked to the coulombic repulsion- a structural constraint that can be used for approximation of the inter-charge distance for various stereoisomers.</p>

The work in this thesis has demonstrated the advantages and limitations of using MS based technologies in protein and peptide structural studies. Tandem MS, specifically electron capture dissociation (ECD) have shown the ability to provide structural insights in molecules containing the slightest of all modifications (D-AA substitution). Additionally, it can be concluded that charge localization in molecular ions is best identified with ECD and to a lesser degree using CAD. Fragment ion abundances are a quantifiable tool providing chiral recognition (RChiral). An analytical model demonstrating the detection and quantification of D-AAs within proteins and peptides has been achieved. ECD has demonstrated the ability to quantify stereoisomeric mixtures to as little as 1%. Chirality elucidation on a nano LC-MS/MS time scale has been shown. The structures of various stereoisomers of the mini protein Trp Cage were explored, each providing unique ECD fragment ion abundances suggestive of gas phase structural differences. The uniqueness of these abundances combined with MDS data have been used in proposing a new mechanism in c and z fragment ion formation in ECD. This mechanism suggests initial electron capture on a backbone amide involved in (neutral) hydrogen bonding. The wealth of solution phase (circular dichroism), transitition phase (charge state distribution, CSD) and gas phase (ECD) data for Trp Cage suggest that at low charge states (2+) the molecule has a high degree of structural similarity in solution- and gas- phases. Furthermore, quantitative information from CSD studies is garnered when using a “native” deuteriated form as part of the stereoisomeric mixture. It has also been shown that the stability of the reduced species after electron capture is indicative of the recombination energy release, which in turn is linked to the coulombic repulsion- a structural constraint that can be used for approximation of the inter-charge distance for various stereoisomers.

High resolution mapping of molecular species, specifically sub-micrometer spatial resolution mapping, is at the forefront of recent interest in Secondary Ion Mass Spectrometry (SIMS). Large projectiles, e.g. C60, Au400, display high quasi-molecular ion yields with reduced fragment ion yields compared to atomic or polyatomic projectiles. However, the application of large projectiles in a sub-micrometer beam is hampered by limitations in source brightness and angular emission characteristics which are incompatible with tight focusing. An alternate approach to a focused beam is to reduce the beam intensity to less than 1000 impacts per second (referred to as the event-by-event mode) and localize each projectile impact via an electron emission microscope. The characterization and performance of such an instrument for localizing individual projectile impacts of 15-75keV C60 with sub-micrometer spatial resolution are described here. The quest for localizing single cluster impacts requires an understanding of the relationship between SI and electron emissions. It was found that electron emission is observed independently of the number or type of secondary ion emitted for flat homogeneous samples. The independence of ion and electron emission confirms the rationale for using the emitted electrons to localize individual projectile impacts. Further investigation of electron emission revealed that the electron yield is characteristic of the class of sample investigated (e.g. metal, organic, semiconductor). The electron yield was found to depend on the size and topology of the sample. Additionally, the electron yield increases with increasing projectile velocity. The use of the novel instrumentation presented here, necessitated the development of custom acquisition and analysis software. The analysis of co-emitted species from nano-metric dimensions is enhanced with the ability to perform multiple coincidence/anti-coincidence calculations. New concepts were implemented for integrating localization and mass spectrometry via software solutions for image analysis and localization and subsequently correlation between emitted ions and electrons. The result is software and instrumentation capable of generating ion maps with sub-micrometer spatial resolution.

Ambient ionization mass spectrometry, which has witnessed a flurry of recent developments, is a set of useful techniques for the analysis of samples under open-air conditions. It allows direct, rapid, real-time, high-throughput analysis with little or no sample pretreatment for the chemicals in solids or liquids. In this study, thermal desorption electrospray ionization mass spectrometry ( TD-ESI/MS ) involving direct insertion probe ( DIP ), thermal desorption ( TD ) and electrospray ionization ( ESI ) was used for the rapid screening of various types of samples. The source mainly consists of the sampling probe device, thermal desorption heating device, electrospray ionization device, ion source and temperature controller. A novel strategy involved in TD-ESI/MS processes where sampling, desorption, and ionization are separated as three independent events. The sampling probe is first used for the sampling of analytes and then inserted into a heat unit for thermal desorption. The desorbed analytes are finally carried into a reaction region with a stream of nitrogen gas, where charged methanol droplets were generated continuously by electrospray for post-ionization. Total analysis time is less than 10 seconds. Traditionally, three standard methods are used for the analysis for pesticide residues, biochemical, immunoassay and instrument. And, the instrument analysis is the most widely used because it provides lots of advantages in particularly accurate quantitative approach. However, its complicated steps take a long period of time for preparation. Here, we used TD-ESI/MS to rapidly screen the pesticide residues on the surface of fruits and vegetables. The MS/MS analysis was also performed to confirm those detected compounds. The experimental results of the standard deviation for reproducibility is 13.2% (n = 10), and the detection limit is approximately 10 ppb. Furthermore, several fruits and vegetables purchased from local market were used as test samples and pesticide residues on the surface of samples can be successfully detected via TD-ESI/MS. In addition, the TD-ESI/MS technique was also applied to the analysis of illegal additives or phthalates in food. In this study, the TD-ESI/MS technique emerges lots of advantages such as direct, rapid, real-time analysis of sample surface and sample pretreatment is not necessary, and shows highly potential for rapid screening of chemicals in food safety.

Drift tube ion mobility spectrometry (IMS) is a powerful, post-ionization separation that yields structural information of ions through an ion-neutral collision cross section. The ion-neutral collision cross section is governed by the collision frequency of the ion with the neutral drift gas. Consequently, ions of different size will have different collision frequencies with the gas and be separated in the drift cell. A significant challenge for IMS, however, is to separate ions with very similar collision cross sections, requiring higher resolution ion mobility spectrometers. Resolution in IMS is of utmost importance for the separation of complex mixtures, e.g. crude oil samples, proteolytic digests, positional isomers, and ion conformers. However, most methods employed to increase mobility resolution significantly decrease ion transmission through the mobility device. Herein, a periodic-focusing DC ion guide drift cell (PDC IG) is presented to display its potential capabilities for higher mobility resolution with increased ion transmission. The PDC IG utilizes unique electrode geometry compared to the conventional uniform field electrode design. Electrode geometry can be defined by the electrode inner diameter (d), thickness (t), and spacing (s). Specifically, the ratio of d : t : s is equal to, or very near, 1:1:1. The PDC IG electrode design creates a non-uniform (fringing) electric field-especially near the electrode walls. The design also causes variations in the radial electric field which provides an effective RF as ions move through the device and a radially confining effective potential that improves ion transmission through the device. In this dissertation the analytical utility of the PDC IG drift cell for ion mobility separations will be explored. The radial focusing properties of the device will be presented along with studies of electrode geometry and its effect on ion mobility resolution and ion transmission through the drift cell. PDC IG drift cell length is also examined to determine its effect on mobility resolution and ion transmission. Finally, the PDC IG drift cell device is coupled to an orthogonal-acceleration time-of-flight mass spectrometer as well as a modular, PDC IG drift cell being adapted to a commercial qTOF mass spectrometer for IM-MS experiments.

The focus of this Ph.D. thesis is the theoretical, computational, and experimental analysis of electrohydrodynamics and ionization in the Array of Micromachined UltraSonic Electrospray (AMUSE) ion source. The AMUSE ion source, for mass spectrometry (MS), is a mechanically-driven, droplet-based ion source that can independently control charge separation and droplet formation, thereby conceptually differing from electrospray ionization (ESI). This aspect allows for low voltage soft ionization of a variety of analytes and flexibility in the choice of solvents, providing a multifunctional interface between liquid chromatography and mass spectrometry for bioanalysis. AMUSE is a versatile device that operates in an array format, enabling a wide range of configurations, including high-throughput and multiplexed modes of operation. This thesis establishes an in-depth understanding of the fundamental physics of analyte charging and electrokinetic charge separation in order to enhance droplet charging and ionization efficiency. A detailed electrohydrodynamic (EHD) computational model of charge transport during the droplet formation cycle in the AMUSE ion source is developed, coupling fluid dynamics, pressure and electric fields, and charge transport in multiphase flow. The developed EHD model presents a powerful tool for optimal design and operation of the AMUSE ion source, providing insight into the microscopic details of physicochemical phenomena, on the microsecond time scale. Analyte charging and electrohydrodynamics in AMUSE are characterized using dynamic charge generation measurements and high-spatial-resolution stroboscopic visualization of ejection phenomena. Specific regimes of charge transport, which control the final droplet charging, have been identified through experimental characterization and simulations. A scale analysis of the ejection phenomena provides a parametric regime map for AMUSE ejection modes in the presence of an external electric field. This analysis identifies the transition between inertia-dominated (mechanical) and electrically-dominated (electrospraying) ejection, where inertial and electric forces are comparable, producing coupled electromechanical atomization. The understanding of analyte charging and charge separation developed through complimentary theoretical and experimental investigations is utilized to improve signal abundance, sensitivity, and stability of the AMUSE-MS response. Finally, these tools and fundamental understanding provide a sound groundwork for the optimization of the AMUSE ion source and future MS investigations.