The K-shell x-ray and ionization cross sections are measured for protons on Ag, Cd, Sn, Sb, Te, Ba, and La over the ion energy range of 0.6 to 2.0 MeV. The data are compared to the predictions of the PWBA, the PWBA with corrections for binding energy and/or Coulomb deflection, the BEA, and the constrained BEA predictions. In general, the non-relativistic PWBA with binding energy correction gives the best overall agreement with the measurements of proton-induced x-ray processes for the K-shell of the elements studied in this work. The data further suggest the need for relativistic PWBA treatment of the interactions in the K-shell for the range of binding energies represented by the elements investigated in this work.

K-Shell ionization cross section for protons over the energy range of 0.4 to 2.0 MeV have been measured on thin targets of the elements Se, Br, Rb, Sr, Y, Mo and Pd. Total x-ray and ionization cross sections for the K-shell are reported. The experimental values of the ionization cross sections are compared to the non-relativistic plane-wave Born approximation, the binary-encounter approximation, the constrained binary-encounter approximation, and the plane-wave Born approximation with corrections for Coulomb-deflection and binding energy effects.

Lignin, the second most abundant naturally occurring polymer found in plant cell wall has the potential of becoming an alternative source for the production of chemical synthons for the pharmaceuticals and other chemical industries. While much gain has been made towards the development of degradation methods to break down lignin, effective analytical methods are still required to rapidly and accurately identify the products of lignin breakdown experiments. The goal of this work was to develop mass spectrometric methods for the characterization of lignin oligomers based on the study of model lignin compounds. Unlike peptides and oligosaccharides, lignin model compounds that could serve as analytical standards for methods developments are not commercially available, and hence, the first project of this dissertation focused on the synthesis of lignin model compounds containing the β-O-4 bond. The priority was to synthesize compounds containing all important functionalities that reflect the structure of native lignin. By employing the known Aldol reaction, lignin oligomers containing the β-O-4 were synthesized. The synthesized β-O-4 lignin oligomers contained the characteristic functional groups of native β-O-4 lignin, that is, the phenolic functionality, the aryl glycerol β-O-4 aryl ether bond and the unsaturated side chain. The second project was aimed at developing alternative ionization methods for the characterization of lignin in the negative ion mode mass spectrometry. A chloride adduct ionization method was developed and used for characterizing and sequencing lignin oligomers. This method proved to be very useful in stabilizing the adduct ion in the full scan spectrum mode and also providing useful structural information upon tandem mass spectrometry. In the third project, a cationization technique was developed to unambiguously assign the sequence in which β-O-4 lignin oligomers are connected. A simple and easy to use sequencing chart was designed and could serve as a guide for predicting the sequence of larger lignin oligomers. This method offers an alternative approach for the characterization of lignin oligomers in the positive ion mode mass spectrometry. The fourth project focused on the ionization response of a new class of β-O-4 lignin compounds. β-O-4 compounds having the same skeletal backbone but different non-polar groups at the a-position were synthesized, and their ESI response studied. Results from this study show that a slight change in the structure of a β-O-4 lignin model compound can change the cationization response to several order of magnitude. Most importantly, this work for the first time has shown a direct correlation between lignin ionization response and lignin structure. The fifth project was aimed at studying the chromatographic behavior of the diastereomer pair in β-O-4 lignin model compounds. Using three commercially available HPLC columns, the chromatographic behavior and factors that affect the separation of the diastereomer pair of the β-O-4 lignin diastereomer on an HPLC column were studied. By performing tandem mass spectrometry on each of the diastereomers, a fragmentation mechanism was developed that could be used to unambiguous assign the configuration (erythro or threo) for the pair of diastereomer in a β-O-4 model. The results presented in this dissertation adds significant knowledge to the lignin mass spectrometry literature, and it offers new ionization techniques for the characterization of lignin oligomers, most importantly, an alternative approach for lignin analysis using adduct ionization mass spectrometry. The developed methods could easily be extended for the characterization of larger lignin oligomers.

Since the introduction of electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI), there has been an unprecedented growth of biomolecule analysis using mass spectrometry (MS). One of the most popular applications for mass spectrometry is the field of proteomics, which has emerged as the next scientific challenge in the post-genome era. One critical step in proteomic analysis is sample preparation, a major bottleneck that is attributed to many time consuming and labor-intensive steps involved. Microfluidics can play an important role in proteome sample preparation due to its ability to handle small volumes of sample and reagent, and its capability to integrate multiple processes on a single chip with the potential for high-throughput analysis. However, to utilize microfluidic systems for proteome analysis, an efficient interface between microfluidic chip and mass spectrometry is required. This thesis presents several methods for coupling of microfluidic chips with ESI-MS and MALDIMS. III Three microfluidic-ESI interfaces were developed. The first interface involves fabricating a polymer based microchannel at the rectangular corners of the glass substrates using a single photolithography step. The second interface was build upon the previous interface in which a digital microfluidic platform was integrated with the microchannel in a “top-down” format. The integrated microfluidic system was used for inline quantification of amino acids in dried blood spots that have been processed by digital microfluidics. The third interface was formed by sandwiching a pulled glass capillary emitter between two digital microfluidic substrates. This method is a simpler and more direct coupling of digital microfluidics with ESI-MS as compared to the method used for second interface. Finally, a strategy using a removable plastic “skin” was developed to interface digital microfluidics with MALDI-MS for offline sample analysis. We demonstrated the utility of this format by implementing on-chip protein digestion on immobilized enzyme depots.

Since the introduction of electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI), there has been an unprecedented growth of biomolecule analysis using mass spectrometry (MS). One of the most popular applications for mass spectrometry is the field of proteomics, which has emerged as the next scientific challenge in the post-genome era. One critical step in proteomic analysis is sample preparation, a major bottleneck that is attributed to many time consuming and labor-intensive steps involved. Microfluidics can play an important role in proteome sample preparation due to its ability to handle small volumes of sample and reagent, and its capability to integrate multiple processes on a single chip with the potential for high-throughput analysis. However, to utilize microfluidic systems for proteome analysis, an efficient interface between microfluidic chip and mass spectrometry is required. This thesis presents several methods for coupling of microfluidic chips with ESI-MS and MALDIMS. III Three microfluidic-ESI interfaces were developed. The first interface involves fabricating a polymer based microchannel at the rectangular corners of the glass substrates using a single photolithography step. The second interface was build upon the previous interface in which a digital microfluidic platform was integrated with the microchannel in a “top-down” format. The integrated microfluidic system was used for inline quantification of amino acids in dried blood spots that have been processed by digital microfluidics. The third interface was formed by sandwiching a pulled glass capillary emitter between two digital microfluidic substrates. This method is a simpler and more direct coupling of digital microfluidics with ESI-MS as compared to the method used for second interface. Finally, a strategy using a removable plastic “skin” was developed to interface digital microfluidics with MALDI-MS for offline sample analysis. We demonstrated the utility of this format by implementing on-chip protein digestion on immobilized enzyme depots.

The adiabatic approximation is a natural approach for the description of phenomena induced by low frequency laser radiation because the ratio of the laser frequency to the characteristic frequency of an atom or a molecule is a small parameter. Since the main aim of this work is the study of ionization phenomena, the version of the adiabatic approximation that can account for the transition from a bound state to the continuum must be employed. Despite much work in this topic, a universally accepted adiabatic approach of bound-free transitions is lacking. Hence, based on Savichev's modified adiabatic approximation [Sov. Phys. JETP 73, 803 (1991)], we first of all derive the most convenient form of the adiabatic approximation for the problems at hand. Connections of the obtained result with the quasiclassical approximation and other previous investigations are discussed. Then, such an adiabatic approximation is applied to single-electron ionization and non-sequential double ionization of atoms in a strong low frequency laser field. The momentum distribution of photoelectrons induced by single-electron ionization is obtained analytically without any assumptions on the momentum of the electrons. Previous known results are derived as special cases of this general momentum distribution. The correlated momentum distribution of two-electrons due to non-sequential double ionization of atoms is calculated semi-analytically. We focus on the deeply quantum regime -- the below intensity threshold regime, where the energy of the active electron driven by the laser field is insufficient to collisionally ionize the parent ion, and the assistance of the laser field is required to create a doubly charged ion. A special attention is paid to the role of Coulomb interactions in the process. The signatures of electron-electron repulsion, electron-core attraction, and electron-laser interaction are identified. The results are compared with available experimental data. Two-electron correlated spectra of non-sequential double ionization below intensity threshold are known to exhibit back-to-back scattering of the electrons, viz., the anticorrelation of the electrons. Currently, the widely accepted interpretation of the anticorrelation is recollision-induced excitation of the ion plus subsequent field ionization of the second electron. We argue that there exists another mechanism, namely simultaneous electron emission, when the time of return of the rescattered electron is equal to the time of liberation of the bounded electron (the ion has no time for excitation), that can also explain the anticorrelation of the electrons in the deep below intensity threshold regime. Finally, we study single-electron molecular ionization. Based on the geometrical approach to tunnelling by P. D. Hislop and I. M. Sigal [Memoir. AMS 78, No. 399 (1989)], we introduce the concept of a leading tunnelling trajectory. It is then proven that leading tunnelling trajectories for single active electron models of molecular tunnelling ionization (i.e., theories where a molecular potential is modelled by a single-electron multi-centre potential) are linear in the case of short range interactions and ``almost'' linear in the case of long range interactions. The results are presented on both the formal and physically intuitive levels. Physical implications of the proven statements are discussed.

The ionization of chemicals in solids or liquids under ambient conditions, known as ambient ionization mass spectrometry, is currently a fruitful research area in mass spectrometry. To classify those ambient ionization techniques from preexisting atmospheric pressure ionization methods, the former are commonly defined as those mass spectrometric ionization methods that operate under ambient conditions and require minimal or no sample pretreatment. A characteristic of this technology is that sample introduction and ionization are usually separate events, thereby allowing independent control of each set of conditions. A two-step ESI-based technique, named electrospray laser desorption ionization (ELDI), has been developed to characterize nonvolatile analyte molecules directly from the surfaces of solid samples in 2005 by J. Shiea and his co-workers. The analyte molecules are produced by laser irradiating of the sample surfaces, and then post-ionized in an ESI plume. However, the pulsed laser used in ELDI-MS system is quite expensive. Our aim in this research is to develop simple, convenient, and cheap desorption methods and coupled them to post-ionization techniques for direct analysis of liquid and solid sample analysis. They includes: (a) the use of continuous wave (CW) laser instead of pulsed laser to desorb analytes in liquid samples and ointments, and (b) the use of thermal probe to desorb analytes in solid and liquid samples. All of the desorbed neutral species like molecules or droplets are then post-ionized via ESI or APCI processes. The first topic of the research is to develop a cheaper laser system to introduce analytes in solids or liquids into reaction region for post-ionization. In this section, we use a CW laser instead of a pulsed laser for the sampling of analytes. The titanium foil and stainless steel foil sample plate is quite useful and shows a great of desorption efficiency for liquid samples while irradiating by a CW laser. The detection limit by using a CW laser for sampling and ESI for post-ionization is 0.1 £gM for Benzethonium chloride and 1 £gM for cytochrome c, respectively. The combination of CW laser desorption and ESI post-ionization mass spectrometry can be applied in drug components, food safety and biomedical sample analysis. As a result of small size, lightness and lower prices of CW laser system, it not only shows large potential to use as a high efficiency desorption device for novel ionization source of mass spectrometer but also available for a wide range of useful application in many fields. The second topic of the research is to develop a new thermal probe for the direct desorption of sample surface. The home-made thermal probe is used to touch surface of solid sample or liquid sample to generate gas phase molecules or micro analyte droplets. Those neutral analytes are then post-ionized via ESI or APCI processes. In this study, the setting temperature of thermal probe is 250¢J. When the thermal probe touches liquid sample, it makes droplets boiling away explosively and then fused with ESI plume to generate ions. The detection limit by using a thermal probe for sampling and ESI or APCI for post-ionization is 1 £gM for both melamine and cytochrome c. This technique is also applied to analyze controversial additives in drinks. It also shows large potential to use as a high efficiency desorption device for novel ionization source of mass spectrometer and useful for a wide range of useful application in many fields.

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.

The adiabatic approximation is a natural approach for the description of phenomena induced by low frequency laser radiation because the ratio of the laser frequency to the characteristic frequency of an atom or a molecule is a small parameter. Since the main aim of this work is the study of ionization phenomena, the version of the adiabatic approximation that can account for the transition from a bound state to the continuum must be employed. Despite much work in this topic, a universally accepted adiabatic approach of bound-free transitions is lacking. Hence, based on Savichev's modified adiabatic approximation [Sov. Phys. JETP 73, 803 (1991)], we first of all derive the most convenient form of the adiabatic approximation for the problems at hand. Connections of the obtained result with the quasiclassical approximation and other previous investigations are discussed. Then, such an adiabatic approximation is applied to single-electron ionization and non-sequential double ionization of atoms in a strong low frequency laser field. The momentum distribution of photoelectrons induced by single-electron ionization is obtained analytically without any assumptions on the momentum of the electrons. Previous known results are derived as special cases of this general momentum distribution. The correlated momentum distribution of two-electrons due to non-sequential double ionization of atoms is calculated semi-analytically. We focus on the deeply quantum regime -- the below intensity threshold regime, where the energy of the active electron driven by the laser field is insufficient to collisionally ionize the parent ion, and the assistance of the laser field is required to create a doubly charged ion. A special attention is paid to the role of Coulomb interactions in the process. The signatures of electron-electron repulsion, electron-core attraction, and electron-laser interaction are identified. The results are compared with available experimental data. Two-electron correlated spectra of non-sequential double ionization below intensity threshold are known to exhibit back-to-back scattering of the electrons, viz., the anticorrelation of the electrons. Currently, the widely accepted interpretation of the anticorrelation is recollision-induced excitation of the ion plus subsequent field ionization of the second electron. We argue that there exists another mechanism, namely simultaneous electron emission, when the time of return of the rescattered electron is equal to the time of liberation of the bounded electron (the ion has no time for excitation), that can also explain the anticorrelation of the electrons in the deep below intensity threshold regime. Finally, we study single-electron molecular ionization. Based on the geometrical approach to tunnelling by P. D. Hislop and I. M. Sigal [Memoir. AMS 78, No. 399 (1989)], we introduce the concept of a leading tunnelling trajectory. It is then proven that leading tunnelling trajectories for single active electron models of molecular tunnelling ionization (i.e., theories where a molecular potential is modelled by a single-electron multi-centre potential) are linear in the case of short range interactions and ``almost'' linear in the case of long range interactions. The results are presented on both the formal and physically intuitive levels. Physical implications of the proven statements are discussed.

Two popular workflows exist for quantitative proteome analysis: two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), with staining to visualize proteins, and multidimensional solution phase separations of isotopically labelled peptides coupled to mass spectrometry (MS). However, the development of an alternative strategy, which combines easy-to-read differential profiling as seen in 2D-PAGE, with the sensitivity of MS for detection and identification, is needed. This thesis presents work towards the development of a workflow for high-throughput protein biomarker discovery. Multidimensional separations are vital to obtain sufficient fractionation of complex proteome mixtures. As a first dimension of separation, ion exchange chromatography (IEC) is a common choice, though it has yet to be thoroughly evaluated in terms of its effectiveness as a proteome prefractionation tool. This study used a defined set of protein standards to establish the resolution and proteome yield obtained through IEC. The evaluation uncovered significant bias in terms of protein recovery and separation. To improve throughput of a multidimensional separation strategy, a multiplexed (8-column) reversed phase liquid chromatography (RPLC) platform was constructed. The system design allowed for even distribution of flow across all columns with limited cross-loading during sample loading. This system was directly coupled to matrix-assisted laser desorption/ionization (MALDI) through a novel well plate device. The Teflon wells allowed for high recovery and no cross-contamination during collection/spotting, improved throughput, and greatly reduced the number of sample manipulation steps. An evaluation of MALDI MS, using the ThermoFisher vMALDI LTQ, for quantitative profiling was performed, employing the multiplexed LC-MALDI platform. The use of MALDI MS allowed for fast (< 5.5 hours) acquisition of quantitative data from isotopically differentiated samples partitioned over 640 fractions from two-dimensional LC. Proteins comprising 0.1% of the proteome were detected and quantified using this method. Finally, the effects of varying concentrations of acetonitrile (ACN) upon the products generated from tryptic digestions were explored. Poor enzymatic efficiency in 80% ACN was found to be responsible for an increased concentration of peptides containing missed cleavage sites. These peptides often contained unique amino acid sequences, which were not detected from complete digestions, resulting in improved protein sequence coverage following MS analysis.