Transport-kinetic processes and surface chemistry in biosensor design

Vijayendran, Ravi Albert University of Illinois at Urbana-Champaign 2001 해외박사(DDOD)

Biosensors are analytical devices that detect a target analyte on the basis of biomolecular recognition. Detection occurs as the consequence of specific interactions between the analyte and complementary biomolecules immobilized on the transducer surface. Several physicochemical factors influence this detection process. This thesis examines the role of these factors in sensor operation and also evaluates specific methods to manipulate these factors and improve sensor performance. We begin by investigating the kinetic and transport processes that underlie analyte recognition. A transport-kinetic model is developed to quantitatively relate these processes to sensor response in a typical biosensor measurement. Predictions from our model are compared with kinetic data from a fiber optic immunosensor. With these experimental comparisons, we demonstrate that our model provides a more physically rigorous description of analyte transport, and is thus better for data analysis and sensor design than competing models. The role of surface effects in biosensor operation is also addressed. We examine how immobilization impacts the activity of the biomolecules on the transducer surface. Although these molecules display homogeneous binding characteristics in solution, they often exhibit heterogeneous binding properties after surface immobilization. We measure binding isotherms and the detection kinetics for several analyte-receptor systems constructed with various immobilization strategies. By comparing theoretical models with experimental data, we elucidate the relationship between protein immobilization chemistry and receptor heterogeneity, and identify methods for constructing more uniformly reactive protein films. Finally, sample mixing is examined as a potential method to improve the performance of microfluidic biosensors. We attempt to mix sections of the sample solution where the analyte concentration is high with other sections where it is low, and thereby reduce the sensor response time when the detection kinetics are diffusion-limited. A serpentine micromixer, originally designed to mix two fluids in bulk solution via “chaotic advection,” is used to mix the sample as it passes through a surface plasmon resonance biosensor. These experiments indicate that such “solution-based” mixing strategies can be effective in microfluidic biosensors.

Relative Quantification of N-linked Glycans in Complex Mixtures via Stable Isotope Labeling and Enhanced Analysis by Liquid Chromatography Coupled Online to Mass Spectrometry

Walker, Steven Hunter North Carolina State University 2013 해외박사(DDOD)

Glycomics is a rapidly emerging field due to the ubiquity and functional importance of glycosylation in biological systems. However, the current analytical tools for studying glycomics and glycoproteomics lag decades behind proteomics and, to a larger degree, genomics. Additionally, the increasing advancements in separations and mass spectrometry technology (e.g. the Orbitrap) are not being fully taken advantage of due to the lack of reproducible, robust, and high-throughput front-end glycomics sample preparation strategies. Thus, this dissertation describes an effort to develop a high-throughput chemical derivatization strategy for the relative quantification of N-linked glycans, which can be coupled to nearly any glycomics sample preparation procedure with minimal monetary and time cost. The motivation for this work is the correlation between aberrations in glycosylation and disease. Thus, a strategy capable of systematically comparing and quantifying glycan profiles between samples (e.g. control and cancer samples) would be invaluable in glycan biomarker discovery efforts. Additionally, this work has been primarily developed in the most complex of biological matrices, blood plasma. There are two main reasons for this: 1) because plasma is one of the most complex matrices, it is likely that this technique will be effective when applied to any other biological matrix, and 2) plasma samples can be acquired without invasive surgery. This means that a screening method derived from biomarkers discovered in plasma will ultimately be inexpensive and non-invasive in practice. Aside from the possible clinical value of this quantification strategy, this work has made significant contributions to the field of glycomics and fundamental analytical chemistry including both experimental and practical advantages. By developing tunable glycan reagents, it has been shown that these tags are capable of both relatively quantifying N-linked glycans and systematically decreasing the detection limits of N-linked glycans in plasma samples using mass spectrometry. Because glycomics strategies often involve numerous sample preparation steps, the addition of chemical derivatization typically only further complicates the preparation. However, the strategy presented herein requires only 4 hours of total additional sample preparation time (samples can be processed in parallel), and the reaction products can be immediately analyzed. This is a significant advantage over traditional glycan derivatization strategies such as permethylation and reductive amination. Finally, this work has also contributed to the fundamentals of analytical chemistry and, more specifically, mass spectrometry. By tuning the glycan reagents with different functional properties, the mechanism for the generation of gas phase ions in electrospray ionization was able to be studied, and using these results, biases in the electrospray process were able to be exploited for the enhanced detection of glycans by mass spectrometry. Furthermore, liquid chromatography of glycans is often coupled online to mass spectrometry for the separation of glycans just before mass analysis, and traditionally, glycans are not able to be retained and separated using reverse phase chromatography (the most robust separation strategy for biological analytes). However, using the reagents developed and presented herein, the separation of glycans by reverse phase liquid chromatography is not only possible, but it is advantageous, allowing for increased separation efficiency and an increase in the total number of glycans detected. A significant practical advantage of this strategy is the ability to analyze glycan samples on the same instrument platform as a majority of proteomic strategies. This significantly increases the efficiency of joint proteomic and glycomic laboratories and facilitates a more comprehensive systems biology approach to bioanalytical chemistry.

Surface-Enhanced Raman Spectroscopy of Analytes in Blood

Campos, Antonio Renteria, II University of Minnesota 2015 해외박사(DDOD)

Although Raman scattering has traditionally been considered a weak process, making analysis of low concentration analytes in complex matrices difficult, both methodological and instrumentation advances in the last couple decades have made Raman spectroscopy a viable and useful analytical tool. This is especially true for analyte species within aqueous environments because the Raman scattering cross-section of water is small; one particular example of a critical aqueous environment is analysis of and in blood. The work detailed in Chapter 1 will analyze much of the literature related to Raman analysis in blood within the last 20 years, including normal Raman, surface-enhanced Raman, and spatially offset Raman analyses. The first section will focus on direct analysis of blood samples, including determining the age of deposited or donated blood and blood content within body fluid mixtures. The second section will discuss intrinsic Raman-based detection of small molecules and protein analytes within blood as well as extrinsic Raman detection of tumors. The last section will review the recent use of spatially offset Raman and surface-enhanced spatially offset Raman spectroscopy to analyze molecular analytes, tissue, bone, tumors, and calcifications, including in vivo analysis. This focal point closes with perspective on critical gaps and upcoming developments for Raman analysis in blood. Raman detection in blood can be applied to different forensic fields and can also be used for the detection of foreign analytes. In current events, ricin has been discussed frequently because of letters sent to high-ranking government officials containing the easily extracted protein native to castor beans. Ricin B chain, commercially available and not dangerous when separated from the A chain, enables development of ricin sensors while minimizing the hazards of working with a bioterror agent that does not have a known antidote. As the risk of ricin exposure, common for soldiers, becomes increasingly common for civilians, there is a need for a rapid, real-time detection of ricin. To this end, aptamers have been used recently as an affinity agent to enable the detection of ricin in food products via surface-enhanced Raman spectroscopy (SERS) on colloidal substrates. One goal of this work is to extend ricin sensing into whole human blood; this goal required application of a commonly used plasmonic surface, the silver film-over-nanosphere (AgFON) substrate, which offers SERS enhancement factors of 106 in whole human blood for up to 10 days. This aptamer-conjugated AgFON platform enabled ricin B chain detection for up to 10 days in whole human blood. Principle component analysis (PCA) of the SERS data clearly identifies the presence or absence of physiologically relevant concentrations of ricin B chain in blood. In addition to the detection of ricin B chain at a relevant concentration, the development of a platform to perform a single experiment calibration curve was performed through the combination of microfluidic devices with SERS substrates. Microfluidic sensing platforms facilitate parallel, low sample volume detection using various optical signal transduction mechanisms. Herein, we introduce a simple mixing microfluidic device, enabling serial dilution of introduced analyte solution that terminates in five discrete sensing elements. We demonstrate the utility of this device with on-chip fluorescence and surface-enhanced Raman scattering (SERS) detection of analytes, and we demonstrate device use both when combined with a traditional inflexible SERS substrate and with SERS-active nanoparticles that are directly incorporated into microfluidic channels to create a flexible SERS platform. The results indicate, with varying sensitivities, that either flexible or inflexible devices can be easily used to create a calibration curve and perform a limit of detection study with a single experiment. In Chapter 4, the synthesis of an ultrastable and reversible pH nanosensor using gold nanosphere aggregates functionalized with 4-mercaptobenzoic acid (MBA) that are encapsulated in mesoporous silica was performed. The pH nanosensor is stable and functional in human whole blood for a period of more than 3 months. With the growing interest in nanoparticles and nanomaterials, a demonstration was organized for a high school AP Chemistry class. Spectrophotometry and colorimetry experiments are common in high school and college chemistry courses. Previous work has demonstrated that handheld camera devices can be used to quantify the concentration of a colored analyte in solution in place of traditional spectrophotometric or colorimetric equipment. Chapter 5 extends this approach to an investigation of a mesogold mineral supplement. With the addition of free Google applications, the investigation provides a feasible, sophisticated lab experience, especially for teachers with limited budgets.

Raman investigations on high pressure phases of carbon based novel networks

Trout, Chad Christopher The Pennsylvania State University 2001 해외박사(DDOD)

Solid-state chemistry plays an important part in everyday life, from the material that coats the blade of your razor to the way your refrigerator keeps cool. The search for new and interesting materials is a broad and exciting area of solid-state chemistry. Carbon plays a large role in life and in solid-state chemistry. Carbon's versatility in bonding gives its compounds various physical, chemical, and biological properties. The versatility of carbon comes from the ability to form novel covalent networks containing sp, sp<super>2</super> and sp<super>3</super> bonds. These networks can exhibit a wide variety of structures and properties. The composition of amorphous carbon can range from only sp<super>2</super> carbon to various amounts of sp<super>2</super> and sp<super>3</super> carbon giving a variety of properties. In the last two decades, several new forms of carbon have been discovered, reopening the interest in carbon chemistry. There is still much to learn about solid-state carbon chemistry. Two aspects of solid-state chemistry are addressed in this thesis. The first aspect, is chemists' ability to make an educated guess about reaction pathways. The pathways of organic reactions are often understood, which allows organic chemists to make educated guesses about these reaction pathways. In solid-state chemistry there is a lack of understanding of the pathways for the reactions to proceed. In topochemical reactions the crystal structure of the monomer controls the final product and a crystal is formed. With these types of reactions a crystal is obtained instead of the usual amorphous or mixed phase material. The crystal's structure can be determined, which can lead investigators to determine the reaction pathway. Together topochemcial reactions may shed light on other reactions. The improved characterization of solid-state carbon materials is investigated in this work. Towards that respect, ultra violet (UV) Raman spectroscopy is being used for the first time on carbon based materials synthesized in the diamond anvil cell. Visible Raman spectroscopy often gives little or no information when dealing with amorphous phases of carbon based materials. This is due to the resonance enhancement of sp<super>2</super> carbon bonds with visible Raman spectroscopy. This resonance enhancement hides other features, such as carbon and nitrogen bonds in carbon nitrides and sp<super>3</super> carbon bonds in amorphous carbon. Previously, materials such as carbon nitrides were synthesized and investigated with other analytical methods. UV Raman spectroscopy allows new features in carbon based networks to be observed that were not detected with the other analytical methods. Vibration modes associated with sp<super>3</super>-boned carbon and nitrogen can be observed, indicating that new covalent networks of carbon and nitrogen have been synthesized. UV Raman is a relatively new technique and has not been applied to diamond anvil cell work previously. Various diamonds were investigated for in situ reactions in the diamond anvil cell with UV. Investigations were also performed on materials synthesized in the diamond anvil cell and then quenched to atmospheric pressure. These quenched samples were then studied with UV Raman.

The use of stable isotopes and particulate matter in the investigation of local and regional atmospheric chemistry

Katzman, Tanya Lynn Purdue University ProQuest Dissertations & Theses 2016 해외박사(DDOD)

The chemical composition of particulate matter (PM), a known contributor to air pollution, is highly variable, and elemental analysis reveals information about local and regional sources, as well as how air masses and climate influence PM compositions. Seasonal changes in climate, such as temperature, amount of daylight, or meteorological patterns influence source emissions (increased residential heating activities, decreased natural soil emissions) and the relative importance of certain chemical pathways in the atmosphere. Since the magnitude of these seasonal changes are highly dependent on location, each sampling site is unique and the chemical composition of PM provides valuable insight into local and regional atmospheric chemistry. Elemental analysis was used to evaluate local atmospheric chemistry at four sites in Southern California (Chula Vista, El Cajon, El Centro, and Brawley) and in Whangarei, New Zealand. PM in Southern California sites revealed seasonal trends, but also how emissions from the 2007 wildfire season impacted local chemistry, producing elevated PM and trace gas concentrations and low O3 concentrations. Analysis of PM collected in Whangarei, New Zealand revealed that local atmospheric chemistry is heavily influenced by marine air masses, seasonal shifts in source contributions (e.g. residential heating activities), and changes in boundary layer height. Stable isotope ratios are often applied as tracers of sources and local chemistry, which is extremely useful for deciphering PM. As the main NO x sink, the stable isotope composition of NO3- reflects NOx sources contributions, oxidation pathways, and other processes that effect the isotope distribution (e.g. equilibrium exchange). However, the use of N isotopes (delta15N) as a tracer is usually split between two schools of thought: the source hypothesis and the chemistry hypothesis. The source hypothesis claims that the delta 15N value of NO3- is solely determined by NOx source delta15N values, and observed variations are due to shifts in source emissions. Alternatively, the chemistry hypothesis argues that the delta15N value of NO3- is impacted by source contributions and chemical reactions occurring in the atmosphere. Here, variations in observed delta15N values are attributed to changes in reaction pathway contribution, as well as shifts in source emissions. Stable isotope analysis of NO3- collected in Southern California and Whangarei, New Zealand was used to evaluate these hypotheses. Using source emission data, known delta15N values of NOx sources, and observed delta15N values of NO3- collected in Chula Vista, CA, isotope mass balance suggests that the source delta15N value is not conserved, requiring a NOx source with an unreasonably large delta 15N value (~ 280‰) to explain observed values. Isotope exchange equilibrium was found to explain observed delta15N values well, but deviations did exist, particularly in the winter. These deviations are likely due to shifts in the importance of this exchange and additional fractionation effects associated with reaction pathways. Additionally, the inverse correlation between delta15N and solar radiation observed in Whangarei further supports the chemistry hypothesis. The research presented in this dissertation is the first known evaluation of these two stable isotope hypotheses, with the results strongly support the chemistry hypothesis. While the oxidation of NO2 is well understood, the mechanism of the oxidation of NO to NO2 is highly uncertain, and so stable isotopes were utilized to determine this reaction mechanism. Laboratory studies found that the remaining O2 became depleted relative to the O2, and followed a strict mass dependent relationship. Complimented by kinetic modeling, results strongly suggest that this reaction proceeds in two steps, with the formation of a peroxynitrate intermediate being favored due to the observed mass dependent relationship. This research is the first to offer support to the peroxynitrate intermediate, whereas previous works favored the energetically more stable nitrogen trioxide form.

Quantifying reactive biogenic volatile organic compounds: Implications for gas- and particle-phase atmospheric chemistry

Bouvier-Brown, Nicole Christine University of California, Berkeley 2008 해외박사(DDOD)

This dissertation describes measurements in branch enclosures and ambient air of previously-unidentified reactive and semi-volatile biogenic volatile organic compounds (BVOCs) and the novel analytical methods used to identify and quantify them. These compounds account for some of the highly reactive BVOCs needed to explain observations of ozone loss, hydroxyl radical production, and BVOC oxidation products above forested ecosystems. To identify and quantify reactive and semi-volatile BVOCs emitted from vegetation in branch enclosures, a new solid phase microextraction (SPME) fiber sampling protocol was developed. Using this technique, 26 different sesquiterpene compounds were quantified from the dominant plant species at Blodgett Forest, a ponderosa pine plantation in the Sierra Nevada Mountains. Branch enclosure measurements reveal significant contributions from sesquiterpenes (34%) and methyl chavicol (20%) to the total terpene+methyl chavicol emission mass. To quantify the reactive and semi-volatile BVOCs in ambient air, modifications were made to reduce interactions between the target analytes and an automated gas chromatograph-mass spectrometer (GC-MS) system. This instrument was used to make the first in-situ direct measurement of a series of speciated sesquiterpenes in ambient air. As compared to the branch enclosure measurements, this method detected small amounts of sesquiterpene mass due to the rapid chemical oxidation of these compounds following their emission from local vegetation. Nevertheless, sesquiterpenes contributed 8.5% to the site's total ozone reactivity above the forest canopy. Assuming that the monoterpene-to-sesquiterpene emission rate in the canopy is similar to that observed in branch enclosure studies at the site, and an average aerosol yield of 10-50% for these sesquiterpene compounds, the amount of sesquiterpene mass lost within the canopy accounts for 8-38% of the total measured organic aerosol mass. Both new analytical techniques were used to characterize the emission and abundance of methyl chavicol for the first time. Methyl chavicol mixing ratios were highly correlated with 2-methyl-3-buten-2-ol (MBO) suggesting that methyl chavicol daytime emissions can be modeled using a similar light- and temperature-dependent algorithm. Because sesquiterpenes and methyl chavicol significantly contribute to total ozone reactivity and aerosol composition, the use of improved instrumentation will reveal the prominent role of reactive and semi-volatile BVOCs in global atmospheric chemistry.

Instrumentation and method development for the interrogation of biomolecules and ion/ion chemistry

Erickson, David Edwin Purdue University 2009 해외박사(DDOD)

Instrumentation and new methods are investigated for their utility in biomolecule analysis as well as the investigation of new ion/ion chemistry. The instrumental emphasis for these investigations have utilized 2D linear ion traps for their improvement in sensitivity, dynamic range, and the ability to mate these analyzers with other pre-existing mass spectrometry requirements. Other instrumental emphasis is placed on resolution and mass accuracy, which is effected by the time-of-flight mass analysis. Developing and implementing methods on these instruments provide a diverse array of approaches in order to solve current analytical problems within the context of biomolecular analysis. Development of a 2D linear ion trap for high-mass biomolecule analysis is discussed for implementing a large range of interrogation techniques. Multiple configurations and ionization sources are available and interchangeable on this highly flexible platform. These methods are discussed primarily within the context of a single quadrupole linear ion trap, along with expansion into configurations including two linear ion traps arranged in nonlinear fashion. Instrumentation for low-mass biomolecules originating from vegetation is also discussed. An instrument is modified to support investigations of monoterpenes in ambient atmospheric concentrations is described. Biomolecule analysis data have been used to identify proteins and peptides to support the proteomics science. Methods and experimental techniques are described to improve the results obtained in bioinformatics and mass spectrometry. Finally, characterization of new ion/ion chemistry in the form of electron/peptide interaction is described. Electron transfer dissociation (ETD) is discussed in the context of charge identity and position within the peptide. A description of product partitioning is formed for the channels of dissociative reaction resulting in backbone and neutral loss as well as nondissociative reaction and proton transfer.

Aerosol chemistry on the early Earth and Titan

DeWitt, H. Langley University of Colorado at Boulder 2010 해외박사(DDOD)

Understanding the atmospheric conditions before and during the period when life first appeared on the planet, approximately 3.5-4 billion years ago (Ga) is an important part of understanding the conditions under which life developed. Titan, a moon of Saturn, is often cited as a possible analogue to early Earth's atmospheric conditions: it is made up of primarily nitrogen (N2) with a few percent methane (CH4) that is photolyzed into a thick organic haze, obscuring the surface of the moon. The evidence of liquid water at 4 billion years ago, despite the faintness of the young sun, necessitates the presence of larger amounts of greenhouse gases in the early Earth's atmosphere. CH4, carbon dioxide (CO 2), and hydrogen (H2) have been proposed to have been present in the early Earth's atmosphere in elevated amounts, varying in amounts with the rise of methanogens on the surface of the Earth. Unlike present Earth, the presence of sulfur mass independent fractionation (S-MIF) in sediments older than 2.45 Ga is thought to be evidence for an early anoxic atmosphere. To preserve this signal, the tropospheric formation of at least two different forms of sulfur-containing aerosols, usually thought to be elemental sulfur (S8) and sulfuric acid (H2SO4), would be necessary. Thus, CH4, CO2, H2, O2, and H2O could influence the chemistry of sulfur-bearing aerosols. In this work, we use aerosol mass spectrometry (AMS) to examine the aerosols formed form the photolysis (to simulate the solar spectrum, at wavelengths from 115-400 nm) and electrical discharge (to simulate lightning on the early Earth and the free electrons present in Titan's upper atmosphere) of varying gas mixtures under different laboratory conditions to probe the chemistry of early Earth and Titan aerosols. We examined the N-incorporation into organic aerosols formed from the electrical discharge of 2% CH4 in N 2 to simulate the haze formed in the upper atmosphere of Titan. We found an N/C ratio of 0.25 and determined that the majority of the N-containing organic signal was derived from nitriles. We also probed the effect of H 2 on the photolysis reactions of CH4 and CO2 in N2 and the effect H2 had on the relative amounts of organic haze formed. We found that H2 reduced organic haze formation and thus would prevent any cooling from scattering of incoming solar radiation away from the lower atmosphere and Earth's surface by an overly thick aerosols layer. Finally, when we examined the chemistry of SO2, CH 4, H2O, and CO2, we found that S8 aerosols formed only under very reduced circumstances and that the pressure of SO2, the amount of H2O vapor present, and the amount of reducing gases (such as CH4 or H2) could change the S-aerosol chemistry. We found that organo-sulfur compounds could be another type of S-bearing aerosol important for the preservation of S-MIF signal and could have been prevalent in the early Earth's atmosphere under reasonable atmospheric conditions. Understanding the chemical properties of these aerosols will broaden our understanding of the conditions under which complex organic molecules were formed and life began to develop.

Developing analytical methodologies for combinatorial chemistry using time-of-flight secondary ion mass spectrometry

Xu, Jiyun The Pennsylvania State University 2003 해외박사(DDOD)

In this thesis, imaging time-of-flight secondary ion mass spectrometry (ToF-SIMS) is applied to the high-throughput analysis of combinatorially synthesized organic molecules, which are normally referred to as libraries. Two issues need to be addressed for a library: the occurrence and structure of the library components and their bioactivity toward certain targets. Since bioassay can be rapidly handled with a variety of strategies, here we focus on identifying the library members using mass spectrometric methodologies. We establish parallel analysis protocols for combinatorial libraries synthesized both in solution phase and on solid phase, such as polymer resin particles. By acquiring molecule-specific images of the analytes densely arrayed either in picoliter-volume silicon vials for liquid samples or on arraying chips for polymer beads, analysis rates of 10 analytes/second on model systems has been achieved with imaging ToF-SIMS. The challenges lie in the development of appropriate treatments for diverse samples or samples presented in complex matrixes. For liquid samples, glass substrates modified with functional groups are employed to separate the analytes from a mixture solution through selective binding. As a result, SIMS sensitivity is greatly enhanced. Solid-bound libraries comprise of an intricate system because of the wide varieties of linker moieties and polymer matrixes involved in the synthesis. We examined the influence of three classes of linkers—acid or base labile linkers, a thermally labile linker and a photochemically cleavable linker, all of which are used to anchor one end of the analyte to the polymer resin. With data obtained using both SIMS, X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM), we conclude that an effective treatment of the resin needs to include cleaving the linker and extracting the unbound analyte to the resin surface. We also demonstrate that the hydrophilicity of the polymeric constituents of a resin particle affects the experiments by changing the location of the analyte molecules during resin treatment. In addition, the spatial localization of the released analytes could be controlled by introducing a hydrophobic supporting substrate such as Teflon tape that confines the diffusion of the cleaving reagent. Encoding a library with tags is necessary when direct mass analysis fails to yield conclusive results due to mass redundancy and inadequate sensitivity. Two different encoding strategies and corresponding tags are designed, synthesized and examined with imaging ToF-SIMS. The dual recursive deconvolution (DRED) strategy differentiates the resins based on the varying concentrations of bromine and chlorine-derivatized polystyrene in their polymer matrixes. The resins are subsequentially decoded using isotopic signal intensities measured with SIMS. This scheme obviates the need for extra synthetic steps and cleaving reactions, thus is highly compatible with high-throughput analysis using imaging ToF-SIMS. (Abstract shortened by UMI.).

Fundamental Study of Gas Phase Ion/Ion Reactions and Mass Spectrometry Instrumentation

Bu, Jiexun Purdue University ProQuest Dissertations & Theses 2017 해외박사(DDOD)

Bu, Jiexun Ph.D., Purdue University, May 2017. Fundamental Study of Gas Phase Ion/Ion Reactions and Mass Spectrometry Instrumentation. Major Professor: Scott A. McLuckey. Mass spectrometry (MS) is one of the most important analytical tools in various scientific fields, including chemistry, physics, biology, and geology. The work described here covers a set of projects ranging from mass spectrometry instrumentation to fundamental gas phase ion chemistry. Structural information acquired from tandem mass spectrometry is highly dependent on the precursor ion type. Ion/ion reactions have been developed as a widely used technique to convert ion type from one to another. Recently selective covalent ion/ion chemistry has been developed to modify the analyte in the gas phase. A series of calculations and experiments were done to probe the potential energy surface of ion/ion reactions, which leads to a better understanding of ion/ion reaction chemistry and has provided means to predict the reactivity of gas phase reagents. It also provides a theory to guide the experiment in order to achieve higher modification yield in the gas phase. Several projects have been carried out to explore novel ion/ion reactions. Triazoles have been developed as an electrophile to modify basic residues of biomolecules in the gas phase. It shows a higher reactivity compared to the previously developed NHS based reagents. This result matches well to the theoretical calculation. Cycloaddition between azide and alkynes, which is also known as Click Chemistry, is realized in the gas phase as well. Click chemistry is widely used in biological fields. The gas phase coupling provides a new way to probe azides or alkynes by mass spectrometry. The relationship between the solution phase analyte and the gas phase analyte ions is cause for debate. Solvated ions are a good subject to study in order to bridge the gap between the solution phase and the gas phase. Also, many reactions in the solution phase require solvent molecules to proceed, which indicates that solvated ions may have unique gas phase reactivity. These interests lead to an instrumentation project to facilitate the study of solvated ions. In order to trap the solvated ions long enough for an ion trap experiments (hundreds of milliseconds), cooling is required. A liquid nitrogen cooled ion trap was designed and built for this purpose. Preliminary results have been demonstrated. Aside from the ion type, activation methods can also change the structure information acquired via tandem mass spectrometry. Ultraviolet photo dissociation is one of the activation methods that has become a hot topic. A lot of reactions can also be activated by UV photons which meet the group's interest for ion/ion reaction. A series of experiments were done to generate peptide radical ion in the gas phase by UVPD and ion/ion reactions. Those radical ions can be subjected to collision induced dissociation and provide complimentary information compared to its protonated analog. A new instrument was also built to avoid noise problems associated with an older instrument design.