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Thesis (Ph. D.)--University of Texas at Austin, 1998. / Vita. Includes bibliographical references. Available also in a digital version from Dissertation Abstracts.

Abstract Experimental synchrotron radiation induced electron- and ion spectroscopies together with electron-ion and ion-ion coincidence techniques as well as electron energy loss spectroscopy have been used to study the electronic properties of several vapor phase samples. In this thesis studies of the electronic structure and fragmentation of Sb4 clusters, photo- and Auger electron spectroscopy of atomic Si and Pb as well as ultra high resolution VUV absorption of vapor phase KF molecules have been performed. The instrumentation and techniques used in the studies, especially the electron energy loss apparatus and the newly built ultra high resolution FINEST beamline branch, are presented.

The advent of electrospray ionization enabled the study of intact protein complexes via MS. For example, in the mid-1990s, the observation that viruses can survive after entering the gas-phase and still retain activity was shown. Advances in sample preparation methodologies, mainly native MS, allowed for the preservation of large non-covalently bound complexes, which led to structural characterization studies that were previously unachievable. However, native MS suffers from complications arising from inherent heterogeneity and severe salt adduction. Consequently, the spectra can consist of broad and overlapping peaks that may even preclude the ability to obtain a mass measurement. This dissertation will focus on a gas-phase technique to address highly complex native MS scenarios that give rise to poorly resolved signals using the E. coli ribosome as one model system. Moreover, brief discussion of improvements made on our QToF platform (SCIEX 5600) will be compared with other state-of-the-art instruments. Lastly, other applications to our ion/ion reaction workflow will be explored.

<div>Heightened awareness regarding the implication of disturbances in lipid metabolism with respect to prevalent human-related pathologies demands analytical techniques that provide unambiguous structural characterization and accurate quantitation of lipids in complex biological samples. The diversity in molecular structures of lipids along with their wide range of concentrations in biological matrices present formidable analytical challenges. Modern mass spectrometry (MS) offers an unprecedented level of analytical power in lipid analysis, as many advancements in the field of lipidomics have been facilitated through novel applications of and developments in electrospray ionization tandem mass spectrometry (ESI-MS/MS). ESI allows for the formation of intact lipid ions with little to no fragmentation and has become widely used in contemporary lipidomics experiments due to its sensitivity, reproducibility, and compatibility with condensed-phase modes of separation, such as liquid chromatography (LC). Owing to variations in lipid functional groups, ESI enables partial chemical separation of the lipidome, yet the preferred ion-type is not always formed, impacting lipid detection, characterization, and quantitation. Moreover, conventional ESI-MS/MS approaches often fail to expose diverse subtle structural features like the sites of unsaturation in fatty acyl constituents or acyl chain regiochemistry along the glycerol backbone, representing a significant challenge for ESI-MS/MS. To overcome these shortcomings, various charge manipulation strategies, including charge-switching, have been developed to transform ion-type and charge state, with aims of increasing sensitivity and selectivity of ESI-MS/MS approaches. Importantly, charge manipulation approaches afford enhanced ionization efficiency, improved mixture analysis performance, and access to informative fragmentation channels.</div><div><br></div><div>Here, gas-phase ion/ion chemistry was developed to transform conventional lipid ion types formed upon direct ESI into structurally informative ion types entirely within the mass spectrometer. Explicitly, gas-phase anionic to cationic charge switching chemistries were first developed for fatty acid profiling, as unambiguous structural elucidation and relative quantitation were achieved. Extensions of this gas-phase charge switch derivatization strategy to glycerophospholipids (GPLs), including ether GPLs, and fatty acid esters of hydroxy fatty acids demonstrates the versatility and flexibility of the ion/ion platforms. In an alternate approach, gas-phase proton transfer ion/ion reactions were employed for the gas-phase separation, concentration, and identification of cardiolipins (CLs) from total lipid extract. In total, benefits for lipid structure elucidation and enhanced detection efficiencies have been demonstrated utilizing the reported gas-phase ion/ion platforms.</div>

Gas-phase ion/ion covalent modification was coupled to ion mobility/mass spectrometry analysis to directly correlate the structure of gaseous ubiquitin to its solution structures with selective covalent structural probes. Collision cross section (CCS) distributions were measured prior to ion/ion reactions to ensure the ubiquitin ions were not unfolded when they were introduced to the gas phase. Ubiquitin ions were electrosprayed from aqueous and methanolic solutions yielding a range of different charge states that were analyzed by ion mobility and time-of-flight mass spectrometry. Aqueous solutions stabilizing the native state of ubiquitin generated folded ubiquitin structures with CCS values consistent with the native state. Denaturing solutions favored several families of unfolded conformations for most of the charge states evaluated. Gas-phase covalent labeling via ion/ion reactions was followed by collision induced dissociation of the intact, labeled protein to determine which residues were labeled. Ubiquitin 5+ and 6+ electrosprayed from aqueous solutions were covalently modified preferentially at the lysine 29 and arginine 54 residues, indicating that elements of secondary structure as well as tertiary structure were maintained in the gas phase. On the other hand, most ubiquitin ions produced in denaturing conditions were labeled at various other lysine residues, likely due to the availability of additional sites following methanol and low pH-induced unfolding. These data support the conservation of ubiquitin structural elements in the gas phase. The research presented here provides the basis for residue-specific characterization of biomolecules in the gas phase

No description available.

Mass spectrometry is a versatile analytical tool for chemical and biomolecule identification, quantitation, and structural analysis. Tandem mass spectrometry further expands the applications of mass spectrometry, making it more than a mere detector. With tandem mass spectrometry, the mass spectrometer is capable of probing reaction mechanisms, monitoring reaction processes, and performing fast analysis on complex samples. In tandem mass spectrometry, after activation the precursor ions fragment into small fragment ions through one or more pathways, which are affected by the ion’s inherit property, the ion type, and the activation method. To obtain complementary information, one can alter the fragmentation pathway by changing the ion via ion charge manipulation and covalent modification to the ion. Gas-phase ion/ion reactions provide an easy approach to changing ion type and facile modification to the analyte ions. It has been extensively used for spectrum simplification and analyte structural studies. In this dissertation, ion/ion reaction facilitated mass spectrometry methods are studied, and explorations into the method development involving front-end mass spectrometer are discussed.<br>The first work demonstrates a special rearrangement reaction for gas-phase Schiff-base-modified peptides. Gas-phase Schiff-base modification of peptides has been applied to facilitate the primary structural characterization via tandem mass spectrometry. A major or minor fragment pathway related to the novel rearrangement reaction was observed upon in-trap collisional activation of the gas-phase Schiff-base-modified peptides. The rearrangement reaction involves the imine of the Schiff base and a nucleophile present in the polypeptide. The occurrence of the rearrangement reaction is affected by several factors, such as ion polarity, identity of the nucleophile in the peptide (e.g., side chains of lysine, histidine, and arginine), and the position of the nucleophile relative to the imine. The rearrangement reaction does not affect the amount of structural information that can be obtained by collisional activation of the Schiff-base-modified peptide, but when the rearrangement reaction is dominant, it can siphon away signal from the structurally diagnostic processes.<br>Efforts have also been put into the method development of peptide and protein aggregation detection via electrospray ionization mass spectrometry (ESI-MS). People have studied peptide and protein aggregation processes to understand the mechanism of amyloid-related diseases and to control the quality of the peptide and protein pharmaceuticals. ESI-MS is suitable for solution aggregation studies because of its compatibility with solution samples and the straightforward result of the analyte’s oligomeric state on the mass spectrum. However, peak overlap issue and nonspecific aggregation in the ESI process can obscure the result. Here, the application of proton transfer ion/ion reaction to the analyte has been found useful to reduce or eliminate the peak overlap issue. A statistical model based on Poisson statistics has been proposed to deal with the ESI-induced nonspecific aggregation in the droplet and to differentiate the solution-phase aggregation from the droplet-induced aggregation. Factors that affect the accuracy of the statistical model have been discussed with MATLAB simulations.<br>In the era of biological system studies, sample complexity is a challenge every analytical chemist has to face. The analysis of complex sample can be facilitated by the combination of separation techniques outside the mass spectrometer (such as differential mobility spectrometry (DMS)) and ion structure probing techniques inside the mass spectrometer (such as tandem mass spectrometry and gas-phase ion/ion reactions). Here the coupling method between DMS and ion/ion reaction is developed and tested with model peptide systems to demonstrate its possible application in complex sample characterization such as isomer identification.<br>

Popular catalytic cycles, such as the Heck, Suzuki, and Negishi, utilize metal centers that oscillate between two oxidation states (II/0) during the three main steps of catalysis: reductive elimination, oxidative addition, and transmetallation. There has been a push to use less toxic, cheaper metal centers in catalytic cycles, leading to interest in first-row transition metals, such as nickel and cobalt. With these metals, the cycles can potentially pass through the +1 oxidation state, which acts as reactive intermediates, undergoing oxidative additions to form products, potentially with radical characteristics. The oxidative addition steps of catalytic cycles are critical to determining overall rates and products, however in many cases, these steps have not been amenable to study, in either condensed phase or gas phase, in the past. Through the use of electron transfer dissociation (ETD) technology on a modified Thermo Electron LTQ XLTM mass spectrometer, it is possible to generate intermediates in these catalytic cycles, including those in unusual oxidation states. Using sequentially coupled ion/ion-ion/molecule reactions, the reduced, reactive intermediate can be readily generated, isolated, and studied.As a model set of reactions, the mono- and bis-phenanthroline complexes of Fe(I), Co(I), Ni(I), Cu(I), and Zn(I) were formed by reduction of the corresponding M(II) species in an ion/ion reaction with the fluoranthenyl radical anion. The chemistry of the M(I) species was probed in ion/molecule reactions with allyl iodide. In order to explore ligand effects and the scope of oxidative addition reagents further, bipyridine and terpyridine were studied with these five first-row transition metal complexes while using an acetate series and other substrates for oxidative additions. Through these studies, the roles of the metal and ligand in dictating the product distributions and reaction rates were assessed. Metal electron count, ligand flexibility, and coordination number are critical factors. The overall reactivity is in accord with density functional theory calculations and mirrors that of proposed intermediates in condensed-phase catalytic cycles. In addition, second- and third-row transition metals (Ru(I), Pd(I), and Pt(I)) were explored with bipyridine, mono- and bis-triphenylphosphine, and 1,2-bis(diphenylphosphino)benzene ligation schemes. A variety of oxidative addition reagents were surveyed to determine the scope of reactivity and preference toward metal-carbon bond formation or carbon radical formation.

PEGASES est un nouveau propulseur conçu et développé au LPP. Un propulseur électrique classique éjecte de la matière positive à grande vitesse depuis un plasma électropositif pour générer la poussée. La nouveauté introduite par PEGASES est le fait que la poussée est générée par l'accélération successive d'ions positifs et d'ions négatifs issus d'un plasma ion-ion continu. Le propulseur PEGASES est composé de trois étages: (i) un étage d'ionisation constitué d'une source radiofréquence (rf) pour le couplage inductif d'un plasma électronégatif à partir d'un gaz contenant des halogènes, (ii) un étage de filtrage magnétique des électrons pour obtenir un plasma ion-ion, et (iii) l'étage d'accélération des ions utilisant des grilles polarisées alternativement pour créer un champ électrique dont le sens varie dans le temps. Durant ma thèse, j'ai travaillé essentiellement sur les premier et troisième étages sur deux prototypes de PEGASES. Un plasma ion-ion a été obtenu dans le premier prototype à partir de SF6 grâce à un filtrage magnétique important. Mais des limitations inhérentes et significatives rendent les performances insuffisantes pour le processus d'accélération voulu. Afin d'obtenir une source d'ions électriquement performante, le second prototype utilise une source inductive plane avec une bobine à noyau de ferrite et une boîte d'accord d'impédance comportant un transformateur à faibles pertes. Le couplage capacitif parasite a été réduit en optimisant la boîte d'accord et les progrès sont évalués grâce à la mesure du spectre du potentiel plasma par sonde capacitive. Le plasma est étudié à l'aide de sondes de Langmuir et d'un analyseur de l'énergie des ions (RFEA) dans les deux prototypes. Le potentiel d'un plasma ion-ion peut être contrôlé par une électrode polarisée en contact avec le plasma. L'accélération des ions issus du plasma ion-ion est étudiée dans le cas continu où la polarisation des grilles est fixée puis en imposant une tension créneau d'amplitude comprise entre 0 et ± 350 V avec une fréquence de 1 kHz. Dans le cas alternatif, les ions positifs et les ions négatifs sont accélérés durant les demi-périodes de polarisation positive et négative respectivement. L'énergie respective des deux populations d'ions peut être contrôlée indépendamment, en continu et en alternatif. Avec ces résultats est démontrée la faisabilité du concept PEGASES et l'étude du propulseur peut passer à l'étape de développement et réalisation.