The results of the laboratory study of reaction rate coefficients of several ion- molecule reactions with atomic and molecular hydrogen and molecular deuterium at low temperatures are presented in the thesis. The reaction rate coefficients of the N+ and H+ reaction with H2 were measured with respect to the nuclear spin configuration and rotational excitation of H2. The reactions of anions were a subject of the isotope exchange and isotope effect study. The measurements of the rate coefficients of H2O and D2O formation in the reaction of O- with H2 and D2, isotope exchange reactions OH- + D2 and OD- + H2, and associative detachment and charge transfer channels of D- + H interaction were performed. Experiments were carried out using an AB-22PT instrument with an ion trap. It has producing, guiding, trapping, and detecting systems for ions and a separate source of atomic H. The cooling system allowed to measure the temperature dependencies of the reaction rate coefficients at temperatures relevant to astrochemistry (10 K - 300 K)

This thesis is concerned about ion-molecular reactions at low temperatures, which are important the fully understand the chemical evolution in interstellar medium. For realization of experimental part of thesis has been used the apparatus of 22-pole radiofrequency ion trap, which allows study the rate constant of reactions at temperatures 10 - 100 K. Thesis contains measuring results of reaction NH+ + H → N+ + H2, which follows the previous study of reaction N+ + H2 → NH+ + H on the same apparatus, description of the apparatus and the general introduction.

In the present work, the results of the experimental study of reactions of ions with molecular hydrogen in the temperature range 15 - 300 K using a 22-pole ion trap apparatus are presented. The reaction of OD- with para-enriched hydrogen was studied using a combination of the 22-pole ion trap apparatus with a para-hydrogen generator. Also reactions of O- with H2, D2, and HD were studied. These reactions have a channel of water production and a channel of hydrogen or deuterium transfer. Another field of study was a sequence of reactions of oxygen hydride cations with H2 and D2 which leads to the production of H3O+ or its isotopic variant, specifically reactions OH+ with H2, H2O+ with H2, D2O+ with H2, and D2O+ with D2. This reaction chain can be followed by the electron recombination of H3O+ or its isotopologue, which has a channel of water production.

4 Title: Reactions of astrophysically important positive ions with molecules and atoms at low temperatures Author: Serhiy Rednyk Department: Department of Surface and Plasma Science Supervisor of the doctoral thesis: prof. RNDr. Juraj Glosík, DrSc, Ph.D., Department of Surface and Plasma Science Abstract: In the present work, the results of the experimental study of reactions of ions with atomic and molecular hydrogen are presented. Experiments were performed using a cold radiofrequency 22-pole ion trap apparatus in the temperature range, relevant for interstellar clouds (from 300 down to 15 K). The present study is devoted to experimental investigation of the reactions of NH+, NH2 + and NH3 + ions with H2. The reaction of NH+ with H2 has two channels, which lead to NH2 + (about 97 %) and H3 + (3 %) formation with nearly constant reaction rate coefficients. The reaction of NH2 + + H2 produces only NH3 + ions and the measured reaction rate coefficient is decreasing with increasing temperature from 6∙10−10 cm3 s−1 to 2∙10−10 cm3 s−1 . The measured reaction rate coefficient of NH3 + with H2, producing NH4 +, is increasing with decreasing temperature from 80 K down to 15 K, confirming predicted mechanism of tunneling through a potential barrier. Reaction of NH+ + H was studied using a combination of the 22-pole...

Here we present the design, assembly and successful ion trapping of a room-temperature ion trap system with a custom designed and fabricated surface electrode ion trap, which allows for rapid prototyping of novel trap designs such that new chips can be installed and reach UHV in under 2 days. The system has demonstrated success at trapping and maintaining both single ions and cold crystals of ions. We achieve this by fabricating our own custom surface Paul traps in the UMass Amherst cleanroom facilities, which are then argon ion milled, diced, mounted and wire bonded to an interposer which is placed in an ultra-high vacuum chamber and baked in a conventional oven for 46 hours. We demonstrate the system’s ability to confine strontium ions and present preliminary data towards calibrating the ion trap parameters for reduced heating rates. Future work will see the system being used to study the effects of various trap geometries, process fabrication steps and surface treatments on anomalous heating rates, and for portable quantum sensing applications, as an optical atomic clock.

The ability to rapidly detect and identify hazardous analytes in the field has become increasingly important. One of the most important analytical detection methods in the field is gas chromatography-mass spectrometry (GC-MS). In this work, a hand-portable GC-MS system is described that contains a miniature toroidal ion trap mass analyzer and a low thermal mass GC. The system is self-contained within the dimensions of 47 x 36 x 18 cm and weighs less than 13 kg. Because the instrument has a small footprint, it was used as the detector for an automated near-real-time permeation testing system. In permeation testing, materials that are used to make individual protective equipment such as gloves, masks, boots, and suits are exposed to hazardous analytes to determine how long the equipment can be worn safely. The system described herein could test five samples simultaneously. A multi-position valve rotated among the various sample streams and delivered time aliquots into the MS for quantitation. Current field air sampling techniques suffer from long desorption times, high pressure drops, artifact formation and water retention. These disadvantages can be avoided by concentrating the analytes in short open tubular traps containing thick films. There are several advantages to using polymer coated capillaries as traps, including fast desorption, inertness and low flow restriction. An air sampling trap was constructed utilizing open tubular traps for the concentration of semi-volatile organic compounds. The system consisted of multiple capillary traps bundled together, providing high sample flow rates. The analytes were desorbed from the multi-capillary bundle and refocused in a secondary trap. The simultaneous focusing and separation effect of a trap subjected to a negative temperature gradient was also explored. In this configuration, analytes were focused because the front of the peak was at a lower temperature than the rear of the peak and, hence, moved slower. In addition to the focusing effect, analytes with different volatilities focused at different temperatures within the gradient, allowing for separation.

<p dir="ltr">Mass spectrometry has been at the forefront of complex mixture analysis and, as a result, has greatly advanced the understanding of biological systems with its application in the biological sciences. One area in which mass spectrometry has succeeded is the area of microbiology and the identification of pathogens and has gained much attention from the biothreat detection community. Although this technology has matured in the past decade, very few systems have been developed for point-of-need analysis in cases such as the detection of biothreats. Current MS systems for the analysis of microbes utilizing MALDI-TOF-MS require large instruments to accommodate a drift tube long enough for high resolution mass analysis and high vacuum which is not amenable to the miniaturization requirements of point-of-need analysis. The previously mentioned methods also require extensive manipulation of the sample which takes time and can pose a risk to instrument operators in the biothreat detection space. Additionally, most mass spectrochemical instruments provide only one-dimension of data which can limits classification accuracy when using classification algorithms to provide an identity on a microbiological sample which could consist of any of the numerous common bacterial pathogens or biothreats.</p><p dir="ltr">A possible solution to this problem is the implementation of two-dimensional tandem mass spectrometry (2D MS/MS) which allows the analysis of the product ions of all precursor ions representing the result in the 2D MS/MS data domain. This methodology is possible with a linear quadrupolar ion trap mass analyzer and can be applied to miniature ion trap technology for portability. In this dissertation, a progression of mass spectrochemical analysis of biological systems from conventional methods to the implementation of 2D MS/MS is demonstrated: by (i) the development of a rapid biomolecule extraction method to analyze bacterial spores, using a (ii) modified linear quadrupolar ion trap mass spectrometer, (iii) then a miniature ion trap mass spectrometer, and (iv) finally adding numerical methods to discriminate between biological systems using data acquired on each 2D MS/MS instrument. This work is then taken a step further by developing a high throughput experimentation method in which DESI is coupled to 2D MS/MS to analyze a moderate number of samples rapidly, automatically, and with high reproducibility.</p>

No / Two-dimensional gel electrophoresis-separated and excised haptoglobin alpha2-chain protein spots were subjected to in-gel digestion with trypsin. Previously unassigned peptide ion signals observed in mass spectrometric fingerprinting experiments were sequenced using the matrix-assisted laser desorption/ionization-quadrupole ion trap-time of flight (MALDI-QIT-TOF) mass spectrometer and showed that the haptoglobin alpha-chain derivative under study was cleaved by trypsin unspecifically. Abundant cleavages occurred C-terminal to histidine residues at H23, H28, and H87. In addition, mild acidic hydrolysis leading to cleavage after aspartic acid residues at D13 was observed. The uninterpreted tandem mass spectrometry (MS/MS) spectrum of the peptide with ion signal at 2620.19 was submitted to database search and yielded the identification of the corresponding peptide sequence comprising amino acids (aa) aa65-87 from the haptoglobin alpha-chain protein. Also, the presence of a mixture of two tryptic peptides (mass to charge ratio m/z 1708.8; aa40-54, and aa99-113, respectively), that is caused by a tiny sequence variation between the two repeats in the haptoglobin alpha2-chain protein was resolved by MS/MS fragmentation using the MALDI-QIT-TOF mass spectrometer instrument. Advantageous features such as (i) easy parent ion creation, (ii) minimal sample consumption, and (iii) real collision induced dissociation conditions, were combined successfully to determine the amino acid sequences of the previously unassigned peptides. Hence, the novel mass spectrometric sequencing method applied here has proven effective for identification of distinct molecular protein structures.

<p dir="ltr">Multiply-charged ions of intact biomolecules generated from electrospray ionization (ESI) have drawn researchers' interest in the field of native mass spectrometry (MS) for decades because these ions carry mass and charge information of the intact molecules and interactions among different units. However, the confinement of multiple charge states in a narrow range of <i>m/z</i> makes mass and charge assignments challenging, especially for analytes with a mass greater than 100 kDa. Gas-phase ion/ion reactions have proven to be powerful techniques that facilitate the interpretation of mass spectra of natively sprayed macromolecular analytes by manipulating the masses and charges of ions detected.</p><p dir="ltr">The proton-transfer reaction (PTR) is the most used gas-phase ion/ion reaction method. It utilizes perfluorinated PTR reagents to "grab" protons away from the analyte ions, thereby reducing their charges. A novel charge state manipulation technique called "ion parking," based on PTR, has been developed. In this method, ion signals are accumulated to one or a range of charge states by selectively inhibiting reactions between the target charge state and the PTR reagents via resonance excitation.</p><p dir="ltr">The multiply-charged ion attachment (MIA) reaction is another gas-phase ion/ion reaction approach. It utilizes the significant <i>m/z</i> displacement caused by the attachment of multiply-charged reagent ions, and it has been proven useful for mass analysis of heterogeneous macromolecular analytes with a mass greater than 1 MDa.</p><p dir="ltr">All gas-phase ion/ion reaction techniques require mutual storage of ions in opposite polarities within an electrodynamic quadrupole ion trap, such as a 3D quadrupole ion trap (QIT) or a linear quadrupole ion trap (LIT). Electrodynamic ion traps use high-voltage (HV) drive radio frequencies (RF) to trap ions in a quadrupolar field, typically employing a sinusoidal waveform (sine wave). A digital quadrupole ion trap (DIT) is an unconventional electrodynamic ion trap that uses a digital waveform (square wave) as the drive RF. The high agility of square waves makes DIT an ideal mass analyzer for studying high <i>m/z</i> ions resulting from gas-phase ion/ion reactions. This dissertation describes the development of a novel home-built digital dual-trap mass spectrometer and ion/ion chemistry studies of large biomolecules within the instrument.</p>

Le long bio-polymère d'ADN est condensé à l’intérieur du noyau des cellules eukaryotes à l'aide de petites protéines appelées histones. En plus de leurs fonctions condensatrices,ces histones sont également la cible de nombreuses modifications post-traductionnelles(MPT), particulièrement au niveau de leur section N-terminale. Ces modifications réversibles font partie d’un code d’histones épi-génétique transmissible qui orchestre et module dynamiquement certains événements impliquant la chromatine, tels l’activation et la désactivation de gènes ainsi que la duplication et la réparation d’ADN. Ces modifications sont impliquées subséquemment dans la signalisation et la progression de cancers, tels que la leucémie. En conséquence, l'élucidation des modifications d’histones est importante pour comprendre leurs fonctions biologiques. Une méthodologie analytique a été mise au point en laboratoire pour isoler, détecter, et quantifier les MPT d’histones en utilisant une approche rapide à deux volets à l’aide d’outils bioinformatiques spécialisés. La méthodologie développée en laboratoire a été validée en utilisant des histones de souche sauvage ainsi que deux types d’histones mutants déficients en enzymes acétyltransferase. Des trois sources d’histones utilisées, la seule MPT qui a démontré un changement significatif est l’acétylation de l’histone H3 à lysine 56 (H3K56ac). L’expression et la stoechiométrie de cette MPT, issue de cellules de souche sauvage et de cellules mutantes, ont été déterminées avec précision et comparées. Les fonctions de balayage polyvalentes d'un instrument à trappe ionique quadrupôle linéaire hybride ont été utilisées pour améliorer la détection de protéines intactes. Le mode de balayage « enhanced multiply charged » (EMC) a été modifié pour contenir et détecter les ions de protéines intactes situées dans la trappe ionique linéaire. Ce mode de balayage nommé « targeted EMC » (tEMC) a permis de quadrupler le niveau de sensibilité (signal/interférence), et quintupler la résolution du mode de balayage conventionnel. De plus, la capacité de séparation des charges du tEMC a réduit de façon significative les effets de « space charge » dans la trappe ionique linéaire. La résolution supérieure du mode tEMC a permis de différencier plusieurs isoformes modifiées, particulièrement pour l’histone H3. L’analyse des peptides d’histones trypsiques à l’aide du mode de balayage « MRM » a permis le séquençage et la quantification de MPT avec un haut degré de précision. La seule MPT qui était sous-exprimée entre l’histone de souche sauvage et le mutant DOT1L fut la méthylation de l’histone H3 lysine 79(H3K79me1). Les effets de deux inhibiteurs d’enzymes HDAC (HDACi) sur l’expression de MPT d’histone ont été évalués en utilisant la méthodologie analytique mentionnée. Les histones extraites de cellules normales et cancéreuses ont été exposées à du Vorinostat(SAHA) ou du Entinostat (MS-275) pour une période de 24 à 72 heures. Deux histones furent principalement affectées, soit H3 et H4. Étonnamment, les mêmes effets n'ont pas été détectés lorsque les cellules normales ont été traitées avec le HDACi pour une période de 48 à 72 heures. Une méthode absolue de quantification avec une courbe d’étalonnage a été développée pour le peptide H3K56ac. Contrairement à certaines publications, nos résultats démontrent que cette MPT est présente dans les cellules mammifères avec une stoechiométrie très basse (< 0,1%) et n'est pas surexprimée de façon significative après le traitement au HDACi. / In eukaryotic cells, the lengthy DNA biopolymer is condensed into the cell nucleus with the aid of small packaging proteins called histones. In addition to their packing functions,histones are also targets of numerous post translational modifications (PTMs), especially on their N-terminus. These reversible modifications are believed to be constituents of a heritable epigenetic “histone code” that dynamically orchestrate and modulate chromatin based events such as gene activation and silencing, DNA replication and repair, and are also involved in the downstream signaling and progression of cancers, such as leukemia. Thus, the elucidation of histone PTMs is important in understanding their biological function. An analytical workflow was designed and set-up in the laboratory to isolate, detect, and quantitate histone PTM, using a two-pronged, unbiased, and rapid approach with specialized bioinformatic tools. The workflow was validated using histones from wildtype, and 2 mutants deficient in acetyltransferase activity. Between the three histone sources, the only PTM that demonstrated any change was acetylation at histone H3 lysine 56 (H3K56ac). The down-regulation and stoichiometry of this PTM was accurately assessed between wild-type and mutant cells. The versatile scan functions of a hybrid quadrupole-linear ion trap instrument were exploited to enhance the detection of intact histone proteins. The enhanced multiply charged (EMC) scan was modified in order to contain and detect intact protein ions within the linear ion trap. This targeted EMC (or tEMC) resulted in not only a 4-fold increase in signal-to-noise, but also a 5-fold increase in resolution. Furthermore, the charge separation capability of the tEMC dramatically reduced space charge effects within the linear ion trap. The superior resolution of the tEMC mode allowed for the discimination of many modified histone isoforms, especially for histone H3. Using the bottom-up strategy with multiple reaction monitoring (MRM), histone peptides were quantified and sequenced with a high degree of precision. The only PTM that was down-regulated between wild-type and DOT1L mutant histones was methylation at histone H3 lysine 79 (H3K79me1). The effects of two clinically relevant small molecule HDAC inhibitors (HDACi) on histone PTMs patterns were assessed using the analytical workflow developed. Histones derived from both normal and cancer cells were exposed to either Vorinostat (SAHA) or Entinostat (MS-275) over a 24- to 72 hour period. The two core histones primarily affected were H3 and H4. Surprisingly, the same effects were not observed when normal cells were treated with three doses of SAHA at 24-hour intervals over a 72-hour period. An absolute quantitation method using a calibration curve was developed for H3K56ac. In opposition to other published literature, our findings demonstrate that this PTM is present in very low stoichiometry (< 0.1%) in mammalian cells, and exhibits no significant up-regulation in different cell lines treated with several types of HDACi.