This thesis presents numerical optimization of geometries of axially symmetric ion trap mass analyzers. The motivation for this thesis is two fold. First is to demonstrate how the automated scheme can be applied to achieve geometry parameters of axially symmetric ion traps for a desired field configuration. Second is, through the Geometries investigated in this thesis, to present practically achievable geometries for mass spectroscopists to use. Here the underlying thought has been to keep the design simple for ease of fabrication (with the possibility of miniaturization) and still ensure that the performance of these analyzers is similar to the stretched geometry Paul traps. Five geometries have been taken up for investigation: one is the well known Cylindrical ion trap (CIT), three are new geometries and the last is the Paul trap under development in our laboratory. Two of these newer geometries have a step in the region of the midline of the cylindrical ring electrode (SRIT) and the third geometry has a step in its endcap electrodes (SEIT). The optimization has been carried out around deferent objective functions composed of the desired weights of higher order multiples. The Nelder-Mead simplex method has been used to optimize trap geometries. The multipoles included in the computations are quadrupole, octopole, dodecapole, hexadecapole,ikosipole and tetraikosipole having weights A2, A4, A6, A8, A10 and A12, respectively.Poincare sections have been used to understand dynamics of ions in the traps investigated. For the CIT, it has been shown that by changing the aspect ratio of the trap the harmful ejects of negative dodecapole superposition can be eliminated, although this results in a large positive A4=A2 ratio. Improved performance of the optimized CIT is suggested by the ion dynamics as seen in Poincare sections close to the stability boundary. With respect to the SRIT, two variants have been investigated. In the first geometry, A4=A2 and A6=A2 have been optimized and in the second A4=A2, A6=A2 and A8=A2 have been optimized; in both cases, these ratios have been kept close to their values reported for stretched hyperboloid geometry Paul traps. In doing this, however, it was seen that the weights of still higher order multipole not included in the objective function, A10=A2 and A12=A2, are high; additionally, A10=A2 has a negative sign. In spite of this, for both these configurations, the Poincare sections predict good performance. In the case of the SEIT, a geometry was obtained for which A4=A2 and A6=A2 are close to their values in the stretched geometry Paul trap and the higher even multipole (A8=A2, A10=A2 and A12=A2) are all positive and small in magnitude. The Poincare sections predict good performance for this con¯guration too. Direct numerical simulations of coupled nonlinear axial/radial dynamics also predict good performance for the SEIT, which seems to be the most promising among the geometries proposed here. Finally, for the Paul trap under development in our laboratory, Poincare sections and numerical simulations of coupled ion dynamics suggest a stretch of 79:7% is the best choice.

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.

In this work are presented results of the experimental study of state selected reactions of H+ and N+(3PJa) ions with molecular hydrogen H2(J = 0, 1) at temperatures in the range 10 - 100 K using 22-pole rf ion trap apparatus. These reactions are important for the formation of interstellar trihydrogen cations and ammonia. To determine the temperature of ions, calibration measurements of the Doppler broadening of spectral lines using N2+ + Ar  Ar+ + N2 laser induced reaction and rate of the ternary association He+ + 2He  He2+ + He were performed. Both ternary and radiative channels of the H+ + H2(J) association reaction were observed at hydrogen number densities in the range 1012 - 1014 cm-3 and 1011 - 1012 cm-3 respectively. Obtained temperature dependences at 11 - 33 K demonstrate substantial role of the H2 rotational energy, results cannot be explained with the existed theories of the stabilization of collisional complexes. Measurements of the rate coefficient of N+(3PJa) + H2(J) reaction at different ortho fractions of H2 show dependence on internal energy of both reactants. State specific rate coefficients of the reaction of nitrogen and hydrogen ions were derived. The adiabatic model and collisional relaxations of N+(3PJa) fine structure levels were considered. Powered by TCPDF (www.tcpdf.org)

This thesis deals with the analysis of micromotion of a single charged calcium ion trapped inside the linear Paul's ion trap and the influence of residual micromotion on the systematic frequency shifts of the clock transition of calcium ion. The fundamental properties of the motion of an ion confined within linear Paul's ion trap are shown in general using a theoretical description. The micromotion component of the overall motion is especially emphasized. A model expressing micromotion in the axial direction of the trap is introduced on the basis of the results of the numerical calculation of electric fields inside the trap. The model is compared to the reality experimentally. Then, the photon-correlation method of detection of micromotion is introduced and subsequently used to minimize and to estimate a measure of residual micromotion in all spacial directions. According to the achievable measure of residual micromotion, the systematic frequency shifts caused by this micromotion are estimated. It can be seen that we are able to reach uncertainties of the relative frequency shifts due to micromotion below 10^20. We expect that uncertainty of total motional systematic frequency shift is in our case limited by thermal motion.

<p>Crude oil is a mixture of hydrocarbons so complex that it is predicted to comprise as many compounds as there are genes in the human genome. Developing methods to not only recover crude oil from the ground but also to convert crude oil into desirable products is challenging due to its complex nature. Thus, the petroleum industry relies heavily on analytical techniques to characterize the oil in reservoirs prior to enhanced oil recovery efforts and to evaluate the chemical compositions of their crude oil based products. Mass spectrometry (MS) is the only analytical technique that has the potential to provide elemental composition as well as structural information for the individual compounds that comprise petroleum samples. The continuous development of ionization techniques and mass analyzers, and other instrumentation advances, have primed mass spectrometry as the go-to analytical technique for providing solutions to problems faced by the petroleum industry. The research discussed in this dissertation can be divided into three parts: developing novel mass spectrometry-based methods to characterize mixtures of saturated hydrocarbons in petroleum products (Chapters 3 and 5), exploring the cause of fragmentation of saturated hydrocarbons upon atmospheric pressure chemical ionization to improve the analysis of samples containing these compounds (Chapter 4), and developing a better understanding of the chemical composition of crude oil that tightly binds to reservoir surfaces to improve chemically enhanced oil recovery (Chapter 6). </p>

Using a cryogenic linear 22-pole rf ion trap, rate coefficients for H/D exchange reactions of OH− with D2 (1) and OD− with H2 (2) have been measured at temperatures between 11 K and 300 K with normal hydrogen. Below 60 K, we obtained k1 = 5.5 × 10−10 cm3 s−1 for the exoergic reaction (1). Upon increasing the temperature above 60 K, the data decrease with a power law, k1(T) [similar] T−2.7, reaching ≈1 × 10−10 cm3 s−1 at 200 K. This observation is tentatively explained with a decrease of the lifetime of the intermediate complex as well as with the assumption that scrambling of the three hydrogen atoms is restricted by the topology of the potential energy surface. The rate coefficient for the endoergic reaction (2) increases with temperature from 12 K up to 300 K, following the Arrhenius equation, k2 = 7.5 × 10−11 exp(−92 K/T) cm3 s−1 over two orders of magnitude. The fitted activation energy, EA-Exp = 7.9 meV, is in perfect accordance with the endothermicity of 24.0 meV, if one accounts for the thermal population of the rotational states of both reactants. The low mean activation energy in comparison with the enthalpy change in the reaction is mainly due to the rotational energy of 14.7 meV contributed by ortho-H2 (J = 1). Nonetheless, one should not ignore the reactivity of pure para-H2 because, according to our model, it already reaches 43% of that of ortho-H2 at 100 K. / Dieser Beitrag ist aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Hochgeladene Ionen stellen einen extremen Zustand der Materie dar, wie sie vornehmlich in kosmischen Plasmen zu finden ist. Die labormäßige Erzeugung und (spektroskopische) Untersuchung hochgeladener Ionen liefert wichtige Daten und Erkenntnisse für die Astrophysik und Fusionsforschung. Aufgrund ihrer zum Teil exotischen Eigenschaften besitzen hochgeladene Ionen ein großes Potential für eine Vielzahl neuer Anwendungen. Die bisher weltweit einzige Elektronenstrahl-Ionenfalle, die hochgeladene Ionen bis hin zu vollständig ionisierten Ionen unter Raumtemperaturbedingungen erzeugen und bereitstellen kann, die Dresden EBIT, ist Gegenstand der vorgelegten Arbeit. Die Dresden EBIT zeichnet sich neben ihrer Kompaktheit und einer einfachen Bedienung durch ihre Langzeitstabilität aus. Sowohl über Röntgenspektren als auch über die Extraktion der Ionen aus der EBIT konnte für eine Reihe von Elementen der Nachweis der Erzeugung von vollständig ionisierten Ionen bis Z=28 erbracht werden. Für schwere Elemente können Ionenladungszustände bis hin zu neonähnlichen Ionen erzeugt werden. Entscheidenden Einfluss auf den erzielten mittleren Ladungszustand hat die Ioneneinschlusszeit. Die zeitliche Entwicklung der Ladungszustandsverteilung, wie sie im Zusammenspiel der verschiedenen atomaren Prozesse simuliert werden kann, ist sowohl an einer Reihe von röntgenspektroskopischen Messungen als auch anhand von Extraktionsspektren untersucht worden. Neben der Beladung der EBIT mit gasförmigen Elementen ist insbesondere die Beladung mit Metallen, d. h. mit einem möglichst breiten Spektrum an Elementen gefordert. Die Beladung mit leichtflüchtigen metallorganischen Verbindungen, die über das Gaseinlassventil eingebracht werden können, hat sich als erfolgreiche und preiswerte Alternative zu einer MEVVA-Quelle erwiesen. Die Beladung mit Metallionen ist am Beispiel verschiedener Untersuchungen gezeigt. Der monoenergetische Elektronenstrahl gestattet neben der Untersuchung von Anregungs- und Ionisationsprozessen insbesondere die der wichtigen Rekombinationsprozesse des Strahlenden Einfangs und der Dielektronischen Rekombination. Der Einsatz eines Kristalldiffraktionsspektrometers erlaubt trotz einer aufwendigen Kalibrierung und sehr langen Messzeiten die Auflösung einzelner Übergänge in hochgeladenen Ionen. Hauptanwendungsfeld der Dresden EBIT wird der Einsatz als Ionenquelle sein. Aus den Untersuchungen des extrahierten Gesamtionenstroms können die Bedingungen für einen möglichst großen Ionenstrom und einen optimalen Ionenstrahltransport abgeleitet werden. Eine optimale Ausnutzung der Eigenschaften hochgeladener Ionen erfordert die Separation der einzelnen Ladungszustände. Der Nachweis der sehr kleinen Ionenströme erfolgt über die kapazitive Messung in einem Faradaycup. Die Messung der Ladungszustandsverteilung in Abhängigkeit von den Parametern der EBIT gibt zusätzliche Aufschlüsse über die Eigenschaften der Ionenfalle.

Two gas-phase ion-molecule reaction systems are presented here based on measurements done in a temperature variable 22-pole trapping machine. In the first case, the proton affinity of methane is determined based on a new technique for measuring the equilibrium constant of the HCO2+ + CH4 <=> CH5+ + CO2 reaction. The second case reports to the (Ar + N2 )+ reaction system, with reaction rate temperature dependencies measurements made both in the forward and reverse direction with different and complementary methods. The temperature variable 22-pole trapping machine allows one to determine equilibrium constants and reaction rate coefficients over a wide range of temperatures. The coupling of an effusive beam to the setup overcomes the problem of neutral gas wall condensation and extends the temperature range measurements beyond condensation point. The introduction (Chapter 1) gives a short overview about the rf technology and parallel experimental techniques developed in order to better characterize and understand the several mechanisms related to ion-molecule reactions. It also focuses some aspects of reaction rate temperature dependencies determination as well as thermodynamical equilibrium in laboratory environment. A short description of the setup and experimental methods are presented in Chapter 2. Based on equilibrium constant measurements, Chapter 3 is dedicated to the proton affinity of methane. This concept has applications on several fields such as atmospheric and combustion modelling, or testing empirical and ab initio theories for electronic structures. The (Ar − N2 )+ system presented in Chapter 4, is known for being a good case study for inferring the role of vibrational excitation in reaction dynamics and to the existence of non-adiabatic coupling. The experimental results here presented for the N2+ + Ar reaction demonstrate that it is possible to avoid parallel reactions with first vibrational excited state of nitrogen (N2 (ν = 1)). On the other hand, the reverse reaction experiments confirm the existence of a minimum of the reaction rate in the 30 to 300 K range, due to the existence of two reaction channels. The question of the high rate coefficient towards lower temperatures being related to the N2 rotational ground state population is raised. A summary and outlook are presented in Chapter 5, where some new possible paths of investigation are pointed out.

Two gas-phase ion-molecule reaction systems are presented here based on measurements done in a temperature variable 22-pole trapping machine. In the first case, the proton affinity of methane is determined based on a new technique for measuring the equilibrium constant of the HCO2+ + CH4 <=> CH5+ + CO2 reaction. The second case reports to the (Ar + N2 )+ reaction system, with reaction rate temperature dependencies measurements made both in the forward and reverse direction with different and complementary methods. The temperature variable 22-pole trapping machine allows one to determine equilibrium constants and reaction rate coefficients over a wide range of temperatures. The coupling of an effusive beam to the setup overcomes the problem of neutral gas wall condensation and extends the temperature range measurements beyond condensation point. The introduction (Chapter 1) gives a short overview about the rf technology and parallel experimental techniques developed in order to better characterize and understand the several mechanisms related to ion-molecule reactions. It also focuses some aspects of reaction rate temperature dependencies determination as well as thermodynamical equilibrium in laboratory environment. A short description of the setup and experimental methods are presented in Chapter 2. Based on equilibrium constant measurements, Chapter 3 is dedicated to the proton affinity of methane. This concept has applications on several fields such as atmospheric and combustion modelling, or testing empirical and ab initio theories for electronic structures. The (Ar − N2 )+ system presented in Chapter 4, is known for being a good case study for inferring the role of vibrational excitation in reaction dynamics and to the existence of non-adiabatic coupling. The experimental results here presented for the N2+ + Ar reaction demonstrate that it is possible to avoid parallel reactions with first vibrational excited state of nitrogen (N2 (ν = 1)). On the other hand, the reverse reaction experiments confirm the existence of a minimum of the reaction rate in the 30 to 300 K range, due to the existence of two reaction channels. The question of the high rate coefficient towards lower temperatures being related to the N2 rotational ground state population is raised. A summary and outlook are presented in Chapter 5, where some new possible paths of investigation are pointed out.

Das Proteasomensystem der Zelle ist für die Degradation von Proteinen verantwortlich und spielt eine zentrale Rolle bei der Generierung von Epitopen, die auf MHC-Klasse-I Molekülen den cytotoxischen T-Lymphozyten (CTLs) präsentiert werden. Die Stimulation von Zellen mit Interferon-gamma (IFNgamma) führt zu der Bildung von Immunoproteasomen, die im Vergleich zu den konstitutiven Proteasomen eine verbesserte Generierung vieler MHC-Klasse-I Epitope aufweisen. In gesunden Mäusen werden Immunoproteasomen vorwiegend in den lymphatischen Geweben exprimiert, wohingegen nicht-lymphatische Gewebe hauptsächlich konstitutive Proteasomen enthalten. In der vorliegenden Arbeit wurde der Einfluss der Listeria monocytogenes Infektion auf die aus der Leber, der Milz, dem Dünndarm und dem Colon stammenden murinen 20S Proteasomen untersucht. Die Struktur der isolierten 20S Proteasomen wurde mittels zweidimensionaler Gelelektrophorese und Westernblot ermittelt, während die Funktion durch in vitro Prozessierung von drei oligomeren Peptidsubstraten analysiert wurde. Die Prozessierungsprodukte wurden mittels HPLC-ESI-Ionenfalle massenspektrometrisch identifiziert sowie quantifiziert. Die vorliegende Arbeit zeigt zum ersten Mal, dass nach einer Infektion die aus den nicht-lymphatischen Organen und Zellen isolierten 20S Proteasomen eine strukturelle und funktionelle Plastizität aufweisen: Nach der Infektion wurde die Bildung von Immunoproteasomen induziert, was mit der gesteigerten Generierung der immunrelevanten Fragmente korreliert werden konnte. Dies verlief unabhängig von der direkten Präsenz von Listeria monocytogenes in den Organen und wurde ausschließlich durch das Cytokin IFNgamma reguliert. Es konnte außerdem eine Zunahme der posttranslationalen Modifikation von Leberproteasomen mit dem Monosaccharid N-Acetylglucosamin nach der Infektion nachgewiesen werden. Des Weiteren wurde eine detaillierte Analyse der massenspektrometrischen Daten hinsichtlich des Schnittverhaltens der konstitutiven und Immunoproteasomen etabliert. Die Auswertung ergab, dass die Immunoproteasomen nach der Infektion durch schnellere und veränderte Nutzung bestehender Spaltstellen an der verbesserten Epitoppräsentation beteiligt sind. / The proteasome system of the cell is responsible for the degradation of proteins and plays a central role in the generation of epitopes which are presented to cytotoxic T-lymphocytes (CTLs) on MHC-class-I molecules. The stimulation of cells by interferon-gamma (IFNgamma) leads to the formation of immunoproteasomes that show an improved generation of many MHC-class-I epitopes compared to constitutive proteasomes. In healthy mice, immunoproteasomes are mainly expressed in the lymphatic tissues, whereas the non-lymphatic organs predominantly contain constitutive proteasomes. In this project the effect of Listeria monocytogenes infection on murine 20S proteasomes derived from the liver, spleen, small intestine and colon were investigated. The structure of the isolated proteasomes was analyzed by two-dimensional gel electrophoresis and western blots while the function was studied by in vitro processing of three oligomeric peptide substrates. Identification and quantification of the processing products was performed by HPLC-ESI-ion trap mass spectrometry. The project showed for the first time, that after infection 20S proteasomes isolated from non-lymphatic organs as well as from non-lymphatic cells displayed structural and functional plasticity: immunoproteasomes were induced post infection which could be correlated with the enhanced generation of immuno-relevant fragments. This was independent of the direct presence of Listeria monocytogenes in the organs and solely controlled by the cytokine IFNgamma. In addition, an increased posttranslational modification with the monosaccharide N-acetylglucosamine could be detected in liver-derived proteasomes after infection. Furthermore, a detailed analysis of the mass spectrometry data was established according to the cleavage site usage of constitutive and immunoproteasomes. The result was that immunoproteasomes are involved in improved generation of the immuno-relevant fragments by the faster cleavage and the changed usage of existing cleavage sites after infection.