Íons polihalogenados de Si, X3Si+ (X = F, Cl), são fragmentos facilmente gerados em espectrometria de massas por ionização eletrônica de compostos de silício polihalogenados. Estes cátions possuem um elevado caráter eletrofílico e desempenham um papel importante como intermediários em processos de corrosão auxiliados por plasma utilizados na fabricação de dispositivos em microeletrônica. Esta dissertação apresenta um estudo sobre a reatividade dos íons +SiCl3, em fase gasosa, perante uma série de substratos neutros simples como água, alcoóis, amônia, aminas e algumas bases doadoras de elétrons π. As reações íon-molécula em fase gasosa foram caracterizadas do ponto de vista experimental por espectrometria de massas de ressonância ciclotrônica de íons por transformada de Fourier (FTICR) a pressões da ordem de 10-8 Torr. As reações foram acompanhadas em função do tempo de reação na cela do espectrômetro, o que permitiu a elucidação de uma série de reações sequenciais. O perfil de energia das reações e as estruturas dos íons silicênios formados nestas reações foram também caracterizados por métodos de química computacional, usando métodos ab initio e métodos baseados na teoria do funcional da densidade, a fim de elucidar o mecanismo das reações. Observou-se que o cátion +SiCl3 reage rapidamente em fase gasosa com os diversos substratos neutros através de processos semelhantes a reações de solvólise que resultam na adição do neutro seguida de eliminação de HCl. Em vários dos casos, foi possível observar a solvólise total do cátion com substituição dos três átomos de cloro. Os cálculos revelam que estas reações se processam inicialmente pela adição do eletrófilo aos centros ricos em densidade eletrônica dos substratos neutros e que estes adutos são mais estáveis que os reagentes isolados. O estado de transição destas reações envolve uma migração 1,3 de um hidrogênio e a energia calculada para o estado de transição é consideravelmente menor que a energia dos reagentes, fato este comum para reações rápidas íon/molécula em fase gasosa. Os cálculos para a espécie correspondente +CCl3 revelam que este tipo de reação não é favorável para os cátions metílicos substituídos e experimentalmente reações semelhantes não são observadas para +CCl3. No caso dos íons ClnSi(OH)3-n+ (n=1, 2 e 3), oriundos das reações de hidrólise do íon +SiCl3, observou-se reações secundárias de condensação com SiCl4 que levam a formação de espécies iônicas com ligações tipo siloxanas (-Si-O-Si-). Os cálculos teóricos sugerem que estas reações se processam inicialmente através de um intermediário tipo clorônio, R1-Cl+-R2 seguida de uma transferência formal de um átomo de Cl e rearranjo para uma estrutura tipo siloxana. / Polyhalogenated silicenium ions, X3Si+ (X = F, Cl), are common fragment ions in the mass spectra of polyhalogenated silanes obtained by electron ionization. These ions are powerful electrophiles and are believed to play a role in plasma enhanced corrosion processes and plasma enhanced chemical vapour deposition processes. In this dissertation, we present some new results on the gas-phase reactivity of the +SiCl3 ion with a number of simple n electron donor bases such as water, alcohols, ammonia, amines and some π electron donor bases. Ion-molecule reactions were characterized experimentally by Fourier transform ion cyclotron resonance mass spectrometry (FTICR) at pressures in the 10-8 Torr range. Reactions were followed as a function of trapping time of the ions in the cell of the spectrometer and this allowed for the identification of subsequent reactions of the primary product ions. The energy diagram and structure of the different silicenium ions were also characterized by computational chemistry using both ab initio and density functional theory methods in order to understand the mechanism of these reactions. +SiCl3 reacts rapidly in gas phase with various neutral substrates through processes similar to solvolysis in which the neutral substrate adds onto the silicenium ion followed by elimination of HCl. In some cases, complete solvolysis is observed with substitution of all three chlorine atoms. The calculations show that reactions proceed by initial addition of the electrophile onto the electron center of the neutral substrates giving rise to stable adducts. The transition state for these reactions involve a 1,3 hydrogen migration and the calculated energy for these transition states is less than the energy of the isolated reactants, a fact that is common to fast gas-phase ion-molecule reactions. Similar calculations for +CCl3 reveal similar solvolysis reactions to be energetically unfavourable, and in fact these reactions are not observed experimentally. Secondary reactions have been observed for the product ions ClnSi(OH)3-n+ (n = 1, 2 and 3), obtained from successive hydrolysis of +SiCl3, with the parent SiCl4 neutral. These secondary condensation reactions yield ionic species containing a siloxane type linkage (-Si-O-Si-). The theoretical calculations suggest that is that these secondary condensation reactions initially proceed via chloronium ion intermediate, R1-Cl+-R2 , followed by formal Cl transfer and rearrangement to a siloxane type structure.

<p>In this thesis, methods for studying different aspects of proteomics were developed with Fourier Transform Ion Cyclotron Resonance, (FTICR), mass spectrometry. The FTICR technique provides ultra-high mass resolving power, mass accuracy at sub ppm level and sensitivity in the attomole region.</p><p>Methods for quantifying biomarkers in body fluids such as cerebrospinal fluid, (CSF), and plasma were developed. Two sets of global markers with different properties were used for quantitative analysis; S-Methyl Thioacetimidate, (SMTA), and S-Methyl Thiopropionimidate, (SMTP), and [H₄]- and [D₄]-1-Nicotinoyloxy succinimide ester. Reduced ion suppression and higher sensitivity was obtained by coupling a High Performance Liquid Chromatography, (HPLC), system to the FTICR mass spectrometer.</p><p>In body fluids, proteins and peptides are present in a broad dynamic concentration range. Therefore, depleting abundant proteins prior to analysis results in decreased ion suppression and increased sensitivity. Two commercial depletion kits were evaluated with the SMTA- and SMTP-markers.</p><p>For both types of global markers, the experimental error for quantitative analysis of abundant proteins was less than 30%. This provides a lower limit for the protein up- and down regulations in complex solutions that can be monitored with HPLC-FTICR mass spectrometry.</p><p>Together with the identity and quantity of selected proteins the structure, dynamics and interactions with other molecules are of great importance. The later can be elucidated with Hydrogen/Deuterium Exchange, (HDX), mass spectrometry. Structural information at high resolution can be obtained with Collision-Induced Dissociation, (CID), HDX mass spectrometry. In this thesis, exchange rates of amide hydrogens in peptides were in excellent agreement with NMR results.</p><p>In some cases, the CID-fragments have different gas-phase exchange properties and as a consequence the solution phase exchange process can not be monitored. By applying Electron Capture Dissociation, (ECD), at ultra-high vacuum, the exchange process at a specific residue could be monitored.</p>

<p>Studies of protein and peptide expression are vital in order to understand complex biological systems. As demonstrated in this thesis, on-line packed capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR MS) is a useful analytical tool for such studies.</p><p>A proteomics method, based on global tryptic digestion and subsequent separation and detection of the peptides by LC-FTICR MS, was developed for qualitative analysis of body fluids. Initial experiments on cerebrospinal fluid (CSF) provided results that were comparable or superior to those achieved by more time- and sample-consuming techniques. The method was also successfully applied on plasma and amniotic fluid. One of the major challenges in proteomics is the broad dynamic range of proteins in biological matrices. The advantages of removing high-abundant components from CSF and plasma prior to MS were demonstrated.</p><p>In order to search for potential biomarkers, mass chromatograms of CSF from patients suffering from amyotrophic lateral sclerosis (ALS) and controls were compared using an in-house constructed pattern recognition program. ALS-specific patterns were observed, and four out of five unknown samples were correctly assigned. Alternative strategies to quantitatively compare two pools of samples rely on differential chemical labeling. The performance of one such method, quantification-using-enhanced-signal-tags, was investigated in complex sample analysis. The experimental intensity ratios were proven to be consistent with the prepared concentration ratios of abundant proteins in CSF.</p><p>Finally, the thesis reports on the first experiments where electron capture dissociation (ECD) was successfully incorporated in on-line LC-MS experiments. ECD and nozzle-skimmer fragmentation were applied to a sample of endocrine peptides extracted from mouse pancreatic islets. The two fragmentation methods provided complementary information. However, the method needs further optimization before it can be applied in the analysis of more complex samples, such as body fluids.</p>

In this thesis, methods for studying different aspects of proteomics were developed with Fourier Transform Ion Cyclotron Resonance, (FTICR), mass spectrometry. The FTICR technique provides ultra-high mass resolving power, mass accuracy at sub ppm level and sensitivity in the attomole region. Methods for quantifying biomarkers in body fluids such as cerebrospinal fluid, (CSF), and plasma were developed. Two sets of global markers with different properties were used for quantitative analysis; S-Methyl Thioacetimidate, (SMTA), and S-Methyl Thiopropionimidate, (SMTP), and [H4]- and [D4]-1-Nicotinoyloxy succinimide ester. Reduced ion suppression and higher sensitivity was obtained by coupling a High Performance Liquid Chromatography, (HPLC), system to the FTICR mass spectrometer. In body fluids, proteins and peptides are present in a broad dynamic concentration range. Therefore, depleting abundant proteins prior to analysis results in decreased ion suppression and increased sensitivity. Two commercial depletion kits were evaluated with the SMTA- and SMTP-markers. For both types of global markers, the experimental error for quantitative analysis of abundant proteins was less than 30%. This provides a lower limit for the protein up- and down regulations in complex solutions that can be monitored with HPLC-FTICR mass spectrometry. Together with the identity and quantity of selected proteins the structure, dynamics and interactions with other molecules are of great importance. The later can be elucidated with Hydrogen/Deuterium Exchange, (HDX), mass spectrometry. Structural information at high resolution can be obtained with Collision-Induced Dissociation, (CID), HDX mass spectrometry. In this thesis, exchange rates of amide hydrogens in peptides were in excellent agreement with NMR results. In some cases, the CID-fragments have different gas-phase exchange properties and as a consequence the solution phase exchange process can not be monitored. By applying Electron Capture Dissociation, (ECD), at ultra-high vacuum, the exchange process at a specific residue could be monitored.

New biomarkers are needed to improve knowledge about pathophysiology, in order to provide earlier correct diagnosis and to follow disease progression of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD). The aim of this thesis was to find new biomarkers for these diseases. First, increased serum levels and unchanged levels in postmortal spinal cord of vascular endothelial growth factor (VEGF) were demonstrated. VEGF was not detected in cerebrospinal fluid (CSF) in ALS. Second, increased levels of fibroblast growth factor 2 were found in the CSF and serum of ALS patients. Both studies used enzyme-linked immunoassays. Third, a proteomics method for CSF analysis was explored, based on tryptic digestion and subsequent separation and detection of the peptides by on-line liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry. ALS-specific patterns were observed. Four out of five samples were correctly assigned, but no single protein biomarker could be identified. Fourth, [11C](L)-deprenyl-D2 (DED) positron emission tomography (PET) demonstrated increased retention in the pons and white matter in ALS. DED binds to monoamino oxidase B, which in the brain is primarily located in astrocytes. Thus evidence was provided that astrocytosis may be detected in vivo in ALS. Fifth, normal [11C]-PIB binding in five nondemented patients with PD was reported, in contrast to previous findings of increased retention in Alzheimer's disease reflecting amyloid aggregation. Finally, the combined use of fluorodeoxyglucose and L-[β 11C]-DOPA PET for the differential diagnosis of parkinsonian syndromes was evaluated. PET provided support for the clinical diagnosis in 62 out of 75 patients, and served to exclude suspected diagnoses in another five patients.

This thesis concerns heating and current drive in tokamak plasmas using the fast magnetosonic wave in the ion cyclotron range of frequencies. Fast wave heating is a versatile heating method for thermonuclear fusion plasmas and can provide both ion and electron heating and non-inductive current drive. Predicting and interpreting realistic heating scenarios is however difficult due to the coupled evolution of the cyclotron resonant ion velocity distributions and the wave field. The SELFO code, which solves the coupled wave equation and Fokker-Planck equation for cyclotron resonant ion species in a self-consistent manner, has been upgraded to allow the study of more advanced fast wave heating and current drive scenarios in present day experiments and in preparation for the ITER tokamak. Theoretical and experimental studies related to fast wave heating and current drive with emphasis on fast ion effects are presented. Analysis of minority ion cyclotron current drive in ITER indicates that the use of a hydrogen minority rather than the proposed helium-3 minority results in substantially more efficient current drive. The parasitic losses of power to fusion born alpha particles and beam injected ions are concluded to be acceptably low. Experiments performed at the JET tokamak on polychromatic ion cyclotron resonance heating and on fast wave electron current drive are presented and analysed. Polychromatic heating is demonstrated to increase the bulk plasma ion to electron heating ratio, in line with theoretical expectations, but the fast wave electron current drive is found to be severely degraded by parasitic power losses outside of the plasma. A theoretical analysis of parasitic power losses at radio frequency antennas indicates that the losses can be significantly increased in scenarios with low wave damping and with narrow antenna spectra, such as in electron current drive scenarios. / QC 20100506

Studies of protein and peptide expression are vital in order to understand complex biological systems. As demonstrated in this thesis, on-line packed capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR MS) is a useful analytical tool for such studies. A proteomics method, based on global tryptic digestion and subsequent separation and detection of the peptides by LC-FTICR MS, was developed for qualitative analysis of body fluids. Initial experiments on cerebrospinal fluid (CSF) provided results that were comparable or superior to those achieved by more time- and sample-consuming techniques. The method was also successfully applied on plasma and amniotic fluid. One of the major challenges in proteomics is the broad dynamic range of proteins in biological matrices. The advantages of removing high-abundant components from CSF and plasma prior to MS were demonstrated. In order to search for potential biomarkers, mass chromatograms of CSF from patients suffering from amyotrophic lateral sclerosis (ALS) and controls were compared using an in-house constructed pattern recognition program. ALS-specific patterns were observed, and four out of five unknown samples were correctly assigned. Alternative strategies to quantitatively compare two pools of samples rely on differential chemical labeling. The performance of one such method, quantification-using-enhanced-signal-tags, was investigated in complex sample analysis. The experimental intensity ratios were proven to be consistent with the prepared concentration ratios of abundant proteins in CSF. Finally, the thesis reports on the first experiments where electron capture dissociation (ECD) was successfully incorporated in on-line LC-MS experiments. ECD and nozzle-skimmer fragmentation were applied to a sample of endocrine peptides extracted from mouse pancreatic islets. The two fragmentation methods provided complementary information. However, the method needs further optimization before it can be applied in the analysis of more complex samples, such as body fluids.

The subject of this thesis is high-precision mass-measurements performed with Penning trap mass spectrometers (PTMS). In particular it describes the SMILETRAP I PTMS and the final results obtained with it, the masses of 40Ca and that of the proton. The mass of 40Ca is an indispensible input in the evaluation of measurements of the bound electron g-factor, used to test quantum electrodynamical calculations in strong fields. The value obtained agrees with available literature values but has a ten times higher precision. The measurement of the proton mass, considered a fundamental physical constant, was performed with the aim of validating other Penning trap results and to test the limit of SMILETRAP I. It was also anticipated that a measurement at a relative precision close to 10-10 would give insight in how to treat certain systematic uncertainties. The result is a value of the proton mass in agreement with earlier measurements and with an unprecedented precision of 1.8×10-10. Vital for the achieved precision of the proton mass measurement was the use of the Ramsey excitation technique. This technique, how it was implemented at SMILETRAP I and the benefits from it is discussed in the thesis and in one of the included papers. The second part of the thesis describes the improved SMILETRAP II setup at the S-EBIT laboratory, AlbaNova. All major changes and upgrades compared to SMILETRAP I are discussed. This includes, apart from the Ramsey excitation technique, higher ionic charge states, improved temperature stabilization, longer run times, different reference ions, stronger and more stable magnetic field and a more efficient ion detection. Altogether these changes should reduce the uncertainty in future mass determinations by an order of magnitude, possibly down to 10-11. / At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 9: Accepted.

Mass spectrometry has in recent years been established as the standard method for protein identification and characterization in proteomics with excellent intrinsic sensitivity and specificity. Fourier transform ion cyclotron resonance is the mass spectrometric technique that provides the highest resolving power and mass accuracy, increasing the amount of information that can be obtained from complex samples. This thesis concerns how useful information on proteins of interest can be extracted from mass spectrometric data on different levels of protein structure and how to obtain this data experimentally. It was shown that it is possible to analyze complex mixtures of protein tryptic digests by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and identify abundant proteins by peptide mass fingerprinting. Coupling on-line methods such as liquid chromatography and capillary electrophoresis increased the number of proteins that could be identified in human body fluids. Protein identification was also improved by novel statistical methods utilizing prediction of chromatographic behavior and the non-randomness of enzymatic digestion. To identify proteins by short sequence tags, electron capture dissociation was implemented, improved and finally coupled on-line to liquid chromatography for the first time. The combined techniques can be used to sequence large proteins de novo or to localize and characterize any labile post-translational modification. New computer algorithms for the automated analysis of isotope exchange mass spectra were developed to facilitate the study of protein structural dynamics. The non-covalent interaction between HIV-inhibitory peptides and the oligomerization of amyloid β-peptides were investigated, reporting several new findings with possible relevance for development of anti-HIV drug therapies and understanding of fundamental mechanisms in Alzheimer’s disease.

QC 20100622