N/A / Thesis / Master of Science (MS)

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Thesis (M.A.)--Boston University / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / The general theory of the operation of a mass spectrometer is described with particular attention to the second order focusing. The equations wherever applicable are used for a symmetrical type, 90° deflection mass spectrometer with a radius of 4.6 centimeters. Since errors in the magnetic field are more serious (by a factor of 2) than errors in the electrostatic potential, a current regulator is constructed which can correct an error signal to few parts in 10^3. The beam is provided by surface ionization and the analysis of possible masses is limited by such factors as ionization potential, maximum magnetic field, and accelerating potential. A few mass spectra are given with voltage scanning, and the results are analyzed in terms of the equations derived in part I. The Bediasite sample used for analysis is from the Grimes County, Texas, and such elements as Fe, Si, Al, Mg, Na, Ne, O, N, and possibly Ti and carbon have been identified in its spectrum. The existence of elements with high ionization potential is explained to be due to a discharge process in the ionization chamber. The experimental duration of peaks due to Ne, 0, N is about 2 hours with N the most intense and Ne the least intense element. These peaks seem to be the contents of the microscopic bubbles present in the sample. The presence of neon oxygen, and helium has been confirmed by the spectroscopic analysis of O'Keefe, Dunning, and Lowman. Helium was not recorded due to the limited range of the accelerating power supply. It is suggested that in order to carry out the research further, some improvements be made on the instrument. / 2031-01-01

進入後基因時代，蛋白質體學成為很多科學家有興趣的主題。蛋白質鑑定成為重要的一環，而質譜儀在縮氨酸分析及蛋白質鑑定中扮演重要的角色。腫瘤、卵巢癌及攝護腺癌等研究亦已成為質譜儀上的應用。Coombes 等人 (2004) 提出了一個線性的數學質譜儀模型，而且建議這個模型可被應用在建立質譜儀的模擬中。本文中，我們利用虛擬的質譜儀產生虛擬質譜資料並加以研究。虛擬的質譜實驗包括了前、後兩部份。樣本資料要放入虛擬質譜儀之前，可能出現的蛋白質其強度(intensity)必須先隨機地被決定，之後強度必須被轉換(calibration)變成離子化的個數(abundance) ；之後將樣本資料丟入虛擬質譜儀中，每一個蛋白值的飛行時間(time of flight， TOF) 將會被紀錄。另外一個轉換(calibration)是將飛行時間(TOF)轉成質量電荷比(mass-to-charge ratio，m/z)。質譜儀和兩個轉換都會在資料中產生誤差。在本文中，一個完整的模擬過程將會一步一步被介紹。同時，兩個轉換的方法所產生的誤差也會被探討。之後，我們將此模擬方法應用於模擬一組攝護腺癌中。 / Entering the post genomic era, proteomic has become the topic that scientists are interested in. The authentication of protein has been an important item of the topics. Mass spectrometry (MS) has become an important tool for peptide analysis or proteomic authentication. There are many applications of MS such as oncology, ovarian cancer, and prostate cancer. Coombes et al.(2004) proposed a mathematical model of a virtual spectrometer and suggested that the virtual spectrometer can be applied in conducting a MS simulation. In our study, we focus on designing a simulation study of spectrum data from a virtual MS experiment. The virtual experiment includes two stages: pre- and post-virtual spectrometer. Before the sample data are put into the virtual spectrometer, a virtual population of the intensity of all possible proteins should be determined; a virtual sample is randomly drawn; and the generated sample of intensity should be calibrated to abundance, which is the number of molecules ionized and desorbed from the biological sample. The sample data are then put into the virtual spectrometer and the time of flight (TOF) of each ionized molecule is recorded. Another calibration is employed to transfer a TOF to a mass-to-charge ratio (m/z). The spectrometer and the calibration processes produce variation in MS data. In this study, a complete simulation design of mass spectra will be introduced step by step. Moreover, the calibration effects caused from the two calibration procedures will be investigated. A simulation based on a real data set from a prostate cancer study will be also given as an illustration.

The study of proteomics holds the hope for detecting serious diseases earlier than is currently possible by analyzing blood samples in a mass spectrometer. Unfortunately, the statistics involved in comparing a control group to a diseased group are not trivial, and these difficulties have led others to incorrect decisions in the past. This paper considers a nested design that was used to quantify and identify the sources of variation in the mass spectrometer at BYU, so that correct conclusions can be drawn from blood samples analyzed in proteomics. Algorithms were developed which detect, align, correct, and cluster the peaks in this experiment. The variation in the m/z values as well as the variation in the intensities was studied, and the nested nature of the design allowed us to estimate the sources of that variation. The variation due to the machine components, including the mass spectrometer itself, was much greater than the variation in the preprocessing steps. This conclusion inspires future studies to investigate which part of the machine steps is causing the most variation.

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This thesis describes a non-magnetic mass spectrometer incorporating the following components: a heated filament source, an electrostatic energy analyser, and a time-of-flight velocity analyser. The last component measures the time required for an ion to go between two small condensers by means of a radio frequency voltage applied to the condensers. If an ion passes successively through both condensers when the field in them is zero, it is collected and detected. It is then possible to relate the e/m to the frequency of the applied voltage when the energy of the ion and the distance between the centres of the condensers is known. Theory is presented which permits the calculation of resolution and current intensities. The values so obtained are realized experimentally. / Thesis / Master of Science (MSc)

The focus of this dissertation is the introduction of surface-induced dissociation (SID) into a commercially available quadrupole time-of-flight mass spectrometer as an alternative ion fragmentation method. The performance of the SID device was characterized and its applications were demonstrated by dissociating peptides, proteins, inorganic salt clusters and non-covalent protein complexes. The SID setup allowed direct comparison of SID with conventional collision-induced dissociation (CID) on the same instrument, taking advantage of the characteristics of Q-TOF instrumentation, including extended mass range, high sensitivity and resolution. With the SID setup installed, no significant reduction of the ion transmission was evident. SID fragmentation patterns of peptides are, in general, similar to CID, with slight differences in the relative intensities of immonium ions, backbone cleavage b- versus y- type ions, and y- versus y-NH3 ions. This suggests enhanced accessibility to high energy/secondary fragmentation channels with SID. SID studies on cesium iodide clusters (CsI) also revealed that SID deposits more internal energy.The utility of mass spectrometric methods to probe the gas phase cyclization process was studied with [D-Ala2]-Leucine Enkephalin amide. This peptide showed prominent formation of the [M-NH3]+ ion which is believed to be the linear b5 ion with a C-terminal oxazolone structure. Other fragments in the spectra indicate that the linear b5 ion undergoes cyclization, subsequent ring opening and further dissociation to rearranged fragments that cannot be explained by the initial sequence. The similarities between the cyclic and b5-ion from the linear peptide indicated the formation of a heterogeneous ion population and this is further supported by gas-phase H/D exchange experiments. An ion funnel interface to improve ion transmission at high pressures was tested in a custom built quadrupole-surface-quadrupole instrument. The ion transmission efficiency for selected bio-molecules such as YGGFLR, insulin chain-B, ubiquitin and cytochrome c showed to approach almost 90%, with the funnel interface installed. The ion transmission efficiency was effected by several factors including: the size of the analyte, the DC gradient, the RF frequency, and the RF amplitude. The higher fragmentation efficiencies for SID in the presence of the funnel interface indicated higher internal energy deposition for the funnel interface.

Detection of organic molecules present on the surface of dust particles is important in homeland security, agriculture, and several other applications. The research presented reports the ability of the aerosol mass spectrometer (AMS) to detect molecules on the surface of dust particles without detecting the particle core. Experiments were carried out to detect semi-volatile organic compounds adsorbed onto the surface of particulates without interference from the dust particle core. Methyl salicylate, oleic acid, and organophosphorus pesticides such as Malathion were detected on the surface of particles representative of dust-type materials. Zeolite powders were used as aerosol support, representative of a typical silica mineral aerosol present in the atmosphere. Mass spectral fingerprint information was gained by first directly detecting atomized species to record their clean electron impact mass spectrum. This facilitated detection during later experiments of organic molecules coated on an inorganic support. Spectra obtained give mass spectrometric signatures of molecules coated on inorganic particles without detection of the particle core. An important feature of the AMS is the ability to equate an ion rate detected in the mass spectrometer to a mass concentration of a given chemical species in a sample using its ionization efficiency. Based on an average inlet flow rate of 1.2 cm 3sec -1 the ionization efficiencies obtained were 5.89x10-5, 1.15x10-6, and 1.62x10-5 for Malathion, methyl salicylate, and oleic acid, respectively. These experiments and the results obtained show that detection and characterization of organic species adsorbed onto inorganic dust particles are possible at µg m-3 concentrations using the AMS.

Résumé : Les instruments de spectrométrie de masse à ionisation secondaire (SIMS) doivent être améliorés afin de satisfaire les exigences et tendances dans de nombreux domaines qui demandent des outils d'analyse pouvant cartographier les échantillons à la fois avec une excellente résolution et une haute sensibilité chimique, mais également avec des temps d’analyse plus court. Les objectifs de cette thèse sont : rechercher à améliorer la résolution en masse des spectromètres de masse à double focalisation en remplaçant le secteur sphérique standard par une nouvelle géométrie sphéroïde ayant de meilleures propriétés de focalisation, et d’étudier la réduction du temps d'analyse en imagerie SIMS, par la preuve de concept du système SIMS à multifaisceaux d'ions. Une comparaison des principales propriétés de focalisation du secteur sphérique, de la géométrie sphéroïde et d’une géométrie de sphéroïde hybride, a été réalisée en utilisant le logiciel SIMION. Une comparaison dans une configuration Nier-Johnson entre le secteur sphérique et le sphéroïde, a montré que le faisceau présente une rotation de 90 ° à la sortie de l'aimant nuisant à la résolution de masse dans la configuration sphéroïde. En ajoutant un élément électrostatique pouvant tourner le faisceau à 90 ° les performances du spectromètre de masse pourrait être amélioré. Toutefois, une comparaison des performances entre les secteurs sphériques et hybrides dans une configuration Mattauch-Herzog a montré que lorsque la double condition de focalisation est optimisée, une meilleure résolution de masse pourrait être obtenue avec la géométrie sphéroïde. Un système multi-faisceau ionique a été étudié pour l'analyse SIMS. La simulation à travers l’optique secondaire d'un Cameca IMS XF de neuf faisceaux a montré une transmission réussie des faisceaux, résultant en neuf points concentrés sur le détecteur plaque à canaux multiples (MCP). La preuve de concept a été achevée expérimentalement dans l'IMS 6F de Cameca, où une ouverture à trous multiples était montée dans la colonne principale, générant 9 et 16 faisceaux de tailles comprises entre 4 µm à 10 µm. Des images d'une grille AlCu ont été obtenues en balayant l'échantillon par le système de multifaisceaux d’ions. Ces résultats montrent que le système multi-faisceau d'ions est une technique possible pour l'imagerie SIMS et qu'en optimisant leur conception les multi-nano-faisceaux d'ions seront une solution permettant de réduire considérablement le temps d'analyse. / Secondary ion mass spectrometry (SIMS) instruments need to be improved in order to satisfy the demands of trends in many fields that require analytical tools that can map samples with both excellent resolution and high-sensitivity chemical information, but also with shorter time of analysis. The objectives of this thesis are: investigate the enhancement of the mass resolution of double focusing mass spectrometers by replacing the standard spherical sector with a novel spheroid geometry which has better focusing properties, and to investigate the reduction of the time of analysis in imaging SIMS by the proof-of-concept of the SIMS multi-ion- beam system.A comparison of the main focusing properties of the spherical sector, the spheroid geometry and a hybrid spheroid geometry, was made using the SIMION software. A comparison in a Nier-Johnson configuration between the spherical sector and the spheroid, showed that the beam presents a rotation of 90° at the exit of the magnet harming the mass resolution in the spheroid configuration. By adding an electrostatic element that can rotate the beam 90° the performance of the mass spectrometer could be improved. However, a comparison of the performances between the spherical and hybrid sectors simulated in a Mattauch-Herzog configuration, showed that when the double focusing condition is properly satisfied, better mass resolution could be achieved with the spheroid geometry.A multi-ion-beam system was investigated for SIMS analysis. A simulation through the secondary optics of a Cameca IMS XF showed successful transmission of nine beams through the optics resulting in nine well focussed spots on the multi channel plate (MCP) detector. The proof-of-concept was completed experimentally in the Cameca IMS 6F, where a multi-hole aperture was mounted in the primary column generating 9 and 16 beams of sizes between 4 μm to 10 μm. Images of an AlCu grid were obtained when t the multi-ion-beam system was scanned over the sample. These results showed that the multi-ion-beam system is a feasible technique for imaging SIMS and by optimizing the design multi-nano-ion-beams will be a solution for reducing drastically the time of analysis.