This thesis reports on the development of a novel mass spectrometer combining image charge detection with surface induced dissociation for real-time analysis of intact viruses. Protonated viruses produced using electrospray are accelerated and subsequently impact on a solid surface. Capsid peptides released during the impact are analyzed using time-of-flight mass spectrometry. Image charge detection is used to measure the mass and charge states of structurally intact, electrosprayed viruses prior to impact. Since virus capsids are composed of loosely-bound proteins, collision of viruses with surfaces at moderate impact energies could release intact proteins. The masses and numbers of different protein types combined with the mass of the intact virus represent a unique signature useful for accurate, real-time virus identification. The progress of instrumentation developed thus far is reported. Techniques were developed for electrospraying intact viruses, including electrospray capillaries with small tips and methods for achieving complete desolvation. Significant reduction of low-frequency and other noise was achieved in the image charge detector as well as determination of accurate methods for mass and charge measurement. Improved focusing and transmission efficiency was achieved via an aerodynamic lens. Suitable surfaces were also obtained including conductive diamond and fluorinated self-assembled monolayer (SAM) surfaces.

Charge detection is essential for a large number of commercial and scientific applications. A charge amplifier is one of the most fundamental building blocks for a detector system. This thesis describes the design, circuit implementation, and post-silicon testing of two different charge amplifier designs, analog and digital, that address some commonly seen fundamental challenges in the charge detection application. In particular, the proposed designs can be integrated with an image charge detector (ICD) to study the characteristics of dust on Mars. The proposed charge amplifier design utilizes a small 10 fF feedback capacitor to achieve a high gain. The fully integrated custom differential charge amplifier design improves the accuracy and robustness of its charge gain, and provides a compact method to extract detector capacitance for gain calibration. Conventional charge amplifiers' charge-to-voltage gain is a function of the detector parasitic capacitance. Therefore, a high precision photo-current calibration method is proposed here to enable an accurate gain calibration. In addition, a novel "digital amplifier" with close to rail-to-rail output swing is proposed to realize an infinite equivalent open-loop gain. Consisting of an ADC and charge pump as the amplifier core, this proposed design maintains a consistent closed-loop gain independent of the input parasitic capacitance. The ADC is realized as a single comparator, i.e. a 1-bit ADC, which, together with an SR latch and a differential charge pump, replaces the conventional analog amplifier core.

Image-charge detection is emerging as an important tool to analyze heavy and heterogeneous samples because of its unique advantages in measuring highly charged microparticles. Conventional image-charge detection instruments include at least three fundamental components: an ionization source, an aerodynamic particle delivery system, and an image-charge detector. Here I report research efforts that investigated the mechanisms of image-charge detection and proposed some instrumental developments of these components to suit specific research purposes. In Chapter 2, I report an investigation of the electrospray ionization (ESI) mechanism based on an observation that a certain portion of charged particles generated with an ESI source carried charges opposite to the needle which is biased with a high voltage. Both biological and non-biological samples were used to shed a light on the complex process of droplet evolution in ESI. In Chapter 3, I present two novel designs of printed circuit board (PCB) based image-charge detectors. With these detectors, not only the charge and velocity of each microparticle were investigated, but also the two dimensional trajectories, with applications in aerosolized particle beam diagnostics. Chapter 4 shows several designs of the microparticle delivering system aiming to achieve a faster acceleration of sample microparticles. Finally, Chapter 5 presents some thoughts on future directions for these projects.

Image-charge detection is an analytical technique in which a highly-charged particle is detected by the magnitude of the image current that it generates in a detecting electrode. This current is represented as a voltage between the charged particle and the sensing electrode. It is a single particle detection method, ideal for the analysis of large, variable mass particles such as biological cells. Some of the physical properties of Bacillus subtilis spores were explored using different applications of image-charge detection. B. subtilis is a gram-negative spore-forming bacteria that has been shown to exhibit extremophile behavior. The particular extremophile behavior that was investigated in this study is the resistance to extreme mechanical stress. The effects of high-velocity impacts upon these spores were studied using image-charge detection. The elastic properties of these spores as well as spore survivability to high-velocity impacts were investigated. Spores were shown to survive impacts at velocities up to 299 ± 28 m/s. The average kinetic energy loss experienced by impacting spores, regardless of velocity at impact, was between 71 and 72%. Both conventional and novel image-charge detection techniques were used for these studies. The novel version of a charge detector that was demonstrated was fabricated using patterned metal electrodes on printed circuit boards. The simplicity and versatility of this method was demonstrated with a multi-stage charge detector, a unique bouncing detector, and charge-detection mass spectrometry detector which is capable of measuring the absolute mass of a single highly-charged particle.

Image charge detection is a non-perturbative pre-detection approach for deterministic ion implantation. Using low energy ion bunches as a model system for highly charged single ions, we experimentally studied the error and detection rates of an image charge detector setup. The probability density functions of the signal amplitudes in the Fourier spectrum can be modelled with a generalised gamma distribution to predict error and detection rates. It is shown that the false positive error rate can be minimised at the cost of detection rate, but this does not impair the fidelity of a deterministic implantation process. Independent of the ion species, at a signal to-noise ratio of 2, a false positive error rate of 0.1% is achieved, while the detection rate is about 22%

Charge detection mass spectrometry (CDMS) is a single particle technique capable of simultaneously measuring charge and mass-to-charge ratios for individual ions or particles. The linear array CDMS design theoretically has no upper mass limit and is therefore a choice method for the analysis of high mass and heterogeneous samples, such as dust microparticles in the Martian atmosphere. This dissertation describes the development of a novel charge detection mass spectrometer made of printed circuit boards (PCB) for the analysis of dust microparticles in the Martian atmosphere. Development of this device has required investigations in analysis methods and the engineering design of both the PCB device and the vacuum chamber system used in laboratory experiments. Accurate velocity analysis is crucial in determining correct particle mass in linear array CDMS. By combining the Shockley-Ramo theorem–which allows for the calculation of instantaneous image current for a system of electrodes when a point charge passes them–and SIMION ion optics simulations effective electrode length can be determined for any given charge detector geometry and aid in charge detector engineering and design process. Applying these simulation results to experimental data yields velocity agreement for a PCB charge detector within 0.44% RSD. The novel PCB CDMS device was demonstrated for the analysis of multiple types of microparticles of varying size and charge similar to that expected of atmospheric Mars dust. This device is able to measure particle charge above 1,500 elementary charges of either polarity. Simulations show that for microparticles having a size and density close to that which is expected for Mars dust, the device is able to ideally measure the mass of particles ranging from 0.2–2.5 μm in diameter, providing broad coverage of particles too small to be observed by optical scattering and other techniques that have been previously used on Mars.

Image charge detection is presented as a possible candidate to realise deterministic ion implantation. The deterministic placement of single impurities in solid substrates will enable a variety of novel applications, using their quantum mechanical properties for sensors or qubit registers. In this work, experimental techniques are used together with theoretical calculations to develop, characterise and optimise the detection of charged objects in a single pass through an image charge detector. In the main experimental part, ion bunches are employed as a model system for highly charged ions in proof-of-principle measurements with detector prototypes built in our labs. Image charge signals are characterised in the time and frequency domain. Using a statistical measurement and data analysis protocol, the noise and signal probability density functions are determined to calculate error and detection rates. It was found that even at an extremely low signal-to-noise ratio of 2, error rates can be suppressed effectively for high fidelity implantation. Aiming to improve the sensitivity, the maximum possible signal-to-noise ratio is calculated and discussed in dependence on the design parameters of an optimised image charge detector and the kinetic ion parameters. Lastly, a new ion implantation set-up combining focused ion beam technology with a source able to produce highly charged ions is introduced.

abstract: Obtaining local electrochemical (EC) information is extremely important for understanding basic surface reactions, and for many applications. Scanning electrochemical microscopy (SECM) can obtain local EC information by scanning a microelectrode across the surface. Although powerful, SECM is slow, the scanning microelectrode may perturb reaction and the measured signal decreases with the size of microelectrode. This thesis demonstrates a new imaging technique based on a principle that is completely different from the conventional EC detection technologies. The technique, referred to as plasmonic-based electrochemical imaging (PECI), images local EC current (both faradaic and non-faradaic) without using a scanning microelectrode. Because PECI response is an optical signal originated from surface plasmon resonance (SPR), PECI is fast and non-invasive and its signal is proportional to incident light intensity, thus does not decrease with the area of interest. A complete theory is developed in this thesis work to describe the relationship between EC current and PECI signal. EC current imaging at various fixed potentials and local cyclic voltammetry methods are developed and demonstrated with real samples. Fast imaging rate (up to 100,000 frames per second) with 0.2×3µm spatial resolution and 0.3 pA detection limit have been achieved. Several PECI applications have been developed to demonstrate the unique strengths of the new imaging technology. For example, trace particles in fingerprint is detected by PECI, a capability that cannot be achieved with the conventional EC technologies. Another example is PECI imaging of EC reaction and interfacial impedance of graphene of different thicknesses. In addition, local square wave voltammetry capability is demonstrated and applied to study local catalytic current of platinum nanoparticle microarray. This thesis also describes a related but different research project that develops a new method to measure surface charge densities of SPR sensor chips, and micro- and nano-particles. A third project of this thesis is to develop a method to expand the conventional SPR detection and imaging technology by including a waveguide mode. This innovation creates a sensitive detection of bulk index of refraction, which overcomes the limitation that the conventional SPR can probe only changes near the sensor surface within ~200 nm. / Dissertation/Thesis / Video for Figure 3.2 C to H / Video for Figure 3.5 / Video for Figure 5.5 / Video for Figure 6.7 / Video for Figure 6.11 / Ph.D. Electrical Engineering 2011

La spectrométrie de masse est devenue un outil indispensable pour la recherche en protéomique, notamment grâce au développement récent de nouveaux spectromètres de masse comme l’Orbitrap et de nouvelles méthodes de dissociation. La stratégie « bottom-up » (analyse des mélanges de peptides protéolytiques) est la plus utilisée par son efficacement et sa simplicité par rapport à la stratégie top-down (analyse des peptides plus longs ou des protéines intactes), mais cette dernière permet une caractérisation plus complète des isoformes de protéines et des modifications post-traductionnelles.Les méthodes de dissociation utilisant des photons, comme la photodissociation dans le domaine ultra-violet (UVPD) et la dissociation multiphotonique infrarouge (IRMPD), ont reçu une grande attention comme approches alternatives aux méthodes de dissociation par collision. L'absorption du photon UV à haute énergie peut être « diluée » sur l'ensemble du peptide ou de la protéine et provoque une fragmentation étendue du squelette peptidique (liaisons C-C), tandis que les photons IR à faible énergie augmentent progressivement l'énergie interne et dissocient préférentiellement les liaisons amide (C-N) les plus labiles.Cette thèse est centrée sur le développement de méthodes et les applications pour une caractérisation structurale de biomolécules par des méthodes d'activation utilisant des photons. L'intérêt de combiner des photons infrarouges à faible énergie et des photons UV à haute énergie dans un spectromètre de masse Orbitrap, pour la caractérisation de petites protéines, a été évalué. En outre, la dissociation infrarouge multiphotonique a été implémentée dans un piège à ions électrostatique afin d’étendre les méthodes de fragmentation aux macromolécules de très haut poids moléculaires dans le domaine mégadalton. L'une des principales avancées de cette thèse a été d'adapter ces méthodes de spectrométrie de masse aux objets biomoléculaires, allant des petits peptides (dans la gamme de masse de kilodalton) à des fibres de protéines entières (dans la gamme de masse de mégadalton) / The structural characterization of proteins often required them to be fragmented into small units containing only few amino acids. In bottom-up approach, proteins are cleaved into small peptides by enzyme then these peptides are subjected to further fragmentation in a collision cell of a tandem mass spectrometer. However, in top-down approach, proteins can directly be dissociated (without enzyme) into small fragments by collision, electron and photon-driven dissociations. Photon-based activation methods including ultraviolet photodissociation (UVPD) and infrared multiphoton dissociation (IRMPD) have received great attention as an alternative to electron-driven and collision induced dissociation methods. Absorption of the high-energy UV photon is dispersed over the whole peptide or protein and stimulates extensive C?Ca backbone fragmentation while the low-energy IR photons gradually increases the internal energy and thus favorably dissociates the most labile amide (C?N) bonds. This thesis focuses on the method development and applications for characterizing biomolecules by photon-based activation methods. The interest of combining high-energy UV photons and low-energy IR photons in an Orbitrap mass spectrometer, for protein and post-translationally modified peptide characterization, has been evaluated. Moreover, infrared multiphoton dissociation has been implemented in a gated electrostatic ion trap to push forward the limit of fragmentation methods to large megadalton ions. One of the main breakthroughs in this thesis is the ability to adapt these method developments and applications to biomolecular objects ranging from small peptides (in kilodalton mass range) to entire protein fibrils (in megadalton mass range)