Quantification and Simulation of Liquid Chromatography-Mass Spectrometry Data

Computational mass spectrometry is a fast evolving field that has attracted increased attention over the last couple of years. The performance of software solutions determines the success of analysis to a great extent. New algorithms are required to reflect new experimental procedures and deal with new instrument generations. One essential component of algorithm development is the validation (as well as comparison) of software on a broad range of data sets. This requires a gold standard (or so-called ground truth), which is usually obtained by manual annotation of a real data set. Comprehensive manually annotated public data sets for mass spectrometry data are labor-intensive to produce and their quality strongly depends on the skill of the human expert. Some parts of the data may even be impossible to annotate due to high levels of noise or other ambiguities. Furthermore, manually annotated data is usually not available for all steps in a typical computational analysis pipeline. We thus developed the most comprehensive simulation software to date, which allows to generate multiple levels of ground truth and features a plethora of settings to reflect experimental conditions and instrument settings. The simulator is used to generate several distinct types of data. The data are subsequently employed to evaluate existing algorithms. Additionally, we employ simulation to determine the influence of instrument attributes and sample complexity on the ability of algorithms to recover information. The results give valuable hints on how to optimize experimental setups. Furthermore, this thesis introduces two quantitative approaches, namely a decharging algorithm based on integer linear programming and a new workflow for identification of differentially expressed proteins for a large in vitro study on toxic compounds. Decharging infers the uncharged mass of a peptide (or protein) by clustering all its charge variants. The latter occur frequently under certain experimental conditions. We employ simulation to show that decharging is robust against missing values even for high complexity data and that the algorithm outperforms other solutions in terms of mass accuracy and run time on real data. The last part of this thesis deals with a new state-of-the-art workflow for protein quantification based on isobaric tags for relative and absolute quantitation (iTRAQ). We devise a new approach to isotope correction, propose an experimental design, introduce new metrics of iTRAQ data quality, and confirm putative properties of iTRAQ data using a novel approach. All tools developed as part of this thesis are implemented in OpenMS, a C++ library for computational mass spectrometry

Application of novel technologies for the development of next generation MR compatible PET inserts

Multimodal imaging integrating Positron Emission Tomography and Magnetic Resonance Imaging (PET/MRI) has professed advantages as compared to other available combinations, allowing both functional and structural information to be acquired with very high precision and repeatability. However, it has yet to be adopted as the standard for experimental and clinical applications, due to a variety of reasons mainly related to system cost and flexibility. A hopeful existing approach of silicon photodetector-based MR compatible PET inserts comprised by very thin PET devices that can be inserted in the MRI bore, has been pioneered, without disrupting the market as expected. Technological solutions that exist and can make this type of inserts lighter, cost-effective and more adaptable to the application need to be researched further. In this context, we expand the study of sub-surface laser engraving (SSLE) for scintillators used for PET. Through acquiring, measuring and calibrating the use of a SSLE setting we study the effect of different engraving configurations on detection characteristics of the scintillation light by the photosensors. We demonstrate that apart from cost-effectiveness and ease of application, SSLE treated scintillators have similar spatial resolution and superior sensitivity and packing fraction as compared to standard pixelated arrays, allowing for shorter crystals to be used. Flexibility of design is benchmarked and adoption of honeycomb architecture due to geometrical advantages is proposed. Furthermore, a variety of depth-of-interaction (DoI) designs are engraved and studied, greatly enhancing applicability in small field-of-view tomographs, such as the intended inserts. To adapt to this need, a novel approach for multi-layer DoI characterization has been developed and is demonstrated. Apart from crystal treatment, considerations on signal transmission and processing are addressed. A double time-over-threshold (ToT) method is proposed, using the statistics of noise in order to enhance precision. This method is tested and linearity results demonstrate applicability for multiplexed readout designs. A study on analog optical wireless communication (aOWC) techniques is also performed and proof of concept results presented. Finally, a ToT readout firmware architecture, intended for low-cost FPGAs, has been developed and is described. By addressing the potential development, applicability and merits of a range of transdisciplinary solutions, we demonstrate that with these techniques it is possible to construct lighter, smaller, lower consumption, cost-effective MRI compatible PET inserts. Those designs can make PET/MRI multimodality the dominant clinical and experimental imaging approach, enhancing researcher and physician insight to the mysteries of life.La combinación multimodal de Tomografía por Emisión de Positrones con la Imagen de Resonancia Magnética (PET/MRI, de sus siglas en inglés) tiene clara ventajas en comparación con otras técnicas multimodales actualmente disponibles, dada su capacidad para registrar información funcional e información estructural con mucha precisión y repetibilidad. Sin embargo, esta técnica no acaba de penetrar en la práctica clínica debido en gran parte a alto coste. Las investigaciones que persiguen mejorar el desarrollo de insertos de PET basados en fotodetectores de silicio y compatibles con MRI, aunque han sido intensas y han generado soluciones ingeniosas, todavía no han conseguido encontrar las soluciones que necesita la industria. Sin embargo, existen opciones todavía sin explorar que podrían ayudar a evolucionar este tipo de insertos consiguiendo dispositivos más ligeros, baratos y con mejores prestaciones. Esta tesis profundiza en el estudio de grabación sub-superficie con láser (SSLE) para el diseño de los cristales centelladores usados en los sistemas PET. Para ello hemos caracterizado, medido y calibrado un procedimiento SSLE, y a continuación hemos estudiado el efecto que tienen sobre las especificaciones del detector las diferentes configuraciones del grabado. Demostramos que además de la rentabilidad y facilidad de uso de esta técnica, los centelladores SSLE tienen resolución espacial equivalente y sensibilidad y fracción de empaquetamiento superiores a las matrices de centelleo convencionales, lo que posibilita utilizar cristales más cortos para conseguir la misma sensibilidad. Estos diseños también permiten medir la profundidad de la interacción (DoI), lo que facilita el uso de estos diseños en tomógrafos de radio pequeño, como pueden ser los sistemas preclínicos, los dedicados (cabeza o mama) o los insertos para MRI. Además de trabajar en el tratamiento de cristal de centelleo, hemos considerado nuevas aproximaciones al procesamiento y transmisión de la señal. Proponemos un método innovador de doble medida de tiempo sobre el umbral (ToT) que integra una evaluación de la estadística del ruido con el propósito de mejorar la precisión. El método se ha validado y los resultados demuestran su viabilidad de uso incluso en conjuntos de señales multiplexadas. Un estudio de las técnicas de comunicación óptica analógica e inalámbrica (aOWC) ha permitido el desarrollo de una nueva propuesta para comunicar las señales del detector PET insertado en el gantry a un el procesador de señal externo, técnica que se ha validado en un demostrador. Finalmente, se ha propuesto y demostrado una nueva arquitectura de análisis de señal ToT implementada en firmware en FPGAs de bajo coste. La concepción y desarrollo de estas ideas, así como la evaluación de los méritos de las diferentes soluciones propuestas, demuestran que con estas técnicas es posible construir insertos de PET compatibles con sistemas MRI, que serán más ligeros y compactos, con un reducido consumo y menor coste. De esta forma se contribuye a que la técnica multimodal PET/MRI pueda penetrar en la clínica, mejorando la comprensión que médicos e investigadores puedan alcanzar en su estudio de los misterios de la vida.Programa Oficial de Doctorado en Ingeniería Eléctrica, Electrónica y AutomáticaPresidente: Andrés Santos Lleó.- Secretario: Luis Hernández Corporales.- Vocal: Giancarlo Sportell

Technical Design Report for the PANDA Micro Vertex Detector

This document illustrates the technical layout and the expected performance of the Micro Vertex Detector (MVD) of the PANDA experiment. The MVD will detect charged particles as close as possible to the interaction zone. Design criteria and the optimisation process as well as the technical solutions chosen are discussed and the results of this process are subjected to extensive Monte Carlo physics studies. The route towards realisation of the detector is outlined

A versatile imaging system for in vivo small animal research

In vivo small animal imaging has become an essential technique for molecular biology studies. However, requirements of spatial resolution, sensitivity and image quality are quite challenging for the development of small-animal imaging systems. The capabilities of the system are also significant for carrying out small animal imaging in a wide range of biological studies. The goal of this dissertation is to develop a high-performance imaging system that can readily meet a wide range of requirements for a variety of small animal imaging applications. Several achievements have been made in order to fulfill this goal.;To supplement our system for parallel-hole single photon emission computed tomography (SPECT) based upon a 110 mm diameter circular detector, we have developed novel compact gamma cameras suitable for imaging an entire mouse. These gamma cameras facilitate multi-head (\u3e2) parallel-hole SPECT with the mouse in close proximity to the detector face in order to preserve spatial resolution. Each compact gamma cameras incorporates pixellated Nal(Tl) scintillators and a pair of Hamamatsu H8500 position sensitive photomultiplier tubes (PSPMTs). Two types of copper-beryllium parallel-hole collimators have been designed. These provide high-sensitivity imaging of I-125 or excellent spatial resolution over a range of object-detector distances. Both phantom and animal studies have demonstrated that these gamma cameras perform well for planar scintigraphy and parallel-hole SPECT of mice.;To further address the resolution limitations in parallel-hole SPECT and the sensitivity and limited field of view of single-pinhole SPECT, we have developed novel multipinhole helical SPECT based upon a 110 mm diameter circular detector equipped with a pixellated Nal(Tl) scintillator array. A brass collimator has been designed and produced containing five 1 mm diameter pinholes. Results obtained in SPECT studies of various phantoms show an enlarged field of view, very good resolution and improved sensitivity using this new imaging technique.;These studies in small-animal imaging have been applied to in vivo biological studies related to human health issues including studies of the thyroid and breast cancer. A re-evaluation study of potassium iodide blocking efficiency in radioiodine uptake in mice suggests that the FDA-recommended human dose of stable potassium iodide may not be sufficient to effectively protect the thyroid from radioiodine contamination. Another recent study has demonstrated that multipinhole helical SPECT can resolve the fine structure of the mouse thyroid using a relatively low dose (200 muCi). Another preclinical study has focused on breast tumor imaging using a compact gamma camera and an endogenous reporter gene. In that ongoing study, mammary tumors are imaged at different stages. Preliminary results indicate different functional patterns in the uptake of radiotracers and their potential relationship with other tumor parameters such as tumor size.;In summary, we have developed a versatile imaging system suitable for in vivo small animal research as evidenced by a variety of applications. The modular construction of this system will allow expansion and further development as new needs and new opportunities arise

COMPUTATIONAL ANALYSIS OF CODE-MULTIPLEXED COULTER SENSOR SIGNALS

Nowadays, lab-on-a-chip (LoC) technology has been applied in a variety of applications because of its capability to perform accurate microscale manipulations of cells for point-of-care diagnostics. On the other hand, such a result is not readily available from an LoC device and typically still requires a post-inspection of the chip using traditional laboratory equipment such as a microscope, negating the advantages of the LoC technology. To solve this dilemma, my doctoral research mainly focuses on developing portable and disposable biosensors for interfacing with and digitizing the information from an LoC system. Our sensor platform, integrated with multiple microfluidic impedance sensors, electrically monitors and tracks manipulated cells on an LoC device. The sensor platform compresses information from each sensor into a 1-dimensional electrical waveform, and therefore, further signal processing is required to recover the readout of each sensor and extract information of detected cells. Furthermore, with the capability of the sensor platform, we have introduced integrated microfluidic cytometers to characterize properties of cells such as cell surface expression and mechanical properties.Ph.D