Mass spectrometry facilitates cutting edge advancements in many fields. Although instrumentation has advanced dramatically in the last 100 years, data processing algorithms have not kept pace. Without sensitive and accurate signal segmentation algorithms, the utility of mass spectrometry is limited. In this dissertation, we provide an overview and analysis of mass spectrometry data processing. A tutorial to ease the learning curve for those outside the field is provided. We draw attention to the lack of critical evaluation in the field and describe the resulting effects, including a glut of algorithm contributions of questionable novel contribution. To facilitate increased critical evaluation, we show the importance of a modular paradigm for mass spectrometry data processing through highlighting the impact of data processing algorithm choice upon experimental results. Our novel controlled vocabulary is presented with the aim of facilitating literature reviews for comparisons. We propose a novel nomenclature and mathematical characterization of mass spectrometry data. We present several novel algorithms for mass spectrometry data segmentation that outperform existing standard approaches. We end with an overview of future research which will continue to advance the state of the art in mass spectrometry data processing.

Fiber loop ring down (FLRD) spectroscopy is a sensitive spectroscopic technique that is based on absorption and it is convenient for trace chemical detection. Different FLRD systems are being improved in order to increase their sensitivity. In FLRD spectroscopy, detection of a sample is done by measuring of a leaking light at each trip within an optical cavity. Intensity of leaking light has an exponential decay where it is reduced by absorption of sample and scattering of light. In this project, two FLRD set-ups at 1535 nm and 808 nm were designed. In both set-ups, optical fiber and optical fiber couplers are used to form a cavity. At 1535 nm, a FLRD set-up is constructed by utilizing a pulsed laser and used for characterization of thin films, various pure liquids and fluorescein solutions. Two different sensor regions are designed with free space collimators and ferrules for the measurement of thin films and liquids, respectively. The future endeavor of the set-up is improvement for reliability and reproducibility of the system. For visible and NIR regions, a fiber coupled laser with four colors as 642 nm, 785 nm, 808 nm and 852 nm laser is used to design of a FLRD set-up. 808 nm laser is selected to build a prototype of the FLRD system. The construction of a closed loop FLRD set-up is completed and the system is characterized. Ultimate aim in our project is to be able to do trace detection at visible and NIR regions where the chemical sensitivity is higher.

Ce travail de thèse a permis le développement et la caractérisation d'instruments basés sur la technique "OF-CEAS" dans le moyen infrarouge pour la détection de traces dans différents mélanges en phase gazeuse. Le Laser à Cascades Inter-bandes (ICL) est la dernière innovation des lasers à semi-conducteurs dans cette zone spectrale. La compatibilité des ICL avec l'OF-CEAS ouvre la voie vers de nouvelles applications pour la réalisation d'instruments compacts et robustes avec un temps de réponse rapide tout en présentant une très bonne limite de détection.Une démonstration de la bonne sensibilité et stabilité des instruments OF-CEAS aété réalisé avec la mesure de continua d'absorption (de la vapeur d'eau et de l'azote). Mais également avec la détection d'une raie quadrupolaire de l'azote de très faible intensité (3x10-29 cm-1/(moléc cm-2). L'objectif principale de ces travaux consistait au développement d'un instrument dédié à la détection de monoxyde d'azote pour l'analyse du gaz exhalé. L'analyseur ainsi réalisé présente une sensibilité de 6x10-10 cm-1 en une acquisition de 180 ms. Sa limite de détection sur le NO est à l'état de l'art, avec à court terme (180 ms) un minimum de 50 ppt est atteint. Celui-ci parvient à un niveau sub-ppt (0.9 ppt) en 12 min d'intégration. / This work of these has made it possible to develop and characterize the use of instruments on the "OF-CEAS" technique in the mid-infrared for traces' detection in different mixtures in the gas phase. Inter-band Cascade Laser (ICL) is the latest innovation in semiconductor lasers in this spectral region. Compatibility of ICL with OF-CEAS offers new applications for compact and robust instruments with fast response time and a low detection limit. A demonstration of the good sensitivity and stability of the OF-CEAS instruments was performed with continua absorption measurements (water vapor and nitrogen). But also with the detection of a very low intensity quadrupole line of nitrogen (3x10-29 cm-1/(moléc cm-2). The main objective of this work was to develop an instrument dedicated to nitrogen oxide detection for the analysis of exhaled breath. The analyzer is presented at the sensitivity of 6x10-10 cm-1 in an acquisition of 180 ms. Its limit of detection on NO is at the state of the art, with short term (180 ms) limit of 50 ppt. It reaches the sub-ppt level (0.9 ppt) with 12 min of integration.