<p>The research described in this dissertation focuses on several areas: developing analytical methods to distinguish structural isomers, identifying the chemical compositions of aviation fuels and evaluating the effectiveness of organic dopants to swell aircraft o-ring seals. Chapter 2 discusses fundamental aspects of mass spectrometry, and ionization methods and the instrumentation used to complete this research. </p> <p>Chapter 3 discusses and compares two activation methods used to distinguish ionized structural isomers. Ionized naphthene-containing aromatic structural isomers were subjected to collision-activated dissociation (CAD) in an ion trap (ITCAD) and to medium-energy collision-activated dissociation (MCAD) in an octupole collision cell, both in the energy-resolved mass spectrometry mode (ERMS). MCAD was shown to be superior over ITCAD at the structural differentiation of the ionized isomers. </p> <p>Determination of the chemical compositions of petroleum-based jet and diesel fuels, potential alternative fuels and fuel blending components by using a GCxGC/(EI)TOF MS is discussed in chapter 4. The ability to determine the chemical compositions of fuels and to correlate the identified compounds and their concentrations to the physical and chemical properties and aircraft performance of the fuels is vital for the development of future resilient, alternative fuels. The chemical compositions of petroleum-based fuels were found to be different from potential alternative fuels.</p> <p>Chapter 5 discusses the effectiveness of aromatic and nonaromatic compounds in swelling air craft o-ring seals, which prevents leaks in the fuel circulation systems. The aim of this study was to identify aromatic and nonaromatic compounds that most effectively swell o-ring seals. Steric effects were shown to decrease the efficiency of the compounds to swell seals. Ethylbenzene and indane were found to swell o-ring seals more effectively than any other compounds studied, including a currently approved alternative fuel. </p>