<p>Aviation fuels are complex mixtures that mostly consist of a wide range of different hydrocarbons but also contain small amounts of heteroatom-containing compounds. Different fuels can have very different physical and chemical properties (e.g., storage and thermal stabilities are influenced by the heteroatom-containing compounds), with some performing better as fuels than others. To address this situation, correlations need to be developed between the chemical composition of fuels and their properties. This requires that the chemical compounds in fuels are correctly characterized, which is challenging. Because of the large number and many different types of organic compounds present in fuels, separation of these compounds by using techniques such as one- (GC) and -two-dimensional gas chromatography (GC×GC) is necessary before mass spectrometric characterization. Furthermore, analysis using traditional electron ionization (EI) mass spectrometry is hampered by excessive fragmentation that often leads to complete absence of a stable molecular radical cation, thus preventing the determination of the molecular weight (MW) of the analyte. To explore alternative methods, GC coupled with methane chemical ionization (CI) triple quadrupole mass spectrometry and GC×GC coupled with methane CI time-of-flight high-resolution mass spectrometry, both in the positive-ion mode, were tested. While both chromatographic techniques separate volatile organic chemicals via boiling point and intermolecular forces, GC×GC methods incorporate a greater level of separation by taking advantage of secondary column of different polarity. This additional level of separation can help separate overlapping compounds that would be impossible in GC. What comes to mass spectrometry analysis, methane CI was found to be more predictable and “softer” than the traditionally employed EI. Several ions revealing the MW of the analyte, e.g., M+•, [M+H-H2]+, and/or [M+H]+, were generated for almost every compound studied with some associated fragmentation. These fragmentation patterns provided invaluable structural information. When combined with the number of carbon atoms in the diagnostic ions, double bond and ring equivalent (DBRE) values, and elemental compositions, all obtained from highly accurate mass measurements performed using the time-of-flight mass spectrometer (but not the quadrupole), the classification of the compounds was possible. In some instances, even the unambiguous identification of individual compounds in aviation fuels was possible.</p>