The technique of proton transfer reaction mass spectrometry (PTR-MS) couples a proton transfer reagent, usually H3O+, with a drift tube and mass spectrometer to determine concentrations of volatile organic compounds. Proton transfer reaction-mass spectrometry (PTR-MS) has successfully been applied to a wide variety of matrices to identify and to investigate on the behavior of trace compounds; among the possible field of applications we can find: food, air, energy, etc. Natural gas is considered as a fuel for high energy efficiencies applications such as SOFC generators. The ability to distinguish several isobaric aldehydes, ketones, isoprenoids and other compounds is impossible using PTR-MS instrument. In the present research work, PTR-ToF-MS was coupled to a prototype FastGC system allowing for a rapid (90 s) chromatographic separation of the sample headspace prior to PTR-MS analysis. The system was tested on natural gas trace compounds to individuate the major elements and to identify possible issues for the SOFC generators. In comparison to the results obtained by direct injection, FastGC provided additional information, thanks to a less drastic dilution of the sample and due to the chromatographic separation of isomers. This was achieved without increasing duration and complexity of the analysis.