Five perfluorocompounds [perfluoropentane, 4-(perfluoroethoxy)-perfluorobutane, 5-(perfluoroethyl)-perfluorotetrahydrofuran, 2-(trifluoromethyl)-perfluorotetrahydropyran, and 4-(trifluoromethyl)-perfluorotetrahydropyran] were analyzed by electron ionization (EI) and chemical ionization (CI), using methane and isobutane as reagent gases. Under CI conditions, isobutane does not lead to significative results whereas methane leads to high ionic yields [with respect to both CI (isobutane) and EI]. Under EI conditions, practically only fragment ions are observed, with the complete loss of molecular weight. In contrast under CI(CH(4) ) conditions, [M-F](+) ions are produced. Under these conditions, the behavior of oxygen-containing molecules is strongly different from that of perfluoropentane. This is because oxygen can greatly stabilize the formation of the [M-F](+) carbocation by a π-electron donor effect, especially in the case of cyclic structures. Moreover, π-stabilization can be considered a useful tool to rationalize the position of tertiary carbon atom in trifluoromethyl-perfluoro-pyrane isomeric ions. The experimental data formed the starting point for the theoretical calculation, which allowed us to explore the mechanisms of the reactions of CH(5) (+) ions with selected perfluorocompounds. The computational methods used show that a direct protonation of the perfluoroethers (PFEs) by CH(5) (+) as well as iBu(+) is very unlikely. In the theoretical calculations, the PFE molecule served rather as the F(-) donor, and the elimination of HF molecule occurred when the PFE molecule was placed close to H(+) or CH(5) (+) ions. The fact that the latter is very unstable and decomposes to a proton and methane molecule explains why the use of methane in CI is so successful in the generation of [M-F](+) ion. In contrast, the isobutonium cation rearranges to an isopropyl cation/methane complex rather than that it abstracts F(-) from the PFE molecule. Similar results can be expected for other PFEs and perfluoroalkanes (PFAs) because both CH(5) (+) and H(+) were able to abstract the HF molecule also by attacking along the perfluoroalkyl chain of the PFE.