We investigated a two-stage ion source for proton transfer reaction (PTR) ionization to achieve more selective mass spectrometric (MS) detection of selected volatile organic compounds (VOCs) than that achieved with commonly used PTR-MS instruments, which are based on single-step PTR ionization with H(3)O(+). The two-stage PTR ion source generated reagent ions other than H(3)O(+) by an initial PTR between H(3)O(+) and a selected VOC, and then a second PTR ionization occurred only for VOCs with proton affinities larger than the affinity of the reagent VOC. Acetone and acetonitrile were useful as reagent VOCs because they provided dominant peaks as a protonated form. Using two-stage PTR-MS, we differentiated isomeric VOCs (for example, ethyl acetate and 1,4-dioxane) by means of differences in their proton affinities; protonated acetone formed the [M + H](+) ion from ethyl acetate but not from 1,4-dioxane. The PTR-MS-derived concentrations agreed quantitatively with those independently determined by Fourier transform infrared spectroscopy (FT-IR) at parts per million by volume (ppmv) levels. In addition, interfering fragment ions formed from alkyl benzenes at m/z 79 (C(6)H(7)(+)) could be distinguished from the m/z 79 ion arising from protonation of benzene, and therefore this method would prevent overestimation of benzene concentrations in air samples in which both benzene and alkyl benzenes are present. This two-stage PTR ionization may be useful for distinguishing various isomeric species, including aldehydes and ketones, if appropriate reagent ions are selected.