A discharge-based proton transfer reaction (PTR) ion source was operated using a mixture of H₂O and rare gases such as He, Ne, Ar, and Kr in combination with a custom-built time-of-flight (TOF) mass spectrometer. In contrast to an “H₂O-only” discharge, which usually functions above a field strength (E/N) of 100 Td for a drift tube, an “H₂O-rare gas”-based discharge was operated successfully at E/N values between 30 and 50 Td. (E is the electric field strength (V cm^-1), N is the buffer gas number density (molecule cm^-3), and 1 Td=10^-17 cm² V molecule^-1.) The intensity of primary ions (H₃O⁺·(H₂O)_n) generated in the “H₂O-rare gas” discharge was comparable to that in the “H₂O-only” discharge. Although detection sensitivities decreased for nonpolar molecules such as isoprene, benzene, toluene, and p-xylene, they increased for polar molecules such as acetone and acetaldehyde. This suggests that the operation of the PTR-TOF mass spectrometer at low drift-tube field-strengths improves both the detection sensitivity and selectivity for the polar molecules. In addition, fragmentation in the drift tube was suppressed significantly for fragile species such as methyl nitrate, in the low E/N operation.