Proton transfer reactions (PTR) are important for chemical ionization, especially in trace gas analysis in air. In an effort to extend their application to the analysis of high‐purity inert gases, we studied PTR of N2H+ and ArH+ with various reaction gases, viz. O2, N2, CH4, CO2, NO2, H2O and CH3OH. Oxygen, nitrogen, methane, carbon dioxide, and water undergo non‐dissociative proton transfer, where the original molecule remains intact. PTR to nitrogen dioxide leads to NO+ with release of neutral OH⋅. While PTR from N2H+ to methanol exclusively yields protonated methanol, the reaction with ArH+ exhibits dissociative proton transfer, due to its higher exothermicity. Products include methenium, protonated formaldehyde, and protonated methanol. The latter undergoes a slow secondary reaction to form protonated dimethyl ether. Within error limits, most reactions proceed at or close to collision rate. Quantum chemical calculations provide energetics and reaction pathways. In such highly exothermic proton transfer reactions, identification and quantification of trace compounds require detailed understanding of the fragmentation pathways and branching ratios.