What is Chemical Ionization? The CI ion source consists of a chamber with higher hermeticity than the EI ion source, as well as a filament and a repeller. The reagent gas introduced into the CI chamber is ionized; ionization of the sample occurs by electrons, protons, and other charged species transferring from the ionized reagent gas to the sample molecule (M). Generally, methane, iso-butane, or ammonia is used as the reagent gas. In the case of a proton transfer reaction, we can predict protonated [M+H] + ion generation based on the proton affinity (PA) of both the reagent gas and M. When M has higher PA than the reagent gas, a proton transfer reaction occurs. However, CI can be unpredictable, in that generated ion species differ depending on the reagent gas. In the case of methane or iso-butane as the reagent gas, [M+H] + ions are generally produced by proton transfer. Other ions such as [M-H] + , M + , or [M + reagent ion] + may also be detected.