We show that a combined technique of Cs$^{+}$ reactive ion scattering (Cs$^{+}$ RIS) and low-energy secondary ion mass spectrometry (LESIMS) provides a powerful means for probing molecular films and their surface reactions. Simple molecules, including HCI, NH$_3$, D$_2$O, and their mixtures, were deposited into a thin film of several monolayer thickness on Ru(001) at low temperature in vacuum, and the surface was characterized by Cs$^{+}$ RIS and LESIMS. On pure films, D$_2$O, HCI, and NH$_3$ existed in the corresponding molecular states. When HCI and NH$_3$ were co-deposited, ammonium ion(NH$_4$$^{+}$) was readily formed by proton transfer from HCI to NH$_3$. In the presence of water molecules, HCI ionized first to hydronium ion(H$_3$O$^{+}$), which subsequently transferred proton to NH$_3$ to form NH$_4$$^{+}$. The proton transfer, however, did not occur to a completion on ice, in contrast to the complete reaction in aqueous solutions.s solutions.