Infrared spectroscopy of gas-phase hydrated clusters provides us much information on structures and dynamics of water networks. However, interpretation of spectra is often difficult because of high internal energy (vibrational temperature) of clusters and coexistence of many isomers. Here we report an approach to vary these factors by using the inert gas (so-called “messenger”)-mediated cooling technique. Protonated water clusters with a messenger (M), H
+(H
2O)
4-8·M (M = Ne, Ar, (H
2)
2), are formed in a molecular beam and probed with infrared photodissociation spectroscopy in the OH stretch region. Observed spectra are compared with each other and with bare H
+(H
2O)
n. They show clear messenger dependence in their bandwidths and relative band intensities, reflecting different internal energy and isomer distribution, respectively. It is shown that the internal energy follows the order H
+(H
2O)
n H
+(H
2O)
n·(H
2)
2 > H
+(H
2O)
n·Ar > H
+(H
2O)
n·Ne, while the isomer-selectivity, which changes the isomer distribution in the bare system, follows the order H
+(H
2O)
n·Ar > H
+(H
2O)
n·(H
2)2 > H
+(H
2O)
n·Ne ~ (H
+(H
2O)
n). Although the origin of the isomer-selectivity is unclear, comparison among spectra measured with different messengers is very powerful in spectral analyses and makes it possible to easily assign spectral features of each isomer.