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In this study a thermally sampling atmospheric pressure ionization mass spectrometer is described and characterized. The ion transfer stage offers the capability to sample cluster ions at thermal equilibrium and during this transfer fundamental processes possibly affecting the cluster distribution are also readily identified. Additionally, the transfer stage combines optional collision-induced dissociation (CID) analysis of the cluster composition with thermal equilibrium sampling of clusters. The performance of the setup is demonstrated with regard to the proton-bound water cluster system. The benefit of the studied processes is that they can help to improve future transfer stages and to understand cluster ion reactions in ion mobility tubes and high-pressure ion sources. In addition, the instrument allows for the identification of fragmentation and protonation reactions caused by CID. [ABSTRACT FROM AUTHOR]