Protonation, hydration, and cluster formation of ammonia, formaldehyde, formic acid, acetone, butanone, 2-ocatanone, 2-nonanone, acetophenone, ethanol, pyridine, and its derivatives were studied by IMS-TOFMS technique equipped with a corona discharge ion source. It was found that tendency of the protonated molecules, MH+, to participate in hydration or cluster formation depends on the basicity of M. The molecules with higher basicity were hydrated less than those with lower basicity. The mass spectra of the low basic molecules such as formaldehyde exhibited larger clusters of MnH+(H2O)n, while for compounds with high basicity such as pyridine, only MH+ and MH+M peaks were observed. The results of DFT calculations show that enthalpies of hydrations and cluster formation decrease as basicities of the molecules increases. Using comparison of mass spectra of formic acid, formaldehyde, and ethanol, effect of structure on the cluster formation was also investigated. Formation of symmetric (MH+M) and asymmetric proton-bound dimers (MH+N) was studied by ion mobility and mass spectrometry techniques. Both theoretical and experimental results show that asymmetric dimers are formed more easily between molecules (M and N) with comparable basicity. As the basicity difference between M and N increases, the enthalpy of MH+N formation decreases.