Protonated clusters of alcohols, (ROH) n H +, and alcohol—water heteroclusters, (ROH) n ((H 2O) m H +, where R = C 2H 5, n-C 3H 7, iso-C 3H 7, n-C 4H 9, iso-C 4H 9, sec-C 4H 9 and tert-C 4H 9, were formed in an atmospheric pressure ionization (API) corona discharge source, through proton transfer and displacement ion—molecule reactions with (H 2O) n H +. The cluster ions were then subjected to collision induced dissociation (CID) in a tandem mass spectrometer (API-MS—MS). Stabilities of the clusters were examined through cluster size distribution analysis and CID reaction channels. The results gave insights about the structure and energetics of the clusters. The heteroclusters demonstrated a strong preference for water elimination over alcohol elimination, indicating that the alcohol moiety was the favored protonation site. The CID results indicated that in the heteroclusters water ligands were near the periphery of a chain, along which water and alcohol molecules were hydrogen bonded. This structural model could rationalize product ion formation through a single hydrogen bond cleavage for mild CID conditions and through breaking of two hydrogen bonds or a single bond after proton migration along the chain under enhanced fragmentation conditions. CID of protonated alcohols showed differences in the cleavage of CO vs. OH + bonds, as well as variance in product ion distributions in the alcohols.