Supramolecular recognition of thymine (or its analogs) with various central cations can form magic number clusters. Dual nano-ESI via theta tip emitters was used to on-line synthesize clusters. Even thermodynamically unstable clusters can be detected by MS thanks to the very short life-time (∼ms) of the generated microdroplets. By recording characteristic cluster distributions, isomers can be clearly differentiated in a novel “bottom-up” way. Theoretical calculations were performed to explain the MS results.