Our investigation of the phenylalanine/serine (Phe/Ser) protonated dimer suggests that the intermolecular interaction between the two amino acids is more complex than could have been anticipated from previous studies of similar systems. Isomer-specific infrared (IR) spectra, recorded at an internal temperature of 10 K, demonstrate the presence of at least five isomers with nonzwitterionic structures. Moreover, isotopic substitution experiments provide evidence for different protonation sites among these isomers.