The low-energy region of the potential energy surface (PES) of the protonated phenylalanine/serine dimer is mapped using the basin-hoping search algorithm, and 37 isomers are identified within 180 kJ·mol-1 of the global-minimum structure. Cluster structures are grouped using hierarchical clustering to partition the PES in terms of nuclear configuration. Calculated IR spectra for the various isomers are then compared with the isomer-specific IR spectra by means of the cosine distance metric to facilitate spectral assignment and identify which regions of the PES are populated in the electrospray ionization process.