We report on gas-phase aggregation and structural characteristics of protonated amino acid clusters investigated by ion mobility spectrometry-mass spectrometry (IMS-MS) and infrared multiple photon dissociation (IRMPD) spectroscopy. Amino acids, including valine, isoleucine, phenylalanine, tyrosine, and tryptophan, were studied to understand the formation and stabilization mechanisms of their clusters. The mass spectra reveal the formation of clusters, primarily as zwitterionic assemblies stabilized by extensive hydrogen-bond networks between protonated amine and deprotonated carboxylate groups. IRMPD spectra in the 1000–1900 cm⁻1 region highlight distinctive vibrational features, indicating the presence of zwitterionic structures for clusters larger than octamers. Theoretical calculations support these findings, revealing a transition from non-zwitterionic to zwitterionic with increasing cluster size. Additionally, the charge state distribution analysis indicates that the cluster charge states correlate with their accessible surface area, supporting the applicability of the charged residue model (CRM) for their formation. These results offer valuable insights into the forces governing amino acid cluster assembly and highlight their potential as nanoscale models for studying biomolecular interactions.