Peptides therapeutics are gaining a significant role on the pharmaceutical market due to their high selectivity and efficacy. However, natural peptides often must be optimized to improve their ADME properties by cyclisation, introduction of chemically modified amino acids or other modifications. Moreover, they can be conjugated with small molecule drugs. The result usually is a complex structure that cannot be adequately visualized on atomic level using standard chemical structure visualization tools for small molecules. On the other hand, chemical modifications described above prevents from using standard sequence representation. In MassMetaSite we developed peptide visualization tool for macromolecular representation in which macromolecules can be depicted by monomers and atoms. Every monomer is stored in the internal database and assigned with unique identifier. UI are used for the representation. If it is needed each monomer can be expanded and visualized in standard atomic notation. An exchangeable monomer database allows sharing of data between companies who have assigned different identifiers to monomers. New peptide depiction can be stored and used for the exchange between companies.