The chemical diversity of NRPs and RiPPs with their several possible modifications, make their identification especially difficult, as they are highly stable against several proteases due to their D-or modified amino acids and cyclic structures. In most cases, where such complex peptides were identified, this was based on their good bioactivity (in the case of antibiotics) or after identification of the underlying biosynthetic gene cluster (BGC) encoding characteristic modifying enzymes (e.g., radical SAM-dependent enzymes), followed by heterologous production of the peptide. The identification of the classical linear AMPs is also very challenging, since although they can be cleaved by proteases because of their linear structures, the presence of several cationic amino acid residues often results in peptides too small for definitive identification. The potential benefit of metaproteomics is that it is possible to quantify the abundance of the NRP- producing enzymes even in communities and thus predict their presence and structure, required for their targeted measurement.