Peptides therapeutics are becoming increasingly important on the pharmaceutical market. However, it is known that peptide drugs bioavailability and stability are lower than for small molecules. It is highly important to understand peptide drug metabolism and optimize its clearance as it influences the drug safety and efficacy. Because peptides are mainly cleaved by peptidases, every new candidate must be designed considering the localization of potential protease sites of cleavage. We will demonstrate how to use Mass-MetaSite and WebMetabase to process HRMS data from in vitro incubation samples, to elucidate metabolites structures, to predict cleavage sites and to store the results in a chemically aware database. We will use examples with cyclic and linear peptides, containing nonstandard amino acids collected from different sources to demonstrate that there are no limitations related to peptide structure or chemical modifications of amino acids.