Automatic Monomer detection 

MassMetaSite reads the peptide or protein molecule from a mol file and it can automatically detect the monomers that are present in the compound. The user selects the rules used to generate the monomersi.e., amide bond or disulfide bridge. The system includes a monomer database for the monomers that are automatically recognized adding the one letter or 3 letter code to the monomer nomenclature and visualization. 

For the monomers automatically detected that are not present in the database the user can customize then or leave then with the default naming policy assigned by the program. Once the monomer has been customized the database is updated, and therefore the next time that a peptide with the same monomer is used the monomer would be recognized. In any case the unrecognized monomers are also analyzed.  

The user can define different groups of monomers and can select the metabolic mechanism that would like to be applied to each group. The user may define a small molecule attached to a peptide as a small molecule with all the Phase I and II metabolic reactions and treat the rest of the peptide chain with pure amide hydrolysis reactions. 

Proprietary Peptide visualization tool 

A proprietary algorithm to visualize the peptide in 2D considering the 1 letter code of monomer that simplify the visualization of large molecule. The user can easily move from a collapse form of the amino acid (1 letter code) to all the atoms, by just selecting it from the list on the left panel. The visualization is then applied also to the metabolites structures assign to each of the peak.