Workflow Step3. Users specify the amino acids that they would not like to be included in the resultant peptides (i.e. no M, C due to difficulties with post translational modifications) and the target length of resultant peptide (i.e. between 5 and 30). If there is a phosphorylation site adjacent to an enzyme cleavage site, the cleavage can be missed. This can be simulated by selecting 'Remove cleavages next to phosphorylation sites'. Users can also specify whether or not to consider enzymes that can yield peptides containing some, but not all of the target sites.