1. In the Protein Sequence Editor, select the title bar for the Modification Editor.
  2. The Modification Editor pane opens, displaying all of the N-terminal, C-terminal, and side chain modifications available.
  3. Select Add in the section corresponding to the type of custom modification you want to create (N-terminal, C-terminal, or side chain).
  4. In the Add New Modification dialog box, enter the appropriate information for your custom modification, including a unique modification name, monoisotopic mass, average mass, and chemical formula (optional). For custom side chain modifications, you can also specify the residues for the modification.
  5. See Modification Editor pane parameters.
  6. Select OK.
  7. The application saves the custom modification and the modification appears in purple in the modification list.
  8. You can add your custom modification to the default list of modifications for quick loading.
  9. See Change the default modifications for protein sequences.