In the Protein Sequence Editor, you can assign single-site or global side-chain, N-terminal, and C-terminal modifications to residues in the protein sequence.

Prerequisites

  1. You are editing a protein sequence in the Protein Sequence Editor.
  2. The sequence has the "Peptide Mapping" category for Peptide Mapping Analysis or the "Intact Protein" category for Intact Mass Analysis.

Procedure

  1. In the Protein Sequence Editor, in the Protein Sequence Map pane, position your cursor appropriately and then double-click, as indicated below:
  2. For a side-chain modification, place your cursor to the left of the residue of interest.
  3. For an N-terminal modification, place your cursor to the left of the first residue in the sequence chain.
  4. For a C-terminal modification, place your cursor to the left of the last residue in the sequence chain.
  5. The Residue Properties and Modifications dialog box opens, displaying the properties of the residue in the Residue Properties area.
  6. Residue Properties and Modifications dialog box
    Figure Residue Properties and Modifications dialog box
  7. Assign static modifications as follows:
  8. To assign a single-site side-chain modification to the residue, in the Side Chain Modification area, select a modification from the dropdown list.
  9. To assign a global side-chain modification to all instances of the residue, in the Side Chain Modification area, select a modification from the dropdown list and select the Apply to All checkbox.
  10. To assign an N- or C-terminal modification, in the N- or C-Terminal Modification area, select the modification from the dropdown list.

  11. NOTE

    You cannot assign any static modifications to a disulfide-linked cysteine (C) residue.

  12. The monoisotopic mass of the selected modification appears in the Mono. Mass box.
  13. The average mass of the selected modification appears in the Avg. Mass box.
  14. Select the OK button at the bottom of the dialog box.
  15. The modified residue appears highlighted in blue in the Protein Sequence Map.
  16. Modified residues highlighted in blue
    Figure Modified residues highlighted in blue
  17. Repeat the previous steps to assign more static side-chain, N-terminal, or C-terminal modifications as needed.
  18. To remove a static modification, repeat steps 1 and 2 above to select the appropriate residue, and then in the Residue Properties and Modifications dialog box, do either of the following:
  19. From the appropriate dropdown list of modifications, select None and then select the OK button.
  20. At the bottom of the dialog box, select the Clear button and then select the OK button.
  21. The blue highlight disappears from the affected residue(s) in the Protein Sequence Map.

  22. TIP

    For side-chain modifications, selecting the Apply to All checkbox before you select the Clear button removes the modification from all instances of the selected residue.

  23. TIP

    For efficiency, if you want to apply a static side-chain modification to most of the instances of a residue, use the Apply to All checkbox to apply the modification globally. Then, remove the modification from individual residues as needed.

  24. Save the protein sequence.