In the Protein Sequence Editor, you can create intra- and inter-chain links between cysteine (C) residues in a sequence.

NOTE

You can assign disulfide links to sequences with the "Intact Protein" category only. The feature is disabled for all other categories.

TIP

For Peptide Mapping Analysis experiments, you can perform an automatic disulfide bond search without defining the disulfide links in the Protein Sequence Editor.

When you create a new Peptide Mapping Analysis experiment, select the Perform Disulfide Bond Search checkbox in the Processing Method Editor to enable this feature.

TIP

In the Protein Sequence Map, cysteine (C) residues are traced in yellow for easy visibility.

Prerequisites

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

Procedure

  1. In the Protein Sequence Editor, in the Protein Sequence Map pane, right-click to the left of a cysteine (C) residue and then select Create Link from the shortcut menu.
  2. Next, right-click to the left of the cysteine (C) residue to which you want to link the first cysteine and then select Create Link from the shortcut menu.

  3. NOTE

    When creating disulfide links, a cysteine (C) residue can be linked to only one other cysteine residue. You cannot create multiple disulfide links to a single cysteine residue.

  4. The Protein Sequence Map displays an orange line linking the cysteine residues.
  5. Below the Protein Sequence Map, the disulfide link is added to the Disulfide Link Definitions table. When you select a row in the Disulfide Link Definitions table, the application highlights the selected disulfide link in green in the Protein Sequence Map pane.
  6. Disulfide links in the Protein Sequence Map and Disulfide Link Definition pane
    Figure Disulfide links in the Protein Sequence Map and Disulfide Link Definition pane
  7. Repeat the previous steps to add additional disulfide links as needed.
  8. To remove a disulfide link, do either of the following:
  9. In the Disulfide Link Definitions table, select the row for the disulfide link that you want to delete and then select the Delete button to the right of the table or press the DELETE key.
  10. In the Protein Sequence Map pane, right-click to the left of a cysteine (C) residue with the disulfide link that you want to delete and then select Remove Link from the shortcut menu.
  11. The disulfide link disappears from the Protein Sequence Map and the Disulfide Link Definitions table.
  12. Save the protein sequence.

NOTE

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