You can assign multiple variable modifications to a protein sequence. During data processing, the application looks for sequences that match any combination of the assigned modifications up to the maximum number of modifications.

Procedure

  1. In the Protein Sequence Editor, select the title bar for Variable Modifications for Intact and Peptide Analysis.

  2. NOTE

    To edit the parameters in this pane, you must set the category for the protein sequence to Peptide Mapping, Intact Protein, or Unknown.

  3. On the left side of the pane, the Modifications area shows all of the default variable modifications (in the N-Terminal, C-Terminal, and Side Chain boxes) that you can apply to your sequence.
  4. On the right side of the pane, the Modifications Selected for Search area shows all of the loaded variable modifications to be applied to the experiment.
  5. You can edit and customize the displayed lists of default modifications as appropriate.
  6. You can also create custom modifications to apply to your sequence using the Modification Editor at the bottom of the pane.
  7. In the Max # Modifications area, do the following:
  8. In the Intact Protein box, type a value for the maximum number of modifications to assign to the sequence for intact mass analysis.
  9. In the Peptide Mapping box, type a value for the maximum number of modifications to assign to the sequence for peptide mapping analysis.
  10. Setting the maximum number of modifications to a high value can greatly increase the number of combinations and the search time.
  11. The maximum number of modifications does not include glycosylations.
  12. In the N-terminal, C-terminal, and Side Chain boxes, do the following:
  13. To quickly load the modifications from the default sublist, select Load Default Mods.
  14. You can edit the default sublist of variable modifications used for quick loading.
  15. To assign another modification, select it from the Modifications lists (on the left side), and select Add.
  16. You can assign more than one modification to your sequence, but you can only select one modification at a time.
  17. Continue adding modifications from the Modifications list (left) to the Modifications Selected for Search lists (right) as necessary.
  18. Variable Modifications for Intact and Peptide Analysis pane with default modifications loaded
    Variable Modifications for Intact and Peptide Analysis pane with default modifications loaded
  19. If you want to remove a loaded modification from the Modifications Selected for Search lists, select the modification and select Remove.
  20. Select Save or Save as New in the command bar to save the modifications. Or, if you do not want to save the modifications to the sequence, select Cancel.