When you select the Perform Digestion checkbox at the top right of the Sequence area of the Theoretical Protein/Peptide Manager page, the application activates the Digestion Parameters (optional) tab for you to select the protease to apply to the digestion along with other peptide constraints. The application uses these parameters to predict the theoretical peptide fragments when you process the sequence.


  1. On the Theoretical Protein/Peptide Manager page, input a protein or peptide sequence and select the Perform Digestion checkbox.
  2. See Create or import a protein or peptide sequence.
  3. Select the Digestion Parameters (optional) tab.
  4. The Digestion Parameters (optional) pane opens, displaying the digestion parameters.
  5. Digestion Parameters (optional) pane
    Digestion Parameters (optional) pane
  6. In the Select Protease area, select a protease to apply to the digestion.
  7. The activities at the N-terminal and C-terminal for the selected protease appear in the N-Term and C-Term boxes but are not editable.
  8. This information indicates where the protease will cleave during digestion.
  9. You can add a new protease or edit the protease information using the Parameters > Identification page in the peptide mapping analysis workflow.
  10. See Edit the Identification page in the Peptide Mapping Analysis User Guide.
  11. In the Peptide Length Constraints boxes, specify the lower and upper values for the peptide length range.
  12. The application displays only the peptides that fit the specified length in the Results table .
  13. In the Number of Allowed Missed Cleavage Sites box, specify the maximum number of internal cleavage sites within a peptide fragment that a protease enzyme can miss during the digestion process.
  14. The enzymatic digestion process does not always result in all of the available cleavage sites in a protein being cleaved. Therefore, it is important to specify the number of missed cleavage sites that can be present in a peptide fragment where the enzyme could have cleaved but did not.
  15. If you set the Number of Allowed Missed Cleavage Sites parameter to 0, the application considers the enzyme to have efficiently cleaved at all the possible cleavage sites in a protein with 100-percent specificity.
  16. To perform the theoretical digestion of your sequence without changing the default Add/Edit Target m/z or Add/Edit Modifications, select Process.
  17. The Results table displays the results of the theoretical digestion and experiment.
  18. See Results table parameters.
  19. Otherwise, you can specify the Add/Edit Target m/z and Add/Edit Modifications before processing, as necessary.
  20. See Add/edit target m/z parameters.
  21. See Add/edit modifications.