You can create non-cleavable crosslinkers using the Chemical Modifications view.

Procedure

  1. To open the Chemical Modifications view, do one of the following:
  2. Select Administration > Maintain Chemical Modifications.
  3. Select Maintain Chemical Modifications .
  4. Define the modification (refer to the section “Defining Chemical Modifications,” in the Proteome Discoverer User Guide).
  5. Ensure that the chemical formula in the Substitution field is correct. The XlinkX algorithm uses only the formula to calculate the mass of the modification.
  6. Ensure that the target amino acids for the crosslinker are set.
  7. Select the new modification, and then select Edit to add the crosslinker fragments.
  8. The Add Chemical Modification dialog box opens.
  9. Select the Crosslinking tab and do the following:
  10. Select Non-cleavable Crosslink from the dropdown list.
  11. To add target pairs, select two linkable residues from the Target Pairs dropdown lists, and then select Add.
  12. Repeat this process until you have added all valid pairs.
  14. Select OK.