Use cleavable crosslinkers - Proteome Discoverer Software - Use cleavable crosslinkers - Proteome Discoverer Software - Proteome Discoverer Software

Procedure

1. To open the Chemical Modifications view, do one of the following:
1. Select Administration > Maintain Chemical Modifications.
2. Select Maintain Chemical Modifications .
2. Define the modification (refer to the topics on “Defining Chemical Modifications,” in “Configuring Proteome Discoverer” in the Proteome Discoverer User Guide).
3. 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.
4. Ensure that the target amino acid of the crosslinker is set.
5. The following image shows the addition of a new crosslinker called DSSO_new in the Chemical Modifications view.

3. Select Add to add the crosslinker fragments as necessary for cleavable crosslinkers and to enable the chemical modification in the XlinkX/PD Detect node.
4. The Add Chemical Modification dialog box opens to the General page.
4. On the General page, do the following
1. For Name, enter the name of the crosslinker.
2. For Abbreviation, enter the abbreviation of the name of the crosslinker.
3. For Delta Mass [Da] (the monoisotopic mass), enter a value.
4. For Delta Average Mass [Da], enter a value.
5. For Substitution, enter the chemical formula of the crosslinker.
6. Select the targeted amino acid.
5. Select the Crosslinking tab and do the following:
1. Select Cleavable Crosslink from the dropdown list.
2. The application automatically calculates the fragment masses. If it is not possible to calculate a mass, it displays an error message and does not add the fragment to the list.
1. (Optional) To change the information for a fragment, double-click the field, and then enter the new text.
2. (Optional) To remove a fragment, select Delete on the row.
3. After adding all the fragments, you can connect the fragments.
   For the identification, you must have knowledge of the possible fragment combinations in a cleaved crosslink.
4. Select a fragment, and then select Add Selected Fragment.
5. The first selected fragment is displayed under Left Fragment.
1. Select another fragment, and then select Add Selected Fragment.
2. The second selected fragment is displayed under Right Fragment.
6. Connect any additional fragments if needed.
7. Select OK.