During installation, the Proteome Discoverer application automatically adds several common crosslinkers to the list of modifications that you can use. If the crosslinker used in your experiment is not on the list of crosslinkers in the Chemical Modifications view of the application, you must create it or edit an existing crosslinker.

In the Chemical Modifications view, you can specify that a modification be a crosslink reagent.

See the following topics:

For more information on the Chemical Modifications view, refer to the section “Defining Chemical Modifications,” in the Proteome Discoverer User Guide.