If the crosslinker is specified in the MS Annika Search Node as a fixed or variable modifications (in addition to specifying it as the crosslink modification in the MS Annika Detector Node), an error is thrown. This is intended behaviour because in (almost) all cases this is not what you want. The modifications happening to the two cross-linked peptides during cross-linking are already accounted for by the setting in the MS Annika Detector Node.
For the rare case that you actually additionally want to consider that these peptides might carry an additional crosslinker on one of the other residues (e.g., as a monolink modification) you would have to duplicate the crosslinker in the "Chemical Modifications" window in Proteome Discoverer and give it another unique name and select this one instead. That should solve the issue and the search will run through completely.
If the crosslinker is specified in the MS Annika Search Node as a fixed or variable modifications (in addition to specifying it as the crosslink modification in the MS Annika Detector Node), an error is thrown. This is intended behaviour because in (almost) all cases this is not what you want. The modifications happening to the two cross-linked peptides during cross-linking are already accounted for by the setting in the MS Annika Detector Node.
For the rare case that you actually additionally want to consider that these peptides might carry an additional crosslinker on one of the other residues (e.g., as a monolink modification) you would have to duplicate the crosslinker in the "Chemical Modifications" window in Proteome Discoverer and give it another unique name and select this one instead. That should solve the issue and the search will run through completely.