Proteome Discoverer provides search templates for different purposes, including crosslink templates. The XlinkX templates are analysis templates, that is, they contain both a processing workflow and an appropriate consensus workflow. Thermo Fisher Scientific recommends using a predefined analysis template.
The XlinkX analysis templates are in this directory:
C:\Users\Public\Public Documents\Thermo\Proteome Discoverer 3.1\Common Templates\Crosslink Analysis Templates
See the following topics: