The label-free quantification of crosslinks works in the same way as for peptides and proteins. The processing workflow requires the Minora Feature Detector node to extract the features from the MS1 scans of the .raw file and in the consensus workflow Feature Mapper and Precursor ions quantifier are needed as additional nodes.
The result contains quantification values for CSMs, which are aggregated to quantification values for the crosslinks using the same rules that are also applied for peptides. For label-free quantification of crosslinks, the following views are available: Quan Spectra View, Precursor Isotope Pattern View, Chromatogram Trace View, and Quan Channel View.