Feature Request: Accounting for MS3 data for cleavable Crosslinkers

[atroel01]

Hi xiSearch team, this is a fantastic suits that you have and very much exceed expectations, even for a paid commerical product.

Requested feature: MS3 integration.

Inclusion of peptide spectral matches from MS3 fragmentation into the FDR algorithm would be valuable, especailly for cleavable crosslinkers. Not being familiar with the precise code of how FDR is calculated in xisearch, but from basic principles, MS3 data of linked peptides clearly adds an additional validation to the MS2 annotated spectra used currently for matching. This approach is implemented in XlinkX/Metamorpheus/MSAnnika, though each of them have limitations that xisearch addresses, especially around the control over FDR and crosslinking sites.

Could the addition of MS3 data be implemented as an option in xiSearch/ xiFDR, or at least included down stream, so it can be visible during use of the XiView, showing alignments of the MS3 fragmentation inverted below the chimeric MS2 spectra or overlayed over the chimeric MS2 spectrum?