I would like to use Skyline to generate a spectral library compatible with a library-based DIA search in DIA-NN.
My issue is that when I import an output from MaxQuant (1.6.14) using the "import peptide search" pipeline (msms.txt file in the same folder as the raw files, the mqpar.xml and the modifications.xml containing the list of variable modifications -I added the Ammonium and Ammonia loss in the bottom-), the only modifications that I find in the output are oxidation (M) and carbamydomethylation (C). So several modifications are missing.
I am pretty sure that I miss something but I cannot figure out what.
The idea is to then export a custom report from Skyline that would be in a format that I can make compatible with a DIA-NN input library. This bit works.
I work with Skyline (64-bit) 184.108.40.206 (a0e7323e3).
I have uploaded the MaxQuant outputs I work with on the skyline upload site, with the name "Ticket_MLocardPaulet.zip".
Please let me know if you need more information.
Thank you for your help.