Variable modifications not reported in MaxDIA with predicted library mode

[tpruk]

Variable modifications not reported in MaxDIA with predicted library mode
I am currently using MaxDIA (in MaxQuant v2.6.7.0) in predicted library mode to analyze samples that contain the PQ500 SIS peptide mix. In the parameter settings, I specified Oxidation (M) as a variable modification, and also included Arg10 and Lys8 to account for the heavy-labeled PQ500 peptides. However, in the output, I noticed that no variable modifications were reported, not even Oxidation (M), which typically appears when analyzing the same samples in MaxQuant DDA mode. Is there a recommended workflow to enable the identification of such modifications in MaxDIA?

Thank you very much for your guidance and for developing these powerful tools.

[WalterViegener]

We are still working on PTMs for DIA. Once we support them we will mention it in the changelog