During a tutorial on importing DDA data into Skyline at Dortmund, the instructor pointed out that it is not possible to specify MS/MS extraction in the Import > Peptide Search wizard. We now support a "DDA" isolation scheme where we add fragment transitions that are marked as non-quantitative. And we may soon use that for TMT processing with relative quant based on reporter ions in the MS/MS.

We probably need to add the MS/MS extraction parameters as optional to the wizard. Maybe they should just have the MS/MS "Acquisition method:" combo box with the options "None" and "DDA" as in Transition Settings to allow the user to choose either to include MS/MS transitions or not. This is different from DIA and PRM where MS/MS transitions are required and "Acquisition method" is assumed from the choice. Though, DIA shows the "Acquisition scheme" combo, which PRM does not and DDA would not.