Moving this request from support to the issues list to avoid losing it. Please add your insights, Matt.

I uploaded a BSA digest we run in PRM that includes several modes of fragmentation and is not supported by Skyline at the moment. We use this for our QC of the Lumos and fragment using CID, HCD and ETD. At the moment we can only see the MS1 signal in Skyline, but not the MS2, which we would very much like to.
The file name is FS1LC2_BSA_HCD-IT_28082018_01.raw

https://skyline.ms/announcements/home/support/thread.view?rowId=32997

I'm not seeing any problem reading that file from a ProteoWizard perspective. Loads fine in SeeMS and converts in MSConvertGUI and I can see all the expected activation types. You want me to look into it in Skyline? I suspect it's breaking a heuristic somewhere.

Yes. Please try to reproduce it in Skyline and see what you can come up with. If you don't feel comfortable proposing the fix, then hand off to Nick or Brian Pratt.

On the support thread we decided the current workaround with pre-filtering the file into pseudo-replicates for each activation type was sufficient for now given that this is a very rare use case (although the less rare ETD/CID or ETD/HCD would require similar treatment, so if that gets more common we may revisit this).