Sciex SWATH data we see precursor response but not fragments

Sciex SWATH data we see precursor response but not fragments jlaycock  2022-10-21

Dear Skyline Team:

We have 5 replicates of predigested BSA injected with fixed window SWATH on our Sciex a 7600 ZenoTOF. The BSA Fasta was imported and the 5 .wiff data files were imported. I have tried a several different settings in the Transitions form but still do not see the fragments.

I have confirmed by viewing the data in OS Explorer that there is response for at least some of the fragments.


Data files available to upload if helpful.

Nick Shulman responded:  2022-10-21
Can you send us your some of your .wiff files, as well as the .wiff.scan files that go with them?

If those files are too large to attach to this support request (the limit is 50MB) you can package them in a zip and upload them here:

The usual reason that fragment transitions do not have any chromatograms is that there were no MS2 spectra which matched the precursor.
I see that your isolation scheme at "Settings > Transitions > Full Scan" is "All Ions" which means that all MS2 spectra will match all precursors, so I would certainly expect to see some chromatograms for your fragments.
One thing to keep in mind is that whenever you change the Transition Full Scan settings you typically have to tell Skyline to extract chromatograms again by going to "Edit > Manage Results > Reimport".

We will probably be able to figure out what is going wrong after we see your .wiff and .wiff.scan files.
-- Nick