DIA results from SCIEX 7600 zenoTOF instrument

DIA results from SCIEX 7600 zenoTOF instrument lorrain  2023-02-02

We are testing some standard peptides using SWATH DIA on SCIEX 7600 zenoTOF instrument. Our transition setting is attached. After importing the datafiles, for some peptides we were able to see MS2 fragments; for some peptides, there is no fragment data. I am wondering if this is due to our DIA method settings or skyline transitions settings. Would you please help?

Nick Shulman responded:  2023-02-02
If you send us your Skyline document as well as your .wiff and .wiff.scan files we will be able to figure out what is going wrong.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file and your .wiff and .wiff.scan files are less than 50MB you can attach them to this support request. Otherwise, you can zip them all up together and upload them here:

-- Nick
lorrain responded:  2023-02-02
Hi Nick,
Thanks for getting back to us. I just uploaded the skyline file, the .wiff files are >1GB and are still uploading. There are two samples in each .wiff file and the sample we were looking at is iRT sample. Thanks.
Nick Shulman responded:  2023-02-02
Thank you for sending those files.
The Transition Full Scan settings in your first screenshot are different from what is in the document that you uploaded.
Your screenshot shows a MS/MS Acquisition method "DIA", but the document that you were uploading used "PRM".

"DIA" would be the correct setting to use for the wiff files you uploaded

I can use the menu item:
View > Other Grids > Audit Log
to see what isolation scheme you had before.

You had been using the isolation scheme called "SWATH (15 m/z)". This isolation scheme is one of the ones that gets automatically added to the list of choices when you install Skyline. This scheme is not going to work with your data because your data had 40 or 41 m/z wide windows with a 1 m/z overlap.
I would recommend that you go to:
Settings > Transition Settings > Full Scan
and choose "Results Only (0.5 margin)" in the "Isolation Scheme" dropdown.

After you do that, you can use the "Reimport" button on the "Edit > Manage Results" dialog to tell Skyline to extract chromatograms again.
-- Nick
lorrain responded:  2023-02-02
Hi Nick,
Oh we saved our PRM analyses of the other files over this. I just change it back and use results only isolation scheme. That works!
Many thanks!!