Export Isolation List (DIA) for Bruker timsTOF

Export Isolation List (DIA) for Bruker timsTOF Premy  2022-08-02


I use the Bruker timsTOF Pro, and wanted to export an isolation scheme through Skyline. I created a scheme under Transition settings and did the following:

File --> Export --> Isolation list --> selected Bruker timsTOF and set the run duration

After saving the .csv file, no file seems to be created. I'm not sure if I missed something on my end. Any help would be appreciated!


Nick Shulman responded:  2022-08-02
Can you send us your Skyline document?
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, and spectral and ion mobility libraries.

If that .zip file is less than 50MB you can attach it to this support request.
You can upload larger files here:

It might also be helpful if you could send us a screenshot of the Export Isolation List dialog so that we can see what settings you are using.
-- Nick
Premy responded:  2022-08-02
Hi Nick,

I've attached both. The file itself contains no transitions just the calculated isolation window scheme.

Thanks for the help,
Nick Shulman responded:  2022-08-02
You need to have some transitions in your Skyline document in order for "Export > Isolation List" to work.
The purpose of the Export Isolation List menu item is to export a list of precursor m/z values for a targeted PRM method. I do not believe that there is any way to make it work for a DIA method like you are trying to do.
I am not sure, but I do not believe that Skyline has any features to make generating DIA methods easier-- that is something you need to do inside of your mass spectrometer instrument software.
-- Nick
Nick Shulman responded:  2022-08-02
It turns out there are some types of instruments for which Skyline can export a list of DIA isolation windows like the way that you would like, but, unfortunately, Bruker timstof is not one of them.

If you choose "Thermo Fusion", then Skyline would export a CSV with the DIA isolation windows in it.
-- Nick