DIANN out in Skyline

DIANN out in Skyline tania karasiewicz  2024-02-26 05:17


I have just started to use DIANN for some SWATH-DIA data. I am trying to visualise the data and do the stats in Skyline. I have managed to import the library and the peak boundaries of DIANN in skyline for visualisation of the different acquisitions.
I am having problem to do the stats, since I didn't run mprophet, is it possible to import the obtain q value from DIANN some how ?

Or in anycase if you have any tips for DIANN in Slyline, that would be great.

Have a nice day,


Nick Shulman responded:  2024-02-26 14:22
I am not the expert on DIANN in Skyline, but I do not think there is any way to do what you are asking.

Normally, when you are creating a spectral library from peptide search results, including DIANN, you have the opportunity to specify a score threshold for the peptide to be included in the spectral library. You can see that score value in the Document Grid in Skyline in the "Library Probability Score" column.
If you would like to learn more about the Document Grid you can look at the Custom Reports tutorial:

If Skyline cannot find any score to use in your search results when you are building your library, you might have to resort to setting the score threshold to zero or one so that all peptides end up getting included in the spectral library regardless of how bad they are. If you have done that, then I would not expect that you would be able to see any other library score in Skyline.

If you would like, you could send us your Skyline document and we might be able to give you more feedback.
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 libraries.
Files which are less than 50MB can be attached to this support request.
You can upload larger files here:
-- Nick