Prosit mirror

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Prosit mirror Gerhard Saalbach  2021-07-06
 

Hello,
I use the Prosit prediction, but when I turn on the mirror everything disappears and I see only an empty window saying Spectral infmation not available.
What could be wrong?
Thanks
Gerhard

 
 
Nick Shulman responded:  2021-07-06
I cannot think of a reason that it would do that.

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 spectral libraries.

If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:
https://skyline.ms/files.url

It would also be helpful if you could send us a screenshot so that we can see which peptide you have selected and what that Library Match graph window is looking like.
-- Nick
 
Gerhard Saalbach responded:  2021-07-06
Files are attached.
It happens with all peptides.
With online Prosit there are no doyp values either
I do get a dotp if I use a library in addition to the online Prosit.
Then the mirror shows library versus library.
Thanks,
Gerhard
 
Brendan MacLean responded:  2021-07-06
This is simply telling you that you do not have a library spectrum for the selected precursor. Perhaps we should fix this to show the Prosit spectrum only below the x-axis. Though, as you point out, you can see this by turning "Mirror" off. Then Skyline will show you the Prosit spectrum above the x-axis. A dotp value is not appropriate, because all Skyline can get for this precursor is the Prosit prediction, which would have a dotp of 1.00 with itself.

The message is telling you that there is no library spectrum.
 
Gerhard Saalbach responded:  2021-07-06
Of course, there is no library spectrum because I do not want to compare a library spectrum with a Prosit spectrum.
I want to compare the individual experimental spectrum with the Prosit or with a library spectrum.
If I turn off Prosit and set up a library the same problem occurs.
Now there is a library, but I can still not mirror it with the experimental spectrum.
It is right that I can mirror the library spectrum with the Prosit spectrum but that's not really useful.

What I expect from this mirror function is that I can compare a predicted spectrum (or a library spectrum) with the individual experimental spectra.
 
Brendan MacLean responded:  2021-07-07
Okay. Fair point. We have a developer working on what we call our "Full-Scan" view where if your chromatograms come from extraction from spectra (and not SRM), you can click on any point and see its spectrum. For Skyline 21.1, she made it so that these spectra can be annotated like the spectra found in the "Library Match" view. I had also been thinking that it would be good to make this view provide the ability to show a Prosit mirror the way the "Library Match" view does.

For now, if you lack a library for your experiment and you want to see comparisons with Prosit spectra, you should build a Prosit library as shown in this presentation:

https://youtu.be/xm7Niu3lyZA?t=7137

That will give you the ability to make comparisons with your experimental data in the "Peak Areas" view, where Skyline will calculate dotp with the Prosit predictions for every run and show an "Expected" distribution.

Hope this helps. Thanks for your feedback.
 
Gerhard Saalbach responded:  2021-07-07
Thanks for the suggestions.
I already thought I could make a library (non-curated) from every single run, then load all of them in the global document.
Then I can mirror each run-specific library with Prosit.
Just a bit tricky with many files.
Thanks,
Gerhard