dotp value after Prosit integration in Skyline

dotp value after Prosit integration in Skyline meharunnissakohli  2021-07-22

Hello Support Team,
I want to analysis a data in skyline in which I want to match the spectral data obtained in an MRM experiment with the Prosit predicted library.
I could see that the Prosit is making predictions for my target peptides but dotp value is not shown.

However, if I monitor precursors ions also, then only dotp value is shown (but in my data, i have product ions for which I actually need the dot p value).
Could you please help me resolve this.

Looking forward to hearing from you.
Mehar Un Nissa

Nick Shulman responded:  2021-07-22
I am not sure that I understand your question.

If you want to get the prosit dot product values, I think the thing to do is to create a .blib file from Prosit.
That is, go to:
Settings > Peptide Settings > Library
and push the "Build" button and choose "Prosit" as the "Data source".

This will create a spectral library (.blib) file containing the peptides in your Skyline document where the spectra have the intensities that were predicted by Prosit.
Then, when you are using the library in your Skyline document the Library Dot Product values will be the dot product against the predicted prosit spectra.

Does that answer your question?
I might have misunderstood your question. Could you post a screenshot of what you are looking at?

It might also help me understand if 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.

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

-- Nick