How to make skyline pick the peak with highest dot product?

How to make skyline pick the peak with highest dot product? pavel shliaha  2022-04-22

I am not sure how skyline picks which peak corresponds to the peptide from library (I use extremely high RT tolerance) but it picks a peak which has a low dot product (0.3-0.5), but there are other candidates which have dot product as high as 0.95 (which I think is my actual peptide). Is there a way to specify skyline to select the peak with highest dot product?

NOTE: I am NOT asking about filtering on dot product score. If skyline selects a peak with dot product of 0.4, while there is a candidate which is 0.95 and I specify the threshold of 0.9 in refine > advanced > min dot product skyline simply removes the selected peak, but it does not help identify the peak with 0.95 dot product

Nick Shulman responded:  2022-04-22
The library dot product is one part of the peak scoring function that Skyline uses to decide which candidate peak to choose.

The next version of Skyline is going to have some features that make it much easier to see how Skyline scored each of the candidate peaks, and exactly why Skyline picked the peak that it did.

If you want Skyline to use different peak scoring criteria, the only thing that Skyline lets you do is collect data with decoys and train a peak scoring model. There was some information about how to do that at the bottom of this support request:

If you send us your Skyline document I might be able to give you more information about why Skyline is making the bad choices that it is.

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.

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

Let me know an example of a peptide and replicate where Skyline is picking the wrong peak. It might be that you are correct and things would be better if Skyline weighted the library dot product more heavily, but it also might be that there is something else going wrong which is why Skyline is picking the wrong peak.
-- Nick