There is currently no way to do this in Skyline.
We have talked about adding this as a feature because it would then make it easy to compare quantification by spectral counting to chromatogram peak areas.
For now, I think you would have to use some other tool to look at your peptide search results and tell you what the spectral counts were for each peptide.
I will look into whether it would be easy for us to add this feature to Skyline.
-- Nick

Hey,

Is there any update on this thread, I would really like to have the spectral counts for a given modified sequence to be able to apply filtering on my data.

Best,
Wouter

I did start working on implementing this. We would love to hear your feedback about how exactly this should work.
You can install a special build of Skyline-daily here:
https://proteome.gs.washington.edu/~nicksh/SkylineDailySpectralCounting/
This special build of Skyline-daily is currently newer than any official Skyline-daily which has been released. The documents that it saves will not be compatible with older Skyline's or Skyline-daily's, but you can always use the "File > Share" menu item to save the document in an older format that would be compatible with older Skylines.

This special build of Skyline adds a "Peptide Spectrum Match Count" column to the "Peptide Result" section in the Document Grid.
You can see some screenshots showing what that looks like here:
https://github.com/ProteoWizard/pwiz/pull/2481

Let us know if this feature is what you are looking for and whether there is any disconnect between how it works and how you were either hoping or expecting it would work.
-- Nick

Hi,

Thanks for the quick reply, this is exactly what I needed.

Best,
Wouter

Hi,

I've tried it and it works well, but there's one problem still. If I make a table with peptide spectrum match count in a column it counts the PSMs per peptide, but it doesn't count per charge state. so if a peptide is found in two charge states it will sum up the psms for both charge states and then annotate the numbers in both charge states. Is there a way to fix this?

Best,
Wouter