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How to use Peptide spectrum match count?

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How to use Peptide spectrum match count? Juan C. Rojas E.  2024-07-25 07:58
 

Hi there,

I am wondering if there is any default filter being applied for Peptide Spectrum Match Count in the document grid? I see that for some peptides this has 0 despite having a library match. Example in the attached figure.

If data is required I can provide some through Panorama, but this is more of a general inquiry on how this is counted in Skyline and what would happen if there are multiple spectral libraries active in a Skyline document?

I had not seen this PSM counting before, but looks very interesting for generating UpSet plots from a Skyline report.

Sincerely,
Juan C.
 
 
Nick Shulman responded:  2024-07-25 08:18
The "Peptide Spectrum Match Count" column is on the "Peptide Result" and is supposed to tell you the number of PSMs for a peptide in a particular result file.
It was added to Skyline-daily almost a year ago just after Skyline 23.1 was released.

I cannot see the "Replicate" column in your screenshot, so it's possible that the rows that you are looking at do not correspond to the replicate that has those very clear "ID" lines on the chromatogram graph.

But, yes, this does look like a bug. Can you send me your Skyline document?
-- Nick