Feature Score Generations Fails: “Signal to noise missing from chromatogram peak” for particular replicates

Feature Score Generations Fails: “Signal to noise missing from chromatogram peak” for particular replicates peter r mosen  2021-05-02

Dear Skyline team,

During the generation of a peak scoring model Skyline (64bit, v21.0.9.118) reports for one peptide in two of the nine loaded replicates that it is missing the signal to noise for the chromatogram peak, excluding this feature score form the scoring model. However, as you can see (screenshot, lower chromatogram panel the two replicates L01-05 and L01-10) Skyline integrated for the two reported replicates the peak in the light and heavy channel properly (“Integrate all” is active). Also after manual peak integration for the two replicates the noise to signal feature score is still greyed out/inactive. If I exclude the two problem replicates (or delete the affected peptide) and I can build my peak scoring model having the noise to signal feature score included.

Interestingly Skyline is missing the signal to noise only for the two of the nine loaded replicates, though all nine loaded replicates were acquired with the same instrument method in the same acquisition period.

Is there anything what I am missing? What is causing the problem with these two replicates?
Thanks for your help,


Nick Shulman responded:  2021-05-02
I can't think of a reason that that feature would be missing such a small number of peptides like that.

If you send us your Skyline document I could probably tell you what is going wrong.

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.

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

-- Nick
peter r mosen responded:  2021-05-03
Hi Nick,
thank you for your quick response. I am happy to share the document with you, however I would prefer the non-public data transfer. Is there a possibility to share data non-public within the forum, or shall I sent an e-mail?

Best Peter
Nick Shulman responded:  2021-05-03

I have sent you an email directly so that you can share your files with me.
-- Nick
Nick Shulman responded:  2021-05-03

Thank you for sending me your Skyline document.
Skyline is having trouble calculating the Signal to Noise value for peptides where the light and heavy SRM chromatograms cover different retention time ranges.
Skyline looks at the heavy chromatogram first in order to find the list of candidate peaks. For each of those candidate peaks Skyline wants to calculate both the heavy "Standard signal to noise" and the light "Standard to noise" feature scores. Unfortunately, the way that we wrote the code, when Skyline sees that the candidate peak is beyond the end of the light chromatogram, Skyline decides that the feature score should be "unknown".

I will try to fix this in a future version of Skyline. In the meantime, I expect that you will be able to work around this problem by changing your instrument method so that the light and heavy chromatograms are extracted over the same time range.

Thank you for letting us know about this bug.
-- Nick