|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, v18.104.22.168) 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?