Vagisha Sharma responded: |
2017-09-15 10:22:01 |
Hi Tobi,
Measurement for these peptides are missing in your Skyline document for some samples. That is why there are no points in the QC plots. For example, look at the replicate 20170901_55_autoQC01_15 in Skyline. There are no chromatograms for peptides from ALBU_BOVIN. Perhaps these were not injected in the sample?
I also noticed that these samples have been excluded from QC. They show up as light gray on the DLG plot, and if you hover over the point you will see that "Exclude sample from QC from all metrics" has been selected. You will only the excluded points if "Show Excluded Points" is checked.
Thanks,
Vagisha |
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Tobias Kockmann responded: |
2017-09-19 02:56:06 |
Hi Vagisha,
that is exactly the point. I was aware of the fact that the peptides where not extracted by skyline for some reason. My criticism is about how QC folders in Panorama handele missing values and I strongly beliefe that not showing the replicate in individual plots is far from ideal, because the different QC plots loose their alignment in the x (replicate) dimension. Don't you agree?
Greetings,
Tobio |
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Vagisha Sharma responded: |
2017-09-19 08:48:53 |
Hi Tobi,
Yes, I agree that the x-axis should stay consistent in the individual peptide plots. I will add it to our TODO list. I thought you were concerned about missing data points that you thought should have been there!
Thanks for your feedback.
-Vagisha |
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