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x axis for plots in autoQC folder are not kept const. Tobias Kockmann  2017-09-14
 
Hi Panorama support,

I observed the following in

https://panoramaweb.org/labkey/project/Functional%20Genomics%20Center%20Zurich%20-%20Proteomics%20%26%20Protein%20Analysis%20Group/Qcloud/QEXACTIVEHF_2/begin.view?

The QC plots that are displayed do not have the same x-axis (replicates). The DGL... peptides shows several datapoints for the the date 2017-09-03. For the ECC... there is several injections missing. How is this possible? If I co-plot all peptide it gets even more visible (see attachment).

Interestingly, all peptides that are missing belong to the same protein group.

Greetings,
Tobi
 
 
vsharma responded:  2017-09-15
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
 
Tobias Kockmann responded:  2017-09-19
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
 
vsharma responded:  2017-09-19
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