QC Plots are not Displayed

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QC Plots are not Displayed s merker  2018-10-12
 

Dear Panorama team,

first of all, thank you so much for the great work you are doing! We have recently implemented QC for our QTrap 5500 system based on Skyline and Panorama employing the AutoQC client. I have to say that it greatly facilitates the workflow compared to manual data inspection in Skyline. However, since yesterday no QC Plots can be displayed on our dashboard ("no data to plot"). However, samples are being successfully uploaded into the specified Skyline document and also to Panorama, according to the AutoQC log (new sample names also appear in the QC summary, just the plots are gone, s. attached screenshot). When I enter the public Panorama project "U of Melbourne - Proteomics Facility", I can see and manipulate QC Plots there, so this does not seem to be a browser or a general issue. We use regular Skyline release 4.1.0.18169 combined with AutoQC Loader 1.1.0.11725, OS is Windows 7 Professional, 64-bit. Restarting the relevant configuration in the loader did not help. I would very much appreciate any suggestions since we are quite new to Panorama and have never encountered that issue before.

Best regards,

Roman

 
 
s merker responded:  2018-10-12

Hi Roman,
That is strange. When I look at the project you are showing in your screenshot, I see the data just fine, now 59 sample files. When I impersonate you, I also see the no data message. When I impersonate anyone else (Users group for your project or the other project administrator) I can again see the data. So, it appears to be something "sticky" associated with your user account. I can switch to the Runs tab, drill into the two documents listed there and see both chromatograms and summary plots. So, it doesn't seem to be any sort of data access issue, and you are a project administrator.

I am out of ideas, and unfortunately, the people who are likely to have more will be out until Monday. Until then, you could create yourself a new account based on some other email address and either make it also a project administrator or just add it to your Users group. That new user should start off fresh and be able to see the QC data as I can myself or with everyone I impersonate but you. If you then manage to get that other user in this state and you can determine what you did, I may be able to help further. If not, at least maybe you can see the data until Monday when more sophisticated help should return.

Thanks for pointing this out and for your appreciation of PanoramaWeb.

--Brendan

 
Roman Sakson responded:  2018-10-12

Hi Brendan,

thanks a lot for the swift reply. Indeed, the issue is gone when I login with the second admin account we have for the project folder and I can see everything as usual. There must be an issue with the s.merker@zmbh.uni-heidelberg.de-related account only. Therefore, this is not particularly urgent at this point. It would, of course, still be interesting to know what is going on. I will just stick to the working account for now and pay attention just in case that it happens again.

Best regards,

Roman

 
s merker responded:  2018-10-12

Hi Roman,

As you may know, the QC plots remember your previous settings so that when you return, you see the same metric, time window, etc as that time you visited.

It looks like your account is remembering a replicate annotation filter, looking for an annotation named "Vial empty" with a value of "Empty!!". However, we only show you the options to add or remove replicate annotation filters if there are currently annotations in the QC folder, so there's no easy way to clear the filter. However, I was able to remove the sticky filter.

Is it possible that this folder used to have some replicate annotations loaded, but they were later removed from the Skyline document?

Thanks,
Josh

 
jeckels responded:  2018-10-12

Sorry for the confusing post, I was still impersonating you when I clicked submit, so it came across as being from Roman.

Thanks,
Josh

 
Roman Sakson responded:  2018-10-12

Hi Josh,

thank you very much, the issue is gone! However, this has produced some new question marks for me. I was, indeed, playing around with annotations and trying to understand how they work and can be displayed within Levey-Jennings plots. I was doing it only under "Annotations" in Panorama, not in the Skyline document itself (does it make any difference?). It seems that I don't really understand what I am doing when it comes to annotations (the ReplicateAnnotation I created somehow disappeared from the annotations overview a couple of times). Furthermore, what I would like to achieve is a display, possibly with a comment, like in one of the presentations given by Vagisha (s. attachment). Unfortunately, I did not succeed and also could not find any instructions how to do that. Do I need ReplicateAnnotation or QC Annotation for that (the difference between the two is also not really clear to me, sorry about that).

Thanks,
Roman

 
vsharma responded:  2018-10-12

Hi Roman,

What you are looking for are QC annotations. Unlike replicate annotations which are associated with individual replicates in your Skyline document, QC annotations are associated with a date and time. They can be used for marking events such as instrument calibration, new column etc, and show up as colored 'x' markers on the plots.

Here is link to documentation on adding QC annotations:
https://www.labkey.org/Documentation/wiki-page.view?name=QCannotations

Thanks for using the Panorama QC workflow and pointing out the bug related to replicate annotations!

-Vagisha

 
Roman Sakson responded:  2018-10-13

Hi Vagisha,

thank you very much for making that clear (and for very short response times, to all of you!). I did not manage to find that particular documentation folder, it looks exactly like something I was searching for!

Best regards,

Roman