QC trend report

QC trend report jean-christophe prost  2022-11-10 02:27:00

Dear Panorama Team,

I tried quite a long time to generate reports or grids to get a quick overview for SST measurements.
Currently we have to import the data in skyline and extract them a csv report, that is then imported in Excel to get a final SST (see attachment) report and tells you, if your system works properly to measure your run.

Of course, in case we could have everything directly in panorama, it would increase the easiness of our workflow. I do not know, since we use already a set up report from skyline, if we can import it in panorama? or how to set something similar, or a report that gives you the standard deviation of the retention tim, mass error, CV of area and height, in one shot.

In advance thank you for your support and help.
Best, Jean-Christophe

vsharma responded:  2022-11-11 11:54:53

Hi Jean-Christophe,

Thank you for posting your question to the support board. You should take a look at the Panorama AutoQC pipeline if you haven't already done so. This pipeline lets you track the performance of your LC-MS system over time. Skyline documents containing results from system suitability samples are uploaded to a special type of folder on the Panorama server where you can see trends with standard deviations for various metrics, including retention time, mass error etc., in Levey Jennings plots that help you to quickly identify potential issues. Several labs have implemented the AutoQC pipeline for tracking system suitability. You can get more information about the pipeline on this page: https://panoramaweb.org/home/wiki-page.view?name=qc_with_panorama.

The Skyline and LabKey teams did a webinar recently on the "Best practices for evaluating LC-MS system suitability with Skyline and Panorama". This should be a good starting point. Here is the link: https://www.labkey.com/webinar/lc-ms-system-suitability-skyline-panorama/.

Please let us know if you have any questions.


jean-christophe prost responded:  2022-11-30 05:10:56

Dear Vagisha,

Thank you for yourfeedback. I tried to do exact what you show in your wikipage you sent me.
Unfortunately I was not able to setup the autoqc loader.

I send you a print screen of what I did, with a proxy error in the AutoQC configuration, and on this specific working station I use, we are able to go on the toll store. This means something in the config is not correct.

I am not sure, what I have to indicate in the "folder on Panorama".
Is it in our case:
INSELSPITAL-Clinical Chemistry
INSELSPITAL-Clinical Chemistry/test_acylcarnitine
Was unclear for me.

Or maybe there is another problem in the configuration of our autoQC loader?
Thank you in advance for your support.

bconn responded:  2022-12-01 05:59:19

About the "folder on Panorama", in your case it is "INSELSPITAL - Clinical Chemistry/test_acylcarnitine"

The proxy error looks to be the same problem with your PCs proxy configuration that you reported in the other Support ticket (https://panoramaweb.org/home/support/announcements-thread.view?rowId=7828). The URLs which AutoQC is trying to reach are


These URLs will be accessing TCP/443 port on webserver.


jean-christophe prost responded:  2022-12-01 06:13:25

Dear Brian,

Thank you for your help. I know it is exactly the same problem. I tried to explained it to our outsourced IT people.
In the hospital, there are so many firewalls, and proxy settings, it is really annoying. And this makes also very difficult to reach directly the right person to solve your problem.

It is completly crazy, since we have on two different pc's, similar settings, but one goes through and one is blocked.
I will transfer your infos to our IT, hoping they will be able to solve my problem.

Best, Jean-Christophe