Auto QC Trend report

Auto QC Trend report Srujana  2020-04-16 13:11:03


I am working on Metabolomics data files for Skyline/PanoramaWeb/AutoQC. I am looking for answers for below queries.

  1. While installation of AutoQC Loader I am having issues with updated version, which is different from the tutorial version. I don.t see create new configuration tab or panorama settings and has different tabs like import and export. How do I use autoQC loader updated version.
  2. While creating QC trend report, run date tab is showing blocked and without that report doesn't proceed to next step.

Thank you,

Vagisha Sharma responded:  2020-04-16 14:44:00

Hi Srujana,

  1. The "Create a new configuration" button is located in the same place in the latest version of AutoQC Loader as it is in the screenshots in the documentation here: You will find the button at the bottom of the Window. If you don't see it please send us a screenshot of what your AutoQC Loader window looks like. When you respond to this message you can click the "Attach a file" link to include attachments.

  2. You shouldn't need to create QC trend reports in your Panorama QC folders. As far as I can tell, these reports are meant to be used with other types of assays, not with Skyline results. We will be able to help you better if you send us screenshots of what you are trying to do.

You will find links to more detailed documentation on how to use Panorama QC folders here:

Thank you for using the Panorama AutoQC pipeline for your metabolomics workflow.


Srujana responded:  2020-04-17 09:27:01

Hi Vigisha,

Thanks for the response. I have created AutoQC for 3 batches (~430runs) in the PanoramaWeb and would like to check the trend report. I was following the report tutorial to view overall run performance for all batches and export data into excel to proceed for statistics, PCA etc. How can I export data from all 3 batches into one excel file and view QC plots.

And regarding AutoQC, please find attached document. How do i import a run into "create a new configuration" in the latest version. Previously i tried SKyline document. If i have to directly work on AutoQC loader how do i proceed with small molecule data set.

Thank you,


bconn responded:  2020-04-17 11:43:32

Hi Srujana,

I have attached a screen shot of the QC Loader installed on my computer, where you can see the "Create a new configuration" button at the bottom of the application. For some reason your installation is not displaying the button. Does this occur if you restart the AutoQC loader application? If so, can provide me more information about your workstation? What is the OS version?

Which report tutorial are you following? Can you please send the link to the tutorial. This will help us understand the problem you are having.

Thank you,
Brian Connolly

Vagisha Sharma responded:  2020-04-23 17:22:27

I did a quick Zoom call with Srujana. She has Windows 10 Pro on her laptop. The AutoQC Loader window was cropped just like in her screenshot. We changed the display scaling setting "Change the size of text, apps, and other items" from 150% to 100% and that fixed the problem. I can reproduce the problem on my computer if I select anything other than 100% for scaling. This will be fixed in the next release of AutoQC Loader.