Manual integration of SST is not transferred to AutoQC/LabKey

Manual integration of SST is not transferred to AutoQC/LabKey katrin freiburghaus  2020-04-27

Dear Skyline team

I am using Skyline with AutoQC Loader to get my SST uploaded to the Panorama data management system, where I can track the instrument performance (Xevo TQ-S triple quadrupole, Waters). All is working nicely, excpet when the Skyline algorithm picks a wrong peak in my data. I can adjust it manually in the Skyline file, but it is not updated in Panorama.

Could you tell me what I need to do so that my manual adjustments are adapted in Panorama?

Thank you very much and kind regards,

Josh Eckels responded:  2020-04-27

Hi Katrin,

Thanks for your message. I have a guess as to what's going on here, but want to confirm what you're seeing. Is this a file that was imported into your QC folder in Panorama with the original peak from Skyline, and then you made the manual update?

If so, have you already reimport the file manually, or has there been another AutoQC-based import of the file with a new sample? It's possible that there's a bug in Panorama where it's not replacing the peak data like we'd want, but I want to make sure that Panorama knows that it should have imported the updated file first.


katrin freiburghaus responded:  2020-05-01

Hi Josh

Thanks for your help. The file was indeed first uploaded to Panorama and then manually adjusted and reimported using AutoQC. But it did not adapt the file.

I tried to delete the raw files from my Skyline file, reimport them, adjust the peak integration, then upload it to Panorama again using AutoQC Loader. But that did not work either (see attached pdf).

And finally, I deleted the uploaded files in Panorama and tried to upload them again with AutoQC, but nothing happened (no upload anymore).

So I am really not sure what I am doing wrong and look forward to your advice.

Thanks an best regards,

Vagisha responded:  2020-05-01

Hi Katrin,

I want to clarify that AutoQC Loader will only upload a Skyline document to Panorama if it has just imported a new raw file into the document. So, the following sequence of steps has to happen for the manually adjusted peak integration boundaries to show up in Panorama if you are relying on AutoQC Loader for document uploads:

  1. AutoQC Loader imports a new raw file into the document and uploads it to Panorama
  2. User manually adjusts peak boundaries and saves the document on their computer
  3. A new raw file is available to import. AutoQC Loader imports the raw file and uploads the document to Panorama.

After #3 you should see updated peak boundaries on Panorama for results that were present in the document just after step #2.

AutoQC Loader will not upload the document to Panorama if you re-start it after step #2 as it will not see any new raw data to import, and it does not check if the document has changed on the computer since the last time it was uploaded to Panorama. Perhaps this is what you are expecting?

If you want to see the updated peak boundaries after step #2, without waiting for step #3, you can manually upload the document to Panorama. Here is the documentation for doing that:

I hope this helps.