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AutoQC - Verifying peak integration before uploading to Panorama

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AutoQC - Verifying peak integration before uploading to Panorama nbekhti  2024-08-07 14:26:12
 

Hi there,
we are piloting the use of autoQC and Panorama for automated evaluation of our LC-MS system's performance (system suitability). This is for small molecule analysis. We made a sample with a handful of metabolites that we run at the start of each LC-MS batch.

Upon reviewing the Skyline file that contains our system suitability samples and that is linked to Panorama, we noticed that for some samples peak integration was not performed correctly. We use explicit retention times and do observe some retention time shift from one experiment to another. We also have 2 isomers in our sample that have the same transitions and elute closely to each other although they are near baseline separated (see attached PDF). Depending on the retention time shift for that sample, the correct or incorrect peak may be integrated.

Here are my questions:

  1. Is there a way to get more consistent peak integrations across the files and still use AutoQC, for instance be removing explicit retention times (I imagine this can work for some of our molecules although not for our isomer pair)
  2. If the answer to the above question is no, how would your recommend to proceed? Not use AutoQC, but instead review peak integrations manually and then use 'upload to Panorama' under Files?

many thanks!
 
 
Vagisha Sharma responded:  2024-08-07 21:50:44

Hi,

Thank you for your interest in the Panorama AutoQC workflow. Currently, Skyline is not always able to accurately pick the correct peak for closely eluting, isobaric compounds like leucine and isoleucine. Will Thompson and his group at 908 Devices are working on developing algorithms and tools to address this problem. The Skyline team will collaborate with Will's group as soon as they have something that can be implemented in Skyline.

You can watch Will Thompson's talk about this at the 2024 Skyline User Group Meeting using this link: https://skyline.ms/wiki/home/software/Skyline/events/2024%20User%20Group%20Meeting%20at%20ASMS/page.view?name=Will%20Thompson

In the meantime, you will need to manually inspect and adjust peak boundaries in Skyline. You can still use AutoQC Loader to automatically import new raw data into your Skyline document. After new raw files are imported, adjust the integration boundaries in Skyline when required. The document can then be uploaded to your Panorama QC folder via the File > Upload to Panorama menu in Skyline, which is the fastest way to see the adjusted boundaries in Panorama. Alternatively, you can wait for AutoQC Loader to automatically upload the document the next time it imports a new raw file. Panorama will always use the peak boundaries and other metric values from the most recently uploaded Skyline document.

Please let me know if you have any questions.

Best regards,
Vagisha
 
nbekhti responded:  2024-08-08 14:54:34

Thanks so much Vagisha, this is very clear!