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