how to set chromatogram extraction window

how to set chromatogram extraction window yzhu338  2021-10-07

Hi Skyline team,

I'm trying to extract ms1 scan from my 300+ raw files with explicit retention times of 100+ compounds fro quantification purpose. But skyline would often extract and integrate the wrong peak, especially when the compound in a certain file is very low and Skyline would integrate another peak, which can be 10 min far away from the Explicit retention time. It would be impossible for me to do manual integration for all the peaks...
It seems that Explicit retention time window only works when exporting method for SRM or PRM. I'm wondering if there's a way to set the extraction window?


Thank you!

Brian Pratt responded:  2021-10-08

Hi Yunyun,

10 min far away from the Explicit retention time

That's surprising behavior. Normally if Skyline does not find a peak within an explicit RT window, it doesn't pick anything at all (this was not always the case, but has been true for several releases now - are you sure you are using the current release?)

I would be happy to have a look at this. Can you share your Skyline document (use File > Share > Complete to create a file) and one or two of your raw files, especially one where you are getting this 10 minute problem? You can upload to or we can arrange something more private if you prefer.

Thanks for using the Skyline support board!

Brian Pratt

yzhu338 responded:  2021-10-08

Hi brain,

Thank you for the timely response! Yes, I fixed it by updating to the newest version of Skyline, which is really nice. But I have another question about the Explicit retention time window, does it still only work when exporting method or it is to specify the chromatogram extraction window in the newer releases?

Thank you again!


Brian Pratt responded:  2021-10-08

The explicit retention time window is used in chromatogram extraction, yes. Skyline limits peak selection to the explicit RT window when one is provided.