Re-align RT peaks in chromatograms

Re-align RT peaks in chromatograms mhhur  2022-06-17 13:43

Hello Skyline team,

I have a question about the large RT shifting issue among chromatograms. I am trying to find peaks in each other chromatogram for the presence of each RT peak in a chromatogram. I have developed an automated isomer detection algorithm in Skyline and mostly, it works very well but in some cases, it doesn't work because of the large RT shifting issue. By any chance, are there any features in Skyline to realign chromatograms? Or do you know any solutions to fix the large RT shifting issue between chromatograms?

Thank you,

Nick Shulman responded:  2022-06-17 15:03
I believe that it might be possible to accomplish some of what you are describing using the iRT feature:

With iRT, you create a database of normalized retention times, and designate some of the easier-to-detect molecules as "standards", and Skyline knows to look for the other molecules based on the retention time where the standards were found.

Is that what you are asking for?

We might be able to give you better answers if you send us your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms. If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:

-- Nick
mhhur responded:  2022-06-22 13:29
It is helpful. Thank you, Nick!