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apply peak boundaries to all replicates

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apply peak boundaries to all replicates simon daled  2025-08-12 05:18
 

Hi,

Is there an option to apply the peak boundaries of one replicate to all other replicates based on the alligned retention times?
This would be interesting for us to do the analysis of some depletion experiments. For now I have tried the synchronized integration, but it doesn't change or synchronize the peak boundaries unless you manually adjust them. I have possibly found a workaround through the export peakboundaries option and then manually changing them, but enabling this in skyline would be a great help. Unless I overlooked the option of course...

Kind regards

Simon
 
 
Nick Shulman responded:  2025-08-12 07:41
If you have one replicate where you have chosen the boundaries correctly, you can use the menu item:
Edit > Integration > Apply Peak to All

That menu item also even when multiple things are selected are selected in the Targets tree so if you have picked the correct peak for every peptide in one particular replicate, you can select everything in the Targets tree and choose "Edit > Integration > Apply Peak to All".

We are working on a new "Peak boundary imputation" feature which will be available in an upcoming release. You can read about that here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=PeakImputation

-- Nick
 
simon daled responded:  2025-08-12 07:55
That is both simple and effective, thank you very much!