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Multiple peaks view a majcher  2025-11-04 02:34
 

Dear Skyline team,
First of all,
Thank you very much for making skyline great! Its fantastic and I am adapting more and more workflows in Skyline.

I have an issue when I am trying to overlay two peaks (DDA mode). The chromatograms are then not displayed correctly and are distorted.

Is there a way how to fix it? Am I doing something wrong?

I am sending corresponding chromatograms attached.

Best,
Adam
 
 
Nick Shulman responded:  2025-11-04 03:36
When you extract MS2 chromatograms from DDA data, they do end up looking like that with long straight lines connecting the places where a matching precursor happens to have been selected for fragmentation.

MS2 DDA chromatograms are not useful for quantification but Skyline does allow you to extract them mainly so that you can have something to click on in the chromatogram graph to look at spectra.
--Nick