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Flat line instead of peak MRM transition for small molecules

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Flat line instead of peak MRM transition for small molecules yasmin kadyrbekova  2025-11-14 03:14
 

To whom it may concern,

I have a problem with the imported data from SCIEX. I haven't seen it before and I've been using Skyline for 2 years now. In SCIEX files the chromatogram looks normal and there is the small peak at 6.7 min but in Skyline it's just a flat line (see the attached file). I tried to download the newest version and it didn't help. I tried to re-import files and it didn't help either. Could you help me?

Kind regards,
YK
 
 
Nick Shulman responded:  2025-11-14 05:29
In your screenshot, I think the reason that the chromatogram goes flat like that is that the actual chromatogram ended at 6.7 minutes.
If you right-click on the chromatogram and choose "Transform > None" that flat portion will probably disappear.
But if you choose "Transform > Interpolated" then you see that flat portion.

When Skyline is doing peak detection on SRM chromatograms, Skyline first groups all of the chromatograms by Q1 value.
Then, Skyline interpolates the chromatograms so that the points are evenly spaced in the time dimension.
And then Skyline looks for peaks in these grouped chromatograms.

If you send us your Skyline document we can give you a more detailed description of what is going on.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including chromatograms.

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url
-- Nick