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Background correction no longer displayed (absent?)

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Background correction no longer displayed (absent?) niklas40639  2025-07-24 15:22
 

Hello,

I have noticed that skyline no longer displays a grey rectangle under peaks indicating background correction (see attached). I didn't pay very close attention to the timing, but it seems likely that this behavior resulted from the last update (24.1 -> 25.1). As far as I can tell, there is no way to enable/disable background correction during integration; it is a little difficult to tell, but it seems to me that no correction is being performed at all.

Is this a genuine bug, or is there a setting I am missing?

Thanks
Niklas
 
 
Nick Shulman responded:  2025-07-24 15:39
I am not sure why you aren't seeing background.
If you look at the value of "Background" in the Results Grid, is it zero, or some other number?
The Background values will be zero if you have checked the "Triggered chromatogram extraction" checkbox on the "Instrument" tab in "Transition Settings".
If you have checked that checkbox then you should uncheck that and reimport your chromatograms, because Triggered chromatogram extraction does a number of other weird things that you would not want unless you had a SureQuant acquisition method.

If Skyline's user interface is weird you can sometimes get things back to normal using the "Clear all saved settings" button on the "Miscellaneous" tab at "Tools > Options", but that's a drastic thing to do which will also delete all your custom reports, etc.

If you send us your Skyline document we might be able to figure out 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 extracted 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
 
niklas40639 responded:  2025-07-28 09:16
Indeed, 'triggered chromatogram extraction' was checked. Many thanks, I don't think I would have ever figured that out.