In your screenshot, it looks like you have extracted chromatograms for heavy-labeled versions of ADPGlc (C16H25N5O15P2) with between zero and sixteen 13C atoms.
What sort of an experiment was this, and how was the labeling performed?
Skyline does not do a good job working with data where the precise amount of labelling is not known. The place that we usually run into this limitation is when analyzing data from 15N labeling experiments, where many, but not all, of the nitrogen atoms in peptides will be heavy.
In a 15N experiment like that, there are always two populations of molecules which are very clearly separated by several Daltons of mass, but Skyline does not really know how to quantify them because the heavy-labeled population does not have a simple mass distribution that can be modeled as coming from elements with known isotope distributions.
If you would like, you could send us your Skyline document, and we might be able to offer different advice.
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
tempsnip.png