Hi,
I have recently used Skyline for peptide absolute quantitation. Do you have the tutorial for getting started in Skyline with all the parameters (peptide settings, translation, modifications, instrumentation, etc.)?
I am not sure what questions you might have about settings.
If you send us your Skyline document and one or more of your .raw files we could take a look and let you know if anything looks wrong.
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 request.
You can always upload larger files here: https://skyline.ms/files.url
-- Nick