Have you tried using the "Edit > Integration > Apply Peak To All" menu item?
In the most recent Skyline-daily we have improved things so that that menu item works even when you have multiple peptides or molecules selected in the Targets tree.
Other than that, I do not have any good suggestions for improving things.

If you send us your Skyline document and your raw files we might be able to come up with helpful ideas.
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.
The Share Document dialog also gives you the option of including the raw files in the zip file, or you can send them to us separately.

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

Hi Nick,
That helps a lot, thank you!
it does apply the same integration to all the samples from the "Edit > Integration > Apply Peak To All", but unfortunately we need to go through the metabolites one by one and when you have a long list of compounds, it can be time consuming.
I'll check what kind of data I can share, and come back to you if any.
thanks a lot
Nihel