Can you send us your Skyline document?
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.

If that .zip file is less than 50MB you can attach it to this support request.
You can upload larger files here:
https://skyline.ms/files.url

-- Nick

Thank you for getting back to me I have uploaded the zipfile under name SS.

Best,
Sogol

Thank you for uploading that .zip file.

The problem is that you have chosen "Condition" as the "Identity Annotation".
If you do not have technical replicates, then you should probably leave the "Identity Annotation" dropdown blank.

The problem with telling Skyline that "Condition" is the Identity Annotation is that it's telling Skyline that you only have samples from two human beings from each of the conditions. For this reason, Skyline is not able to estimate what the variation might be between different humans with the same condition, so the p-value ends up being 1.

If, instead, you changed the Identity Annotation to blank, Skyline would think that each of your replicates came from a different human being, and would be able to give you a p-value put confidence intervals around the fold change values.
-- Nick

Thank you , but when I leave the annotation blank , it doesn't show me a group comparison grid anymore.

It works for me (see attached screenshots).

If it still does not work for you, then you should send me your new Skyline document.
-- Nick