Is this a multiple injection replicate?
When Skyline looks for the surrogate standard peak area for a particular analyte, Skyline will only look at peak areas that came from the same result file.

We also had a problem in Skyline 4.1 where, even if a standard was measured in all of the injections in a particular replicate, the standard would only be assigned an area for one of those injections (whichever injection had a peak closest to the explicit retention time). This bug has been fixed in Skyline-Daily, so I do not expect that it would be affecting you.

You should probably send us your Skyline document and raw files.

In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files.

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

Please also send us some of your raw files.

Is not a multiple injection replicate.

I shared my extraction results with the name of the file is 'results for skyline team' on sharing support

I am going to need to see your Skyline document in order to figure out what is going wrong.

In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

Can you send me that .zip file?

done see 'Untargeted_polar_BACK_UP_2018_04_18' document

It still does not look like you sent me the correct file.
You sent me a .sky file, but that is for some Skyline document that does not have any results in it.

Hi,

I am sorry but I can not send you the file with the results because they contain the name of the samples, and it's kind of confidential !

I shared a dataset without name see MS184399QEM_Ross_Birsoy_utargeted

It looks like you uploaded a .skyd file.

You should upload a .sky.zip file.

You might be having trouble with the fact that Microsoft Windows hides the filename extensions for some of the files. Here is a page which talks about how to show filename extensions in Windows Explorer:
https://www.cnet.com/how-to/always-show-file-extensions-in-file-explorer/

I uploaded with the .sky.zip file.

with the same name

Thank you for your help

In Skyline, you need to check the checkbox that is on the menu item:
Settings > Integrate All

When "Integrate All" is turned off, Skyline will refuse to integrate transition peaks that are even slightly off-center from the other transitions in the peak group. This is useful if you are designing an SRM experiment, and want to be informed about transitions that might have interference.
However, if you are doing any sort of quantification, then you definitely want to have "Integrate All" turned on.

We have plans to make this feature much less confusing in the next release of Skyline.

I activated 'integrate all' and it works.
thank you very much for your help