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.

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

Thank you for uploading your Skyline document.
The problem is that your heavy and light versions of the molecule are listed as separate molecules, and they need to be different precursors under the same molecule.
Here is a transition list which would work for your deuterium labeled Phenol Rutinoside:
Molecule Name,Molecular Formula,Precursor Adduct,Precursor m/z,Product m/z,Label Type,Product Charge
Phenol Rutinoside,C18 H26 O10,[M-H],401.1453,401.1453,light,-1
Phenol Rutinoside,C18 H26 O10,[M5D-H],406.1767,406.1767,heavy,-1

Here, the heavy and light versions have the same Molecular Formula, but the heavy one has an adduct with "5D" indicating that 5 of the hydrogens have been replaced with Deuterium.

You can learn more about adduct descriptions in Skyline here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=adduct_descriptions
-- Nick

Hi Nick,
Thanks for the help. I have set it up now with the light and heavy. Now when I view the cal curve, its not showing me the 5 levels. Sharing again.

It looks like the problem is that for one of your Unknown samples, the heavy peak area is a very small number.
For this reason, the Light:Heavy peak area ratio is a very big number relative to the values for all of the other replicates.
If you remove the replicate "Sample408090827_IS_SPE AA-r001_DI3.d.HRdm" from your dataset then your calibration curve will look much better.

If you want to remove to completely a point from the calibration curve you can first click on the point on the calibration curve to select that replicate and then right-click on the chromatogram graph and choose "Remove Peak".

-- Nick

Thanks Nick! Cal curve is beautiful!

Hi Nick,
Thanks for all the help! Just one more request. Please delete the shared file.

Best,
Sheher