I am not sure I understand which numbers you want to take the ratio of.
It might be helpful if 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

The "Absolute Quantification" tutorial will show you how to use calibration curves in Skyline:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_absolute_quant
I am not sure whether what you are trying to do is the usual sort of calibration curves that Skyline knows how to do, or whether there is something different about your data.
-- Nick

Hi Nick,

Thank you for your answer. I already did a quantification with the calibration using only light peptides (external calibration) because i do not have heavy peptide to do Ratio light to heavy.

Generally, we compare the ratio found between the two ion (quantification ion and qualification ion) for each peptide in standard and the ratio found in unknown sample. The ratio should be same with an acceptable variation of 20-30%.

I want to generate this Ratio in Skyline. Is it possible.

Thank you,

Skyline will calculate something called the "Qualitative Ion Ratio".
There are some screenshots showing how this works on the following page:
https://github.com/ProteoWizard/pwiz/pull/1165

In order to get Skyline to calculate the Qualitative Ion Ratio you need to mark one of the transitions as non-quantitative, which you can do by right-clicking on a Transition in the Targets tree and unchecking the '"Quantitative" menu item.

Does this answer your question? It might be that you were asking about something else.
-- Nick