Skyline does not have the ability to use the other slope and intercept to calculate the concentration of your peptides like that.
If all that you cared about was the slope, you could achieve this by using the Document Grid to set the "Internal Standard Concentration" for the peptide. Skyline will multiply the Internal Standard Concentration by the ratio to heavy in order to get the calculated concentration.
I could imagine that you might be able to achieve what you want in Microsoft Excel. You can use the Document Grid to export the slope and intercept of the calibration curve.
We have gotten several requests to be able to use other molecules' calibration curves. One example is here:
We might be able to implement this in a future version of Skyline. It might be helpful if you could send us your Skyline document and so we can make sure that the future feature will solve your needs.
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. Otherwise, you can upload it here: