Skyline lets you specify that a particular molecule should be normalized by doing the ratio to a different molecule in the document.
This feature is called "Surrogate Standards".
There is a description of how to use this feature here:
After you have imported your Transition List into Skyline, you can right click on Acetic, But, and Prop in the targets tree and choose "Set Standard Type > Surrogate Standard".
And then you can use the Document Grid to change the Normalization Method of your other molecules to the appropriate value ("Ratio to surrogate Acetic (heavy)" etc.).