I am not sure I understand your question. Can you send me your Skyline document?
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.
If that .zip file is less than 50MB, you can attach it to this support request.
Otherwise, you can upload it here:
What is the relationship between these heavy peptides, and the peptides that you want to measure? If you have spiked in heavy forms of the same peptides that you want to measure, then it would be unusual to call them global standards. You actually want each peptide to be normalized against the heavy form of itself, and the heavy forms of the other peptides would not figure into the calculation. In this case, you want to do "Ratio to heavy" normalization, and you don't want there to be any global standards at all.
Or, is this some collection of peptides that you spiked in that happen to be heavy but that do not have any real relationship to the other peptides in your document? In that case, yes, you would want to make them Global Standards.
I think I was mistaken when I said that Global Standards get removed from the dataset.
MSstats by default removes the iRT standards from the dataset, but the Global Standards remain there.