Dear Skyline team,
I have a question about using MS stats to process PRM experiments in skyline. My proteomics sample is SILAC labeled with heavy lysine. So I need to use the light to heavy ratio for quantification. I have successfully set up the PRM experiment with targeted list in skyline. But I think the MS stats is using the raw intensity instead of the ratio to generate all the plots like profile plot and condition plots, counting all the light and heavy peptides as peptides belong to the protein. As shown in the screenshot, I tried to adjust the MSStats Document Grid to include the ratio and delete the intensity, but the MSstats won't work on the new document grid, showing the error message. Can you help me with this problem?

Thanks a lot!
Ling