This is not currently possible in the Skyline UI. Our multi-peptide chromatogram graph shows only the total chromatograms for the peptides. If you want this graph as a plot for a paper or poster, you would need to create it yourself in a tool like R or Python. You can get the chromatogram points from Skyline in several ways, including:

1. A report using the fields under TransitionResults.Chromatogram
2. Show the plot you want the values from in Skyline, right-click and choose Copy Data. Then paste into Excel or a text editor

Hope this helps. Sorry, we don't have exactly the feature you were hoping for.

--Brendan