How to export figure legends and Skyline transitions' color codes

How to export figure legends and Skyline transitions' color codes wangqingok  2022-03-16

Dear Skyline Team,

We are in the process of analyzing about 2 thousand peptides, and we exported the picture by just Right Click on the image and then choose "Save Image As...". and when we were checking the images, we have 2000+ of them, today and we found that the image we saved is an ".emf" file and THE FIGURE LEGEND WAS NOT ON EACH PICTURE. This is surprising. When we do just copy and paste the Metafile on each picture, the figure legend is preserved into the picture.

So rather than redo everything, I want to ask about is there a way to export just Figure Legends for all the peptides and fragmented ions from a skyline file in a batch process way? And how does skyline decide which color is assigned to which ion? We have a lot of pictures like these, and we already know which peptide sequence each of such picture is representing, but we do not know the transitions and ions without keeping the figure legend. Please help. We have 2k + pictures and sequences like the one attached.

Nick Shulman responded:  2022-03-16
Are you saying that you do not see a legend on the "2909.emf" file that you have attached?
When I open that file in MSPaint, I see a legend at the of each of the two graph panes.
What software are you using to look at that file? Can you post a screenshot of what you see?
-- Nick
Nick Shulman responded:  2022-03-16
By the way, if you want to see the list of colors that Skyline uses, or change the colors, you can go to:
Tools > Options > Display
If you choose "Edit Current" from the dropdown, you can see the two lists of colors that Skyline uses when displaying Transitions or Precursors.
The first transition is given the first color in the list, etc.
-- Nick