Hasmik,

I think the ratio that you are seeing there is probably the ratio to global standards.
In Skyline 21.2, we kind of messed up the display of ratios in the Targets tree. Specifically, the right-click menu which lets you choose which ratio to display is often not available, and so the way to control which ratio is displayed in the Targets tree is with the "Normalized to" right-click menu item on the Peak Areas graph.
This bug is going to be fixed in the next update of Skyline 21.2, which I think is going to be released in a few days.
I believe this all has been fixed in the latest Skyline-Daily.

Can you test this out in the latest Skyline-Daily and let me know if you see anything that does not seem to be working correctly?
Also, if it doesn't appear to be fixed, can you send us your Skyline document? You can use the "File > Share" menu item to create a .zip file and if that .zip file is too large to attach to this support request you can upload it here: https://skyline.ms/files.url

-- Nick

Hi Nick,
Thank you for the quick reply. Right click to normalize to fixed that problem. How about the second problem I am having with the report that's duplicating the transition with a note but doesn't show any values for it.

I don't have the latest version of Daily and prefer using this version so I don't have to change versions very frequently. Glad to hear this will be fixed in the next version.

Thanks again,
Hasmik

The column names are cut off in the screenshot that you posted, so I can't tell what I'm looking at.
Can you post a different screenshot? You can press "Alt-Print Screen" to copy to the clipboard the entire window that you are looking at.
-- Nick

Here is the updated version.

Thanks!

When you pivot on Isotope Label, the "Transition Note" column is supposed to be pivoted, so that you would see the columns "light Transition Note" and "heavy Transition Note".
I am not sure why you are seeing the Transition Note where you are seeing it.
You might be able to fix this by choosing "Reports > Edit Report" and then uncheck and check again the "Pivot Replicate Name" and "Pivot Isotope Label" checkboxes in the Report Editor.

If you would like, you can send me your report definition and Skyline document.
In order to make it so that the Skyline document contains your report definition, you can go to:
Settings > Document Settings > Reports
and check the box next to "PeptideQuant_AllResults".
After you do that, you can do:
File > Share
to create a .zip file containing your Skyline document including that report definition.
Then you can upload that .zip file here:
https://skyline.ms/files.url
-- Nick

Thanks for your help Nick.
unclicking and clicking pivot actually fixed my problem. This is great, and I appreciate your help.

Also, Mike has the daily version and the ratio issue is actually fixed in his latest version of the Daily.

Best,
Hasmik