Chromatogram Graph Properties

Chromatogram Graph Properties bobxiong  2022-06-10

Hi Skyline Team,

I am using Skyline as a visualization tool to display chromatograms for verification of data analysis results produced by vendors' DDA data analysis software. While going about this, I discovered that the chroma graph does not show any peak when my transition list contained say 1000 entries. Is there any way to not show the ion names in the chroma graph? My guess is that the ion names took all the space leaving no room for showing peaks. I have attached a screen shot on 40 entries in the transition list to help explain my experience in Skyline.

Thank you so much,

Bob Xiong, Ph.D.
Joinn Laboratories
Beijing, China
E-mail address:

Nick Shulman responded:  2022-06-10
It sounds like you are asking whether there is a way to hide the Legend on the chromatogram graph.
The Legend is the box which shows you the names of the transitions and which colors they are. If the Legend ever becomes larger than the graph itself, the graph ends up being completely blank.
You can hide the Legend by right-clicking on the chromatogram and unchecking the "Legend" menu item.

By the way, it looks like you might be trying to do something with crosslinked peptides in Skyline. You might find some useful information about crosslinked peptides on this page:

-- Nick
bobxiong responded:  2022-06-10
Hi Nick,

Thank you very much for your quick reply. I was not aware of the 2021 material on crosslink you provided via the url. I was using the small molecule interface in Skyline to handle the manually generated (Perl scripting) transition list. I am now excited about running the transition list using the tools you described.


bobxiong responded:  2022-07-07
Hi Nick,

I tried the crosslinker in Skyline. And I was confused by the automatically generated transitions (see attached). It looks like a bug to me.


Nick Shulman responded:  2022-07-07
Oops! Yes, that is a bug.
I will try to fix that in an upcoming release of Skyline-Daily.
When Skyline is deciding whether a particular fragment ion should be allowed, Skyline is only checking to make sure that either both ends of the crosslinker are contained in the fragment, or neither end of the crosslinker is contained. As you have pointed out, this incorrectly allows fragment ions which consist of two parts which are not attached to each other at all.
Thank you for reporting this bug.
-- Nick