ID marker bobxiong  2022-08-09 01:39

Hi Skyline Team,

Is there a way to manually set the ID marker in the chromatogram? I would like to explore the exported peak area data based on the manually "identified" peaks rather than what Skyline picked out. Screenshot attached.

Thanks a lot,

Bob Xiong, Ph.D.
Joinn Laboratories
Beijing, China
Email address:

Nick Shulman responded:  2022-08-09 07:32
There are a couple of different ways to choose a different chromatogram peak.
One way is to click on the text that is displayed on top of the peak. That is, there are three lines of text above that peak saying "12.5 +0.1ppm (idotp 0.92)". If you click anywhere on that text, Skyline will choose that peak instead of the one that is currently selected.

You can tell which peak is currently selected because Skyline displays a small black triangle which points to the right. Another way to tell which is the currently selected peak is that the vertical dotted lines will be black instead of gray.

A different way to adjust peak boundaries is to point the mouse at one of the black vertical dotted lines, and then click and drag to move the location of that line.

A third way to adjust peak boundaries is to point the mouse at a location below the X-axis, and then click and drag horizontally to indicate the start and end locations of the newly chosen peak.

Your question mentioned the "ID" marker, which made me think that you were going to ask about the lines labeled with the text "ID" which are sometimes shown on a chromatogram. There are no ID lines like that in your screenshot. If you have a spectral library which contain peptide search results from the file that you are looking at, Skyline will display vertical lines with the word "ID" on top of them which indicate the exact times of the peptide spectrum matches. There is no way to move these ID lines, but it sounds like what you really wanted to do was choose a different peak.

-- Nick
bobxiong responded:  2022-08-09 17:53
Hi Nick,

Thanks for your thoughtful explanation. You were right that I was using the term "ID" loosely. I wanted a different peak, like you pointed out.

As always, much appreciated.