Chromatogram information unvailable

Chromatogram information unvailable gazelezi  2024-02-13 12:42


I am a new Skyline user and trying to get some chromatographic information bout several target small molecules. Following the instructions from the site, I was able to insert a transition list and import raw file results from one of my test runs. Initially, I was able to see the chromatogram pieces of information for all the target molecules except for one. After several trials, I wasn't able to fix the issues.
So, I decided to reload the transition list and the raw files. After that, I could not see any chromatogram information for all target molecules. I would appreciate any help.

Attached is the file I am working on.

Nick Shulman responded:  2024-02-13 12:50
Can you send us a file?
In Skyline you can use the menu item:
File > Share
to create a .zip file which will contain your Skyline document (.sky file) as well as some supporting files including the extracted chromatograms (.skyd file) and maybe some other files.

It would also be helpful if you could include some of your .raw files. When you do "File > Share", Skyline will ask you if you want to include .raw files, or you could upload them separately.

Files which are less than 50MB can be attached to this support request. You can upload larger files here:

The usual reason that you get the "Chromatogram information unavailable" might be:
1. In an SRM experiment, the Q1 and Q3 values need to match the precursor and product m/z's in your document. How close they need to match is controlled by the "Method match tolerance m/z" setting at "Settings > Transition Settings > Instrument"
2. With full scan experiments, you might need to do something with the settings at "Settings > Transition Settings > Full Scan".
3. If you have set the "Explicit Retention Time" on any of your molecules, then Skyline may be discarding chromatograms which do not overlap with the Explicit Retention Time.

After we see your Skyline document and raw file(s) we will probably be able to tell you what is going on.
-- Nick
gazelezi responded:  2024-02-13 13:14
Hi Nick,

thank you for the prompt response. Please find attached the zip file.
Nick Shulman responded:  2024-02-13 13:35
Thanks for sending that .zip file.
Part of the problem is that the settings at "Settings > Transition Settings > Full Scan" are telling Skyline to only extract chromatograms from MS1 spectra, but the transitions in your Targets tree are all MS2 transitions.
You should go to:
Settings > Transition Settings > Full Scan
and choose something for the "Acquisition Method" under "MS/MS filtering".

If I could see one of your .raw files I could tell you what to choose for the Acquisition Method, but it should be "DIA" if you have told the mass spectrometer to select wide m/z windows for fragmentation, or "PRM" if you have given the mass spectrometer a list of m/z's to fragment.

After you have changed your Transition Full Scan settings you should tell Skyline to extract chromatograms again by pushing the "Reimport" button at "Edit > Manage Results".
-- Nick
gazelezi responded:  2024-02-13 14:13
It did work. I chose PRM for the acquisition mode based on my mass spectrometry method.

Thank you!