Chromatogram Information Unavailable

support
Chromatogram Information Unavailable sjmzy23  2025-03-08 06:27
 

Hi Support Team,

I'm using Skyline (v23.1) for a targeted lipidomic assay with UPLC-MS/MS data. Waters developed the method, and I obtained the transition list from a former PhD student. There should not be any issues with the transition list. While I can see PA/LPA chromatograms in MassLynx, they show "Chromatogram Information Unavailable" when imported into Skyline. Since all my other results were processed in Skyline, I also need to extract PA/LPA data there. I have attached my example skyline file with one of my raw data. Please let me know if there is a way to resolve this issue.

Best Wishes,
JS

 
 
Nick Shulman responded:  2025-03-08 09:08
Can you send us your Skyline document?
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

Files which are less than 50MB can be attached to these support requests.
You can always upload larger files here:
https://skyline.ms/files.url

The usual reason that you will see "Chromatogram information unavailable" with SRM data like you have is that there really was no chromatogram in the .raw file whose Q1 and Q3 values matched the precursor and product m/z values of the transitions in your document. The closeness that these numbers are required to be for a match is controlled by the "Method match tolerance m/z" setting on the "Instrument" tab at "Settings > Transition Settings".
Another thing to keep in mind is that when Skyline is trying to figure out which group of SRM chromatograms belong to a particular group of transitions in the Skyline document with the same precursor, the Q1 values of the chromatograms in the group must exactly match each other.
Also, if you have set the "Explicit Retention Time" on any of your molecules, Skyline will ignore any SRM chromatogram whose time range does not overlap with the explicit retention time. If you are using Skyline 24.1 then you will usually see a warning about this output to the Immediate Window but earlier versions of Skyline will do this silently.

After I see your Skyline document I will probably be able to tell you exactly what is going wrong.
-- Nick
 
sjmzy23 responded:  2025-03-08 09:20
Please find the attached Skyline doc. I have tried to adjust the transition setting and reimport my results, but the same issue persists with my PA/LPA.

BW,
JS
 
Nick Shulman responded:  2025-03-08 09:36
Most of the molecules in that Skyline document do have a chromatogram. For the molecules that are missing their chromatograms there is nothing in the .raw file whose Q1 and Q3 values are at all close to the precursor and product m/z's of the Transition in the Skyline document

Is there a particular molecule in the document that is missing its chromatogram that you are thinking should have a chromatogram displayed in Skyline but says "Chromatogram information unavailable" instead?
Can you post a screenshot of what you are seeing in Skyline and maybe what you are seeing in MassLynx that makes you think Skyline is displaying the wrong thing?

I used ProteoWizard SeeMS.exe to see the list of chromatograms in the raw data, and it looks like Skyline is correctly displaying everything that you would expect it to.
-- Nick
 
sjmzy23 responded:  2025-03-08 10:52
Thanks for checking. I was expecting PA and LPA molecules, but after reviewing my raw data, it looks like the instrument only recorded targeted MRM/SRM transitions, excluding PA/LPA. I’ll need to verify this on the computer connected to the instrument rather than on Skyline. Apologies for the trouble!