Chromatogram information unavailable - metabolomics sarahmacpherson676  2019-07-10

I am trying to analyze the metabolomics of a 13C-glucose labeling experiment using Skyline. The samples were run on Agilent 7890 GC and the .d directory files seem to upload successfully onto Skyline. However the Chromatograms are not visible with the message "Chromatogram information unavailable". I've increased the method match tolerance m/z, but still no luck.
The files are attached below.
Thanks for your help!

Nick Shulman responded:  2019-07-10

That .zip file contains several Agilent .d directories. When I open those in ProteoWizard SeeMS.exe, it looks like those only contain MS1 scans. Is that what they are supposed to look like?

Can you send us your Skyline document? (no Skyline document was inside of the .zip file you uploaded)

In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files, including whatever chromatograms Skyline managed to extract.

If that .zip file is less than 50MB then you can attach it to this support request.
Otherwise, you can upload it here:

-- Nick
sarahmacpherson676 responded:  2019-07-11
Yes the file does contain a few .d directories. We should be able to get the chromatograms since the lab that sent me the data said that these files work on Masshunter.
Attached is the Skyline document (I only input a small transition list). Samples were run on GC/MS 7890 with 5975 selective detector.
Thanks so much for your help!
Brian Pratt responded:  2019-07-11
As Nick points out, the files contain only MS1 data - but you have Skyline configured to look at only MS2 data.

Go to Transition Settings, select the Filter tab, and change Ion Types from "f" to "f,p" (that is from "fragments" to "fragments and precursors") and you'll see at least some chromatograms.


Brian Pratt
sarahmacpherson676 responded:  2019-07-12
Of course! Working now
Thank you so much!