Shimadzu GC-MS

Shimadzu GC-MS victoria dorrer  2022-09-29

I am currently working with a Shimadzu GC-MS, hence the GCMSsolution Version 4.52. This software creates GC/MS Data File (.qgd) files (see attachement) which I cannot use in Skyline. Even if I try to convert it to mzXML (see attachement) in the software Skyline does not recognize the peaks within the data file. It still tells me chromatogram information unavailable. Did someone have similar problems with the combination Shimadzu and Skyline? If yes how was it solved?


PS: I work with Skyline regularly with files from Bruker and there I have no problems.

Nick Shulman responded:  2022-09-29
Can you send us your mzXML file and your Skyline document? We will figure out what is going wrong.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including whatever chromatograms have been extracted.

If that .zip file and your .mzXML file are less than 50MB you can attach them to this support request. You can upload larger files here:

"Chromatogram information unavailable" often means that there were not MS2 spectra whose isolation window matched the precursors in your Skyline document. This might have something to do with the settings at "Settings > Transition Settings > Full Scan", or it might have something to do with the mzXML file. We will probably be able to give you more information after we see your files.
-- Nick