Skyline not seeing my Waters data

support
Skyline not seeing my Waters data ibrahim abouseada  2026-02-17 09:48
 
Hi,
I have product ion (daughter) scan data from a Xevo TQ I want to use Skyline to parse through the data and pick out and optimize transitions. When I try to import the data I get an error message (see attached file). I've tried importing the .raw file and converting to a .mzML file and still have the same issue.
 
 
Nick Shulman responded:  2026-02-17 12:20
Can you send us your Skyline document and your .raw folder?
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 it managed to read from the imported results.

If you have imported results, the Share Document dialog will allow you to include the .raw folders or .mzML files in the .zip.
Alternatively, you could zip those up and send them to us separately.

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 would see "Chromatogram information unavailable" with triple quad SRM data is that there really were no chromatograms in the raw file whose Q1 and Q3 values matched the precursor and product m/z values of the transitions in your Skyline document.
The setting which controls how closely those numbers need to match is the "Method match tolerance m/z" value on the "Instrument" tab at "Settings > Transition Settings".

After we see your Skyline document and raw data files we will probably be able to figure out what is going wrong.
-- Nick