Chromatogram information unavailable for some peptides in PRM data

support
Chromatogram information unavailable for some peptides in PRM data afshari1  2026-03-12 12:47
 

Hello,
I am analyzing PRM data in Skyline and noticed that for several peptides the message “Chromatogram information unavailable” appears. These peptides were included in my PRM acquisition method, and the precursor m/z and charge state in Skyline match the method settings.

Could you please help me what the reason is?

 
 
Nick Shulman responded:  2026-03-12 12:54
With PRM data, the usual reason to get the "Chromatogram information unavailable" message is that there really were no MS2 spectra whose isolation window matched the precursor m/z of in the document.
The closeness by which the isolated m/z and the calculated precursor m/z need to match is controlled by the "Method match tolerance m/z" value on the "Instrument" tab at "Settings > Transition Settings".

If you send us your Skyline document and raw files we can tell you 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 may have been extracted.

The Share Document dialog gives you the option to include the results files. Alternatively, you can send those to use 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
-- Nick