Chromatograms not displayed in metabolomics SRM analysis

Chromatograms not displayed in metabolomics SRM analysis toonstrac  2018-11-08


I am trying to analyze some metabolomics data using Skyline, but each time I upload the data, none of the chromatograms are visible ('Chromatogram information unavailable'). I can see the chromatograms as the files are uploading, but the chromatograms disappear after they are uploaded. I have uploaded a file (CHL_CE_Heavy_CHL_Palmitate_tr4). I am using a Waters Xevo TSQ. Please let me know if you need anything else. Thank you so much for your help.

Best Regards,


Brian Pratt responded:  2018-11-08
Hi Christian,

May I see the raw Waters file as well?


Brian Pratt
Nick Shulman responded:  2018-11-08
It looks like your chromatograms have m/z's that are whole numbers (e.g. 404, 668, etc).
The m/z's that Skyline has calculated for your molecules are 404.3887, 668.6340 etc.

There is a setting in Skyline that controls how close an SRM chromatogram has to be to the molecule in your Skyline document for Skyline to match them up. That setting is at:
Settings > Transition Settings > Instrument
and it is called "Method match tolerance m/z"

The default value of that setting is 0.055, but you can set it up as high as 0.6.

With the setting at 0.6, Skyline will correctly associate the chromatograms with your Cholesterol molecules. However, the Cholesterol Ester molecules are more than 0.6 units away from what's in your raw file, so the m/z match tolerance settings isn't going to fix those. You might want to delete those molecules, and insert them in a different way where instead of specifying the chemical formula, you just specify the exact m/z value you want Skyline to use.
-- Nick
toonstrac responded:  2018-11-08
Thank you so much Nick, that worked great!

Best Regards,