Chromatogram information unavailable - Metabolomics

Chromatogram information unavailable - Metabolomics erin weisenhorn  2022-02-09


I am using Skyline daily (version to analyze PRM data collected on a Waters Q-Tof. I am starting to develop a PRM method for metabolites and exported an isolation list using Skyline. When I import results per the 'Small Molecule Targets' tutorial I am not able to view any of my chromatograms. I am also a new user to Skyline.

Thanks for your help!

Nick Shulman responded:  2022-02-09
Can you send us one of your .raw files, for instance "20220208_Top11_MRM_RADAR_Pos_1.raw"?
If that file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here:

I see that your settings at:
Settings > Transition Settings > Full Scan
have the MS/MS filtering acquisition method set to "PRM".

The fact that your transitions do not have any chromatograms probably means that there were no MS2 spectra in your raw file that matched a precursor which matched any of the precursors in your document.
After we see your .raw file, we will probably be able to tell you what you need to do to fix this.
-- Nick
erin weisenhorn responded:  2022-02-09
The raw file should be uploaded now.
Nick Shulman responded:  2022-02-09
Thank you for uploading that .raw file.
The m/z's of the precursors that were isolated in your raw file are different from what the m/z's are in Skyline.
For instance, Skyline thinks that Choline has an m/z of 105.1148, whereas the closest precursor in your raw file is 105.975.
Skyline allows you to adjust how closely those numbers need to match. You can change the "Method match tolerance m/z" at "Settings > Transition Settings > Instrument".
However, the maximum number that Skyline allows you to use for the method match tolerance is 0.6, which is not enough to rescue the chromatograms for that particular molecule. However, if you set the match tolerance to a higher number than what it already is (0.055), and then do "Edit > Manage Results > Reimport", you will see chromatograms for some of your molecules.

Do you know why the m/z's of the molecules in your Skyline document are different than what was isolated in your instrument method?
-- Nick
erin weisenhorn responded:  2022-02-10
I have a lot of skyline files and isolation lists I have created so it is possible things got jumbled.

It looks like Skyline can use the molecular formula to calculate precursor mass without inputting a m/z. Would this be a better way to do it moving forward? Using transitions from the literature it was a challenge to get the precursor mass and the mass calculated from the formula to agree when the adduct wasn't provided.
Nick Shulman responded:  2022-02-10
If you tell Skyline the chemical formula of your molecules, Skyline will always calculate the m/z for you.
If you want to use your own m/z values, then you need to not provide a formula when you insert your transition list. That is, your transition list should have the following columns:
Precursor Mz, Product Mz, Precursor Charge and Product Charge
and should not have the following columns:
Molecule Formula, Precursor Adduct, Product Ion Formula, Product Adduct

In your document, if I go to:
View > Document Grid
and choose the "Small Molecule Transition List" from the "Reports" dropdown I can see that you provided a chemical formula for your precursors but not for your transitions. Therefore, Skyline is calculating the m/z's for the precursors, and that might be why they do not match what you expect them to be.
-- Nick
erin weisenhorn responded:  2022-03-13
Hi Nick,

Thanks that helped clear some things up. I have corrected the precursor and product ion masses and also pared down the number of compounds I am looking at to shorten the duty cycle before I finalize the gradient and implement retention time scheduling. With those things, and widening the mass tolerance like you said earlier, I am still getting a 'Chromatogram information unavailable' error. Is there something else that could be causing this? Attached is a new Skyline file, please let me know if I need to upload another raw file.

Thank you
Nick Shulman responded:  2022-03-14
It looks like the problem is still that the precursor m/z's of the MS2 spectra in your .raw file are different than the precursor m/z's of the molecules in your Targets tree. As a result, you are not getting any MS2 chromatograms when you import results.

If you send me one of your raw files (e.g. "20220310_Top30_MRM_RADAR_Pos_1.raw") I could tell you more specifically what is going on.

-- Nick