Missing expected Retention Times

Missing expected Retention Times SW Test  2019-11-11

Hi Skyline Support,

We observe that if Skyline detects maxima at different retention times for the different charge states, it appears to use an Average value for the method for all the charge states. This results into incorrect Scheduled retention times in the MRM method generated by Skyline.

Please advise if this is a feature limitation for the current version? ...

Best Regards

Nick Shulman responded:  2019-11-11
I am not sure I understand your question. Can you send us your Skyline document?

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request. Otherwise you can upload it here:

My understanding is that different charge states always have the same retention time because charge is added to molecules after they have left the chromatography column.

SW Test responded:  2019-11-12
Hi Nick ,

Thanks for the quick response.
I have just uploaded via File > Share the .zip file and also a .doc file with images explaining the issue we have seen.

Best Regards
Nick Shulman responded:  2019-11-12

It looks like you have an SRM experiment, but the mass spectrometer only collected data for intact precursors, and there were no fragment ions.

Because of this, the only chromatograms that you are getting for each precursor is the intact precursor chromatogram itself.

Usually, Skyline makes it very difficult to chromatogram peaks at different times for precursors under the same precursor. However, if each precursor has only one SRM chromatogram, then I think Skyline can get confused during the peak finding part of chromatogram extraction, because Skyline is not confident about how the SRM chromatograms should be associated with the precursors.

It looks like you might not have not told your mass spectrometer to collect the data that you actually want. It might be helpful for you to take a look at the Targeted Method Editing tutorial:

-- Nick