Skyline does not show ion traces anymore

Skyline does not show ion traces anymore dennis jakob  2023-05-09

Dear support,
Uploaded a file '' to file sharing.
The attached file is a skyline template and two raw data files from a Bruker QTOF.
I have been using this skyline template before and it always worked without issues.
It contains molecule lists of different lipid classes and their respective fragmentation precursors.
Now, chromatograms are shown during data import but are not visible afterwards anymore.
For the negative file at least a viel EICs are presented but in a seemingly random way throughout the lists.
Do you have an idea what the issue might be?
Best, Dennis

Nick Shulman responded:  2023-05-09
One thing that can prevent you from getting a chromatogram for a particular molecule is if the "Explicit Retention Time" is set to a number which is outside of the retention time range for which there are spectra available.
When I use the Document Grid to blank out the "Explicit Retention Time" values for all of your molecules and then reimport your file, some molecules (such as "TG 10:0_14:0_18:1") show chromatograms, but some other molecules (such as "MGDG 33:0;3_30:0;O (Isomer 1)") still show "Chromatogram information unavailable").

I will try to figure out what is going on with the molecules that still don't have chromatograms even after I set all of the Explicit Retention Time values to blank.
-- Nick
Nick Shulman responded:  2023-05-09
Actually, I see that you send us two results files for positive and negative ions and each of your molecules is only supposed to have chromatograms extracted from one or the other result file and not both.
It looks like everything will work correctly for you if you make sure that the Explicit Retention Time values are within the retention time range of the available spectra.
-- Nick
dennis jakob responded:  2023-05-24
Thank you very much.
That was exactly the issue. I won't forget this in the future.
- Dennis