Unaligned retention time issue

Unaligned retention time issue dominik kopczynski28488  2022-11-14

We have an issue with Skyline which looks like a potential bug. Maybe you could have a look at it, here is the description:

  • We set up a scheduled targeted method for our lipidomics measurements with (among others) a retention time window from 13.9 to 15.9 min.
  • An example is shown in the attached Image Analyst-correct-retention-time.png. You can see that both chromatograms are aligned.
  • When importing the data (minimal example in: Test.zip), we get a shift in retention times as visible in Image Skyline-incorrect-retention-time.png.
  • However, this shift should not be there, it should be aligned.

Thank you for your support.

Nick Shulman responded:  2022-11-14
Can you send us your wiff files?

That would be "101122_NT_SL_Brain_Screening_conc_1.wiff" and "101122_NT_SL_Brain_Screening_conc_1.wiff.scan"?
If those files are less than 50MB you can attach them to this support request. You can upload larger files here:

-- Nick
dominik kopczynski28488 responded:  2022-11-15
Thank you for the reply. Sure, here are the requested files attached.
Nick Shulman responded:  2022-11-15
Thank you for sending that .wiff file.
I used ProteoWizard SeeMS.exe to look at the chromatograms in that file.
There are three different chromatograms in the file which all have Q1 = 650.645 and Q3 = 632.634
Skyline does not have any way of distinguishing them since the Q1 and Q3 values are exactly the same, so Skyline just uses the first chromatogram that it finds with the closest m/z match.
If you need to have both sets of chromatograms in your wiff file, you will need to do something so that Skyline will be able to figure out which chromatograms to use. In your acquisition method, could you make it so that the the chromatograms for different molecules have different Q1 values? When Skyline is trying to figure out which chromatograms go with which molecules in your document Skyline first groups the chromatograms by Q1 value, and then figures out which group of chromatograms has the most matches of Q3 values to transitions product m/z's.
-- Nick