Ion Mobility Library generation error

Ion Mobility Library generation error Susan Abbatiello  2021-03-16

Hi There!

I'm trying to use Skyline to optimize FAIMS CV values (using CV optimization, similar to CE optimization, from Skyline). After importing the results and observing which CV steps generate the best transmission, I am trying to pull the best FAIMS CV into an Ion Mobility library. When I click "use results", I get the following error. Any advice?


System.Reflection.TargetInvocationException: mismatch in precursor values ---> pwiz.Skyline.Util.AssumptionException: mismatch in precursor values
at pwiz.Skyline.Util.Assume.Fail(String error) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Util\Util.cs:line 2055
at pwiz.Skyline.Model.Results.IonMobilityFinder.ProcessChromInfo(ChromFileInfo fileInfo, ChromatogramGroupInfo chromInfo, PeptidePrecursorPair pair, TransitionGroupDocNode nodeGroup, Single tolerance, LibKey libKey) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\IonMobilityFinder.cs:line 248
at pwiz.Skyline.Model.Results.IonMobilityFinder.ProcessFile(ChromFileInfo fileInfo) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\IonMobilityFinder.cs:line 218
at pwiz.Skyline.Model.Results.IonMobilityFinder.FindIonMobilityPeaks() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\IonMobilityFinder.cs:line 124
at pwiz.Skyline.Model.IonMobility.IonMobilityLibrary.CreateFromResults(SrmDocument document, String documentFilePath, Boolean useHighEnergyOffset, IProgressMonitor progressMonitor) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\IonMobility\IonMobilityLibrary.cs:line 322
at pwiz.Skyline.SettingsUI.IonMobility.EditIonMobilityLibraryDlg.<>c__DisplayClass49_1.<GetIonMobilitiesFromResults>b__0(IProgressMonitor broker) in C:\proj\pwiz_x64\pwiz_tools\Skyline\SettingsUI\IonMobility\EditIonMobilityLibraryDlg.cs:line 582
at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action1 performWork) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 254 --- End of inner exception stack trace --- at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Util\Util.cs:line 1940 at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action1 performWork) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 204
at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 140
at pwiz.Skyline.SettingsUI.IonMobility.EditIonMobilityLibraryDlg.GetIonMobilitiesFromResults() in C:\proj\pwiz_x64\pwiz_tools\Skyline\SettingsUI\IonMobility\EditIonMobilityLibraryDlg.cs:line 586

Brian Pratt responded:  2021-03-16

Hi Sue,

That feature was written with continuously varying ion mobility data formats in mind - that is, data formats where a single retention time is associated with many scans with different ion mobilities (TIMS, drift tube etc.). FAIMS is a bit different since the RT is changing with each step in the CV cycle.

I'll have to look at the code and see how difficult it would be to lump, as it were, the scans within a single CV cycle for these purposes. I believe I already have some data from you that should be suited to that purpose.

At the very minimum it should not give an ugly message like this, of course.

Thanks for using the Skyline support board!

Brian Pratt

Brian Pratt responded:  2021-03-23

Hi Sue,

On reviewing the code, I see that it's actually flexible enough that it should work with FAIMS data, although I can imagine that it would have trouble with low intensity or narrow peaks depending how they break across the CV cycle. If you can point me at the particular file that threw this error that would be most helpful.