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Multiple fragments per line in small molecule transition list import error

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Multiple fragments per line in small molecule transition list import error Chris Ashwood  2026-03-25 16:33
 
Dear Skyline Team,

I hope you're doing well. This is my first time trying the "multiple fragments per line" feature and I'm encountering an error:


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Skyline-daily
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Collection was modified; enumeration operation may not execute.
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OK More Info
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Skyline-daily (64-bit) 26.1.1.083 (019490f698)

System.InvalidOperationException: Collection was modified; enumeration operation may not execute.
   at System.ThrowHelper.ThrowInvalidOperationException(ExceptionResource resource)
   at System.Collections.Generic.List`1.Enumerator.MoveNextRare()
   at System.Linq.Enumerable.<SkipIterator>d__31`1.MoveNext()
   at pwiz.Skyline.FileUI.ImportTransitionListColumnSelectDlg.SetComboBoxTextExtra(List`1 columns, String text) in C:\proj\daily\pwiz_tools\Skyline\FileUI\ImportTransitionListColumnSelectDlg.cs:line 888
   at pwiz.Skyline.FileUI.ImportTransitionListColumnSelectDlg.PopulateComboBoxes() in C:\proj\daily\pwiz_tools\Skyline\FileUI\ImportTransitionListColumnSelectDlg.cs:line 564
   at pwiz.Skyline.FileUI.ImportTransitionListColumnSelectDlg..ctor(MassListImporter importer, SrmDocument docCurrent, MassListInputs inputs, IdentityPath insertPath, Boolean assayLibrary) in C:\proj\daily\pwiz_tools\Skyline\FileUI\ImportTransitionListColumnSelectDlg.cs:line 210
   at pwiz.Skyline.SkylineWindow.ImportMassList(MassListInputs inputs, String description, Boolean assayLibrary, DOCUMENT_TYPE inputType) in C:\proj\daily\pwiz_tools\Skyline\SkylineFiles.cs:line 2191
   at pwiz.Skyline.Menus.EditMenu.Paste(String text) in C:\proj\daily\pwiz_tools\Skyline\Menus\EditMenu.cs:line 408
   at pwiz.Skyline.Menus.EditMenu.Paste() in C:\proj\daily\pwiz_tools\Skyline\Menus\EditMenu.cs:line 347
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And please find below my input text that I'm pasting in:
Molecule List Name    Molecule Name    Molecule Formula    Precursor Adduct    Precursor Mz    Precursor Charge    Product name    Product M/z    Product Charge    Product name    Product M/z    Product Charge
GlyCombo    (Hex)5 (NeuAc)2 (HexNAc)4    C84H140N6O62    [M-2H]    1111.392052    -2    NeuAc Loss    965.892052    -2    NeuGc Loss    957.892052    -2

Cheers,
Chris
 
 
Brian Pratt responded:  2026-03-25 20:46
Hi Chris,

I am able to reproduce the problem using the data you've supplied, thanks. Investigating!

Brian
 
Brian Pratt responded:  2026-03-26 09:06
The fix will appear in the next Skyline-Daily.

For the moment, if you delete the second set of product-related headers then set them by hand after pasting the file into Skyline, it should work just fine - but that's not the point, of course.

Thanks for being a great Skyline collaborator!

Brian
 
Chris Ashwood responded:  2026-03-26 12:58
Hi Brian,

Excellent news, glad you were able to reproduce the problem and identify a fix.

You’re welcome, it’s a cool feature that I’m excited to use.

Cheers,
Chris