Failure attempting to modify the Skyline document with SWATH spectral library search data

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Failure attempting to modify the Skyline document with SWATH spectral library search data Chinmaya k  2021-08-25
 
Hello,

I am trying to search SWATH data against a Prosit-generated spectral library. However, when I tried to reintegrate the peaks using a mProphet model, the Skyline is not able to reintegrate the all peaks with a decoy trained mProphet model.

What could be the reason for this failure? Can you please help me to resolve the issue?

Please find the below error message for your reference.

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Skyline
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Failure attempting to modify the document.
Unexpected document change during operation.
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OK More Info
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System.IO.InvalidDataException: Unexpected document change during operation.
   at pwiz.Skyline.Menus.RefineMenu.<>c__DisplayClass5_1.<ShowReintegrateDialog>b__0(SrmDocument doc) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Menus\RefineMenu.cs:line 76
   at pwiz.Skyline.SkylineWindow.ModifyDocumentInner(Func`2 act, Action onModifying, Action onModified, String description, Func`2 logFunc, AuditLogEntry& resultEntry) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Skyline.cs:line 786
   at pwiz.Skyline.SkylineWindow.ModifyDocumentOrThrow(String description, IUndoState undoState, Func`2 act, Action onModifying, Action onModified, Func`2 logFunc) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Skyline.cs:line 755
   at pwiz.Skyline.SkylineWindow.ModifyDocument(String description, IUndoState undoState, Func`2 act, Action onModifying, Action onModified, Func`2 logFunc) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Skyline.cs:line 732
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Thank you,
Chinmaya
 
 
Nick Shulman responded:  2021-08-25
Chinmaya,

How many times has this error happened to you? This looks like the sort of error that might happen if Skyline happened to be doing something else at the same time as you were using the Refine Dialog. For instance, Skyline uses a web service in the background to go and fill in extra information about the proteins in your document. If Skyline happened to get a response from the web service at the same time as you were using the Refine dialog, this sort of an error might happen. If you were to try to do the same thing again, it might succeed the second time.

If this error keeps happening for you, it would be very helpful if you could send us your Skyline document. (It would probably be helpful to see your Skyline document in any case, so feel free to send it).

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:
https://skyline.ms/files.url

-- Nick
 
Chinmaya k responded:  2021-08-26
Hi Nick,

The reintegration model was kept failing. I observed that the iRT model was kept recalculating or refreshing on its own.

Since the skyline document size is too big (>300 GB), I could not compress it and share it with you.

I have also observed that, though I was trying to refine and reintegrate the peaks, there was no update in the "undo option" as it gets updated accordingly after each step. Finally, I saved the document, closed the Skyline, and reopened it. It worked perfectly.

Thank you for the support.

--
Chinmaya