• Sign In
  1. Requests

Error when Merging Skyline Documents with Same Target lists, when using iRT molecules

support

View Request

view list print
Error when Merging Skyline Documents with Same Target lists, when using iRT molecules Will Thompson  2024-11-19 14:12
 
Hi Skyline Team,

I've got what I think may be a buggy edge case where I can't seem to be able to merge two skyline documents. The documents are attached. The error I get is pasted below, and I think it might be because I have some of the compounds listed twice in each Skyline document, once to use them for iRT alignment, and the second time as an internal standard. (It's a bit of a problem in Skyline currently that you don't allow a molecule to be used both as an iRT marker, and an internal standard for quantitative purposes...therefore I need to list some molecules twice under different molecule groups).

Thanks for looking into this. If it's a bug you can help me work around in the interim by 'force' merging these two documents for me, I'd be indebted.

Cheers

Will

Skyline-daily (64-bit) 24.1.1.284 (bc93c2813)

System.IO.InvalidDataException: The peptide 13C4/15N2 L-Asparagine (Asn ) was found multiple times with user modifications. ---> System.IO.InvalidDataException: The peptide 13C4/15N2 L-Asparagine (Asn ) was found multiple times with user modifications.
   at pwiz.Skyline.Model.SrmDocument.MergeMatchingPeptidesUserInfo(IList`1 peptideGroupsNew) in C:\proj\pwiz\pwiz_tools\Skyline\Model\SrmDocument.cs:line 1353
   at pwiz.Skyline.Model.SrmDocument.ImportDocumentXml(TextReader reader, String filePath, MergeAction resultsAction, Boolean mergePeptides, FindLibrary findLibrary, MappedList`2 staticMods, MappedList`2 heavyMods, IdentityPath to, IdentityPath& firstAdded, IdentityPath& nextAdd, Boolean pasteToPeptideList) in C:\proj\pwiz\pwiz_tools\Skyline\Model\SrmDocument.cs:line 1262
   at pwiz.Skyline.SkylineWindow.ImportFiles(SrmDocument docOrig, ILongWaitBroker longWaitBroker, IList`1 filePaths, MergeAction resultsAction, Boolean mergePeptides, IdentityPath to, IdentityPath& firstAdded) in C:\proj\pwiz\pwiz_tools\Skyline\SkylineFiles.cs:line 2671
   at pwiz.Skyline.SkylineWindow.<>c__DisplayClass833_0.<ImportFiles>b__2(ILongWaitBroker longWaitBroker) in C:\proj\pwiz\pwiz_tools\Skyline\SkylineFiles.cs:line 2621
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\pwiz\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\pwiz_tools\Skyline\Util\Util.cs:line 1920
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\pwiz\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 202
   at pwiz.Skyline.SkylineWindow.ImportFiles(String[] filePaths) in C:\proj\pwiz\pwiz_tools\Skyline\SkylineFiles.cs:line 2629
   at pwiz.Skyline.SkylineWindow.importDocumentMenuItem_Click(Object sender, EventArgs e) in C:\proj\pwiz\pwiz_tools\Skyline\SkylineFiles.cs:line 2579
 
 
Brian Pratt responded:  2024-11-19 14:18

Hi Will,

Can you upload the files to http://skyline.ms/files.url ? I think they were too large to attach here.

Thanks,

Brian
 
Will Thompson responded:  2024-11-19 14:48

Uploading now. Plate 11A and 11B. Thanks Brian!
 
Nick Shulman responded:  2024-11-19 15:32
Thanks for reporting this.
In order for this error to happen, "Merge Matching Molecules" needs to be checked on the "How do you want to handle document results for this import?" dialog.
Skyline is complaining because both Asparagine's have had their peak boundaries adjusted. Skyline could certainly be smarter about this, because I think the peak boundaries for the molecules are identical because the boundaries were adjusted using the "File > Import > Peak Boundaries". Also, the molecules are in different Molecule Lists which are the same in the two documents, but Skyline currently ignores the molecule list when merging molecules.

It will probably take us a few weeks to figure out how to fix this because I am not sure whether we know exactly why it was implemented the way that is right now.
-- Nick
 
Will Thompson responded:  2024-11-19 15:45
Thanks Nick.

Are you saying that if I hadn’t adjusted the peak boundaries, I could have merged the documents? We are using automation to do the peak boundary adjustment, so I think I can merge them and then rerun the algo to fix again, if you think that will work.

Cheers

Will
 
Nick Shulman responded:  2024-11-19 16:22
Yes.

You can reset all of the peak boundaries back to their original boundaries by going to:
Refine > Reintegrate
Make sure that "Peak scoring model" is set to default, "Integrate all peaks" is selected and "Overwrite manual integration" is checked.

If you do that in the Plate B document then you will be able to import the Plate B document into Plate A.
-- Nick