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Error when importing peak boundaries

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Error when importing peak boundaries Yasin  2024-08-04 16:34
 
Hi,

I am trying to import peak boundaries for small molecules. This works most of the time but sometimes I run into errors like the one below. I realize that I can change the names of my molecules (which are in my case just numbers) but this is sub-ideal when I want to retain ids to compare to other tools. Any chance this could be fixed? I have attached the file in case it helps. Also I am on a Windows 11 system.


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Skyline
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Failed reading the file E:\dt_skyline_boundaries.csv.
A protein sequence may not contain the character '5' at 0.
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OK More Info
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System.IO.InvalidDataException: A protein sequence may not contain the character '5' at 0. ---> System.IO.InvalidDataException: A protein sequence may not contain the character '5' at 0.
   at pwiz.Skyline.Model.FastaSequence.ValidateSequence(String seq) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\PeptideGroup.cs:line 293
   at pwiz.Skyline.Model.Peptide.Validate() in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Peptide.cs:line 388
   at pwiz.Skyline.Model.Peptide..ctor(FastaSequence fastaSequence, String sequence, Nullable`1 begin, Nullable`1 end, Int32 missedCleavages, Boolean isDecoy) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Peptide.cs:line 57
   at pwiz.Skyline.Model.ModificationMatcher.GetModifiedNode(String seq, FastaSequence fastaSequence) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 435
   at pwiz.Skyline.Model.PeakBoundaryImporter.Import(TextReader reader, IProgressMonitor progressMonitor, Int64 lineCount, Boolean isMinutes, Boolean removeMissing, Boolean changePeaks) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\ImportPeakBoundaries.cs:line 359
   at pwiz.Skyline.Model.PeakBoundaryImporter.Import(String inputFile, IProgressMonitor progressMonitor, Int64 lineCount, Boolean removeMissing, Boolean changePeaks) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\ImportPeakBoundaries.cs:line 236
   at pwiz.Skyline.SkylineWindow.<>c__DisplayClass793_0.<ImportPeakBoundaries>b__2(IProgressMonitor longWaitBroker) in C:\proj\skyline_23_1\pwiz_tools\Skyline\SkylineFiles.cs:line 1543
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\skyline_23_1\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\skyline_23_1\pwiz_tools\Skyline\Util\Util.cs:line 1920
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 202
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 140
   at pwiz.Skyline.SkylineWindow.ImportPeakBoundaries(String fileName, Int64 lineCount, String description) in C:\proj\skyline_23_1\pwiz_tools\Skyline\SkylineFiles.cs:line 1546
   at pwiz.Skyline.SkylineWindow.ImportPeakBoundariesFile(String peakBoundariesFile) in C:\proj\skyline_23_1\pwiz_tools\Skyline\SkylineFiles.cs:line 1517
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Nick Shulman responded:  2024-08-04 16:48
Can you send us your Skyline document?
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. You can always upload larger files here:
https://skyline.ms/files.url

I believe the way this works is that when you are importing peak boundaries into a small molecule document, Skyline first tries to find the molecule whose name matches what is in the "PeptideModifiedSequence" column, and, if it does not find a molecule with that name it gives you the error that it is not a valid peptide sequence.
It is unfortunate that the error message does not tell you the actual line that it was on when it got this error.

I imagine that one of those molecule names starting with "5" in the "PeptideModifiedSequence" column is not actually in your Skyline document. The one which is causing the problem might be "58" or "546" or "5342", or any of other molecule names which starts with 5.
After I see your Skyline document I will probably be able to tell you exactly which rows in your .csv file are causing problems. I will also try to fix Skyline in the future so that it gives you a more helpful error message.
-- Nick
 
Yasin responded:  2024-08-05 13:52
Thank you. For the quick response! I have attached the .zip file.

Best, Yasin
 
Nick Shulman responded:  2024-08-05 14:34
Thank you for sending that Skyline document.

I see that you are still using Skyline 23.1.
We released Skyline 24.1 a few weeks ago and you should definitely upgrade to it.

In Skyline 24.1 you will get an error message which tells you which line of the .csv file has an error on it.
The error messages involve "5268", "6064" and "9443".
If you remove the lines with those molecule names from your .csv file you will be able to import the peak boundaries without error.
-- Nick
 
Yasin responded:  2024-08-06 16:35
Thank you that solved it!