Please give us more information about the error message you are seeing.
Error message dialogs in Skyline all have a button in the lower left corner which will copy the entire text of the message to the clipboard.
Can you send us the entire text of the message?
-- Nick

Hi, Nick,

Thank you very much. Below is the entire error message:

Best,
Bin-Yan
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Skyline
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Failure opening C:\Binyann\Work\Goldeneyes and eiders_Celine Arzel\2023 autumn\Goldeneye_Batch C\Goldeneye_BatchC.sky.
The file contains an error on line 832 at column 10.
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OK More Info
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System.Reflection.TargetInvocationException: There is an error in XML document (832, 10). ---> System.InvalidOperationException: There is an error in XML document (832, 10). ---> System.InvalidOperationException: Adduct "[M12C13+H]" calls for labeling more C atoms than are found in the molecule C'12C3H11I4NO4
   at pwiz.Skyline.Util.Adduct.ApplyIsotopeValues(ParsedMolecule molecule, Int32 massMultiplier, IDictionary`2 resultDict) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Util\Adduct.cs:line 1471
   at pwiz.Skyline.Model.SequenceMassCalc.GetPrecursorMass(CustomMolecule mol, TypedModifications typedMods, Adduct adductForIsotopeLabels, ParsedMolecule& isotopicFormula) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\SequenceUtil.cs:line 869
   at pwiz.Skyline.Model.TransitionGroupDocNode.CalcSelfPrecursorMZ(SrmSettings settings, ExplicitMods mods, IsotopeDistInfo& isotopeDist, TypedMass& mass) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\TransitionGroupDocNode.cs:line 808
   at pwiz.Skyline.Model.TransitionGroupDocNode..ctor(TransitionGroup id, Annotations annotations, SrmSettings settings, ExplicitMods mods, SpectrumHeaderInfo libInfo, ExplicitTransitionGroupValues explicitValues, Results`1 results, TransitionDocNode[] children, Boolean autoManageChildren) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\TransitionGroupDocNode.cs:line 77
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupXml(XmlReader reader, Peptide peptide, ExplicitMods mods) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1408
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupListXml(XmlReader reader, Peptide peptide, ExplicitMods mods) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1343
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideXml(XmlReader reader, PeptideGroup group, Boolean isCustomMolecule) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 983
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideListXml(XmlReader reader, PeptideGroup group) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 918
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupXml(XmlReader reader) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 888
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupListXml(XmlReader reader) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 667
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadXml(XmlReader reader) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 631
   at pwiz.Skyline.Model.SrmDocument.ReadXml(XmlReader reader) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\SrmDocument.cs:line 2151
   at System.Xml.Serialization.XmlSerializationReader.ReadSerializable(IXmlSerializable serializable, Boolean wrappedAny)
   at Microsoft.Xml.Serialization.GeneratedAssembly.XmlSerializationReaderSrmDocument.Read1_srm_settings()
   --- End of inner exception stack trace ---
   at System.Xml.Serialization.XmlSerializer.Deserialize(XmlReader xmlReader, String encodingStyle, XmlDeserializationEvents events)
   at pwiz.Skyline.SkylineWindow.<>c__DisplayClass746_0.<OpenFile>b__0(IProgressMonitor progressMonitor) in C:\proj\skyline_23_1\pwiz_tools\Skyline\SkylineFiles.cs:line 328
   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 1924
   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.OpenFile(String path, FormEx parentWindow) in C:\proj\skyline_23_1\pwiz_tools\Skyline\SkylineFiles.cs:line 345
---------------------------

Thank you for that error message.
The important part of the message is:
Adduct "[M12C13+H]" calls for labeling more C atoms than are found in the molecule C'12C3H11I4NO4

It sounds like something might have changed in Skyline so that a chemical formula that used to be acceptable now produces an error, but I do not know what it might be that changed.

Can you send me the file "Goldeneye_BatchC.sky"?
If that file is less than 50MB you can attach it to this support request.
You can upload larger files here:
https://skyline.ms/files.url
-- Nick

Hi, Nick,

Thanks. I attached the Skyline Document file here, and also the VIEW file and Skyline Chromatogram Data, just in case you need them.

Best,
Bin-Yan

You would be able to successfully open this document in Skyline 22.2.

You can install Skyline 22.2 by going to this page:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=install-64-disconnected_23_1
and then click on the "I agree" button and then the "Archive" link.

You can download the .zip file for "Skyline (64-bit) 22.2.0.527", unzip it, and run "setup.exe" which is in the unzipped folder.

Skyline version 23.1 cannot open that file.

There is a molecule in the file whose formula is "C'12C3H11I4NO4" and it has a precursor with the adduct "[M12C13+H]".
I am not an expert on adducts in Skyline, but I think that adduct is saying that 12 of the ordinary carbons in the chemical formula are supposed to be heavy carbons, and that is not possible.

Do you know what that molecule was actually supposed to be?
If you open your Skyline document using Skyline version 22.2, you might be able to fix things by either changing the definition of that molecule, or by deleting it from the document.

I will ask my coworkers and see if anyone has a better idea about what to do about this.
-- Nick

Hi,

Yes, it works for Skyline version 22.2. Thank you so much for your help!

Bin-Yan

Hi,

Forgot to say one thing. That chemical with the heavy carbon is essential to our analysis. We use that isotope to track the extraction efficiency. Nevertheless, perhaps it is possible to define that chemical in a different way in Skyline. I will discuss with our technician and see if that is possible. For the time being, I will just use Skyline version 22.

Thank you again very much for your tremendous help!

Bin-Yan

I will investigate the change in behavior. In the meantime you can work around it:
  - open the document in Skyline 22.2
  - right-click on the "T4-13C12-heavy" molecule in the Targets tree
  - choose Modify...
  - change the molecular formula from C'12C3H11I4NO4 to C15H11I4NO4
  - Click OK
  - Save the document (probably you should "Save As" to a new name until you are certain)
  - Open the document in the current Skyline to verify

What Skyline is complaining about is that the formula "C'12C3H11I4NO4" already has labeled carbon in it (C'12), so the adduct [M12C13+H] is asking for additional labeling (12C13) that can't be done.

Normally you declare labels in just the adduct, I'm not sure how Skyline allowed both in this case. Skyline normally handles this while importing the transition list by stripping the labels from the formula and putting them in the adduct description.

Best regards,

Brian Pratt