Error on line XX at column YY

support
Error on line XX at column YY nikolaos psychogios  2025-11-12 10:49
 
Dear Skyline experts,

A Skyline file that I worked on last week suddenly cannot be accessed today. I tried it to open it from several computers, but I'm getting the same error message.
"The file contains an error on line 491 at column 227"

I noticed that other users have seen similar errors, but I'm not sure if I need to edit the relevant .sky file in Text at the specific line, column where the error appears and what exactly should I change. Any help would be appreciated.

Best,
Nick

Below is the message generated from "More info"

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Skyline
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Failure opening Q:\Nick\Act-A_GDF-8\20251107\20251107_ActA_GDF8_C5171006_hum_serum.sky.
The file contains an error on line 491 at column 227.
---------------------------
OK More Info
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Skyline (64-bit) 25.1.0.142 (7401c644b4)

System.Reflection.TargetInvocationException: There is an error in XML document (491, 227). ---> System.InvalidOperationException: There is an error in XML document (491, 227). ---> System.Reflection.TargetInvocationException: Exception has been thrown by the target of an invocation. ---> System.Reflection.TargetInvocationException: Exception has been thrown by the target of an invocation. ---> System.Reflection.TargetInvocationException: Exception has been thrown by the target of an invocation. ---> System.Xml.XmlException: '~', hexadecimal value 0x1A, is an invalid character. Line 491, position 227.
   at System.Xml.XmlTextReaderImpl.Throw(Exception e)
   at System.Xml.XmlTextReaderImpl.ParseAttributeValueSlow(Int32 curPos, Char quoteChar, NodeData attr)
   at System.Xml.XmlTextReaderImpl.ParseAttributes()
   at System.Xml.XmlTextReaderImpl.ParseElement()
   at System.Xml.XmlTextReaderImpl.ParseElementContent()
   at pwiz.Skyline.Model.Results.ChromatogramSet.ReadXml(XmlReader reader) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\Chromatogram.cs:line 773
   at pwiz.Skyline.Model.Results.ChromatogramSet.Deserialize(XmlReader reader) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\Chromatogram.cs:line 709
   --- End of inner exception stack trace ---
   at System.RuntimeMethodHandle.InvokeMethod(Object target, Object[] arguments, Signature sig, Boolean constructor)
   at System.Reflection.RuntimeMethodInfo.UnsafeInvokeInternal(Object obj, Object[] parameters, Object[] arguments)
   at System.Reflection.RuntimeMethodInfo.Invoke(Object obj, BindingFlags invokeAttr, Binder binder, Object[] parameters, CultureInfo culture)
   at System.RuntimeType.InvokeMember(String name, BindingFlags bindingFlags, Binder binder, Object target, Object[] providedArgs, ParameterModifier[] modifiers, CultureInfo culture, String[] namedParams)
   at pwiz.Skyline.Util.XmlElementHelper`1.Deserialize(XmlReader reader) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Util\Xml.cs:line 1179
   at pwiz.Skyline.Util.XmlUtil.ReadElements[TItem](XmlReader reader, List`1 list, IXmlElementHelper`1[] helpers) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Util\Xml.cs:line 858
   at pwiz.Skyline.Model.Results.MeasuredResults.ReadXml(XmlReader reader) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\MeasuredResults.cs:line 1322
   at pwiz.Skyline.Model.Results.MeasuredResults.Deserialize(XmlReader reader) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\MeasuredResults.cs:line 1305
   --- End of inner exception stack trace ---
   at System.RuntimeMethodHandle.InvokeMethod(Object target, Object[] arguments, Signature sig, Boolean constructor)
   at System.Reflection.RuntimeMethodInfo.UnsafeInvokeInternal(Object obj, Object[] parameters, Object[] arguments)
   at System.Reflection.RuntimeMethodInfo.Invoke(Object obj, BindingFlags invokeAttr, Binder binder, Object[] parameters, CultureInfo culture)
   at System.RuntimeType.InvokeMember(String name, BindingFlags bindingFlags, Binder binder, Object target, Object[] providedArgs, ParameterModifier[] modifiers, CultureInfo culture, String[] namedParams)
   at pwiz.Skyline.Util.XmlElementHelper`1.Deserialize(XmlReader reader) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Util\Xml.cs:line 1179
   at pwiz.Skyline.Util.XmlUtil.DeserializeElement[TObj](XmlReader reader, Enum name) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Util\Xml.cs:line 893
   at pwiz.Skyline.Model.DocSettings.SrmSettings.ReadXml(XmlReader reader) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\DocSettings\SrmSettings.cs:line 2228
   at pwiz.Skyline.Model.DocSettings.SrmSettings.Deserialize(XmlReader reader) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\DocSettings\SrmSettings.cs:line 2204
   --- End of inner exception stack trace ---
   at System.RuntimeMethodHandle.InvokeMethod(Object target, Object[] arguments, Signature sig, Boolean constructor)
   at System.Reflection.RuntimeMethodInfo.UnsafeInvokeInternal(Object obj, Object[] parameters, Object[] arguments)
   at System.Reflection.RuntimeMethodInfo.Invoke(Object obj, BindingFlags invokeAttr, Binder binder, Object[] parameters, CultureInfo culture)
   at System.RuntimeType.InvokeMember(String name, BindingFlags bindingFlags, Binder binder, Object target, Object[] providedArgs, ParameterModifier[] modifiers, CultureInfo culture, String[] namedParams)
   at pwiz.Skyline.Util.XmlElementHelper`1.Deserialize(XmlReader reader) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Util\Xml.cs:line 1179
   at pwiz.Skyline.Util.XmlUtil.DeserializeElement[TObj](XmlReader reader, Enum name) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Util\Xml.cs:line 893
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadXml(XmlReader reader) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 613
   at pwiz.Skyline.Model.SrmDocument.ReadXml(XmlReader reader) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\SrmDocument.cs:line 2159
   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__DisplayClass771_0.<OpenFile>b__0(IProgressMonitor progressMonitor) in C:\proj\skyline_25_1\pwiz_tools\Skyline\SkylineFiles.cs:line 325
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\skyline_25_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_25_1\pwiz_tools\Skyline\Util\Util.cs:line 1926
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_25_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_25_1\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 140
   at pwiz.Skyline.SkylineWindow.OpenFile(String path, FormEx parentWindow) in C:\proj\skyline_25_1\pwiz_tools\Skyline\SkylineFiles.cs:line 341
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Nick Shulman responded:  2025-11-12 12:03
Can you send us that file "20251107_ActA_GDF8_C5171006_hum_serum.sky"?
If that 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

-- Nick
 
nikolaos psychogios responded:  2025-11-12 12:42
Thanks Nick,

I have uploaded the skyline file you requested.

Best,
Nick
 
Nick Shulman responded:  2025-11-12 13:24
Thank you for uploading that .sky file.
It looks like a whole 32KB chunk of data in that file has been corrupted and replaced with meaningless bytes.
There probably won't be anything that we could do to recover that data.
-- Nick