Error when opening saved Skyline files antoine lacour  2021-07-22
 

Hi,

I've recently upgraded to Skyline 21.1 (downloaded on 22/7/21) and I have the following error when opening a saved .sky file. This happens with old files from a different Skyline version but also with newly created and saved files.

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Skyline
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Failure opening U:\KTGS\Skyline test sample\Skyline test sample2.sky.
The file contains an error on line 81 at column 9.
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OK More Info
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System.Reflection.TargetInvocationException: There is an error in XML document (81, 9). ---> System.InvalidOperationException: There is an error in XML document (81, 9). ---> pwiz.Skyline.Util.AssumptionException: error reading mz values - declared mz value 325.13691 does not match calculated value 324.129085450091
   at pwiz.Skyline.Util.Assume.Fail(String error) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Util\Util.cs:line 2055
   at pwiz.Skyline.Model.Serialization.DocumentReader.ValidateSerializedVsCalculatedProductMz(Nullable`1 declaredProductMz, TransitionDocNode node) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1623
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionXml(XmlReader reader, TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist, ExplicitTransitionValues pre422ExplicitTransitionValues, CrosslinkBuilder crosslinkBuilder) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1606
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionListXml(XmlReader reader, TransitionGroupDocNode nodeGroup, ExplicitMods mods, ExplicitTransitionValues pre422ExplicitTransitionValues) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1466
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupXml(XmlReader reader, Peptide peptide, ExplicitMods mods) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1335
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupListXml(XmlReader reader, Peptide peptide, ExplicitMods mods) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1261
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideXml(XmlReader reader, PeptideGroup group, Boolean isCustomMolecule) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 908
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideListXml(XmlReader reader, PeptideGroup group) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 843
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupXml(XmlReader reader) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 813
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupListXml(XmlReader reader) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 654
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadXml(XmlReader reader) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 619
   at pwiz.Skyline.Model.SrmDocument.ReadXml(XmlReader reader) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 1998
   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__DisplayClass742_0.<OpenFile>b__0(IProgressMonitor progressMonitor) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 328
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\skyline_21_1_x64\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_21_1_x64\pwiz_tools\Skyline\Util\Util.cs:line 1940
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_21_1_x64\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_21_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 140
   at pwiz.Skyline.SkylineWindow.OpenFile(String path, FormEx parentWindow) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 345
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Any help would be appreciated!

Cheers,

Tony

 
 
Nick Shulman responded:  2021-07-22
If you send us that file "Skyline test sample2.sky" I can fix it for you.

If that file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here:
https://skyline.ms/files.url

This error is always caused by a bug in Skyline where Skyline had calculated a different value for the m/z of a transition when Skyline saved out the file, compared to what Skyline is calculating now. You can read more comments about this bug here:
https://skyline.ms/announcements/home/support/thread.view?rowId=51516

-- Nick