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Failure opening File alessandra tozzi1  2024-07-14 18:45
 
Hello!

I came across the following error, while modifying my transition list. Now I cannot open my transition list anymore.
Thank you in advance for your help!

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Skyline
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Failure opening //mac\Home\Desktop\Griffith University\Milk project\Data Analysis\Experiment 1\N-Glycans\Skyline FINAL TRANSITION LIST 5vs5 Exp 1.sky.
The file contains an error on line 1462 at column 9.
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OK More Info
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System.Reflection.TargetInvocationException: There is an error in XML document (1462, 9). ---> System.InvalidOperationException: There is an error in XML document (1462, 9). ---> pwiz.Skyline.Util.AssumptionException: error reading mz values - declared mz value 1476.524248 does not match calculated value 812.322724
   at pwiz.Skyline.Util.Assume.Fail(String error) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Util\Util.cs:line 2039
   at pwiz.Skyline.Model.Serialization.DocumentReader.ValidateSerializedVsCalculatedProductMz(Nullable`1 declaredProductMz, TransitionDocNode node) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1714
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionXml(XmlReader reader, TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist, ExplicitTransitionValues pre422ExplicitTransitionValues, CrosslinkBuilder crosslinkBuilder) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1692
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionListXml(XmlReader reader, TransitionGroupDocNode nodeGroup, ExplicitMods mods, ExplicitTransitionValues pre422ExplicitTransitionValues) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1552
   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 1421
   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
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Nick Shulman responded:  2024-07-14 19:08
If you send us the file "Skyline FINAL TRANSITION LIST 5vs5 Exp 1.sky" we will be able to fix it for you so that you can open it without error.

Files which are less than 50MB can be attached to these support requests.

You can upload larger files here:
https://skyline.ms/files.url

This error is always caused by a bug in Skyline. Sometimes when settings change Skyline gets confused about what the mass of a molecule is supposed to be and things get in a state where the document cannot be opened.

--Nick
 
alessandra tozzi1 responded:  2024-07-14 20:29
Thank you very much Nick. I attach the file here.
 
Nick Shulman responded:  2024-07-14 20:56
Here is a fixed copy of that file.
You should save this file overtop of the "Skyline FINAL TRANSITION LIST 5vs5 Exp 1.sky" that you already have.
You will then be able to open this file in Skyline without error.
Skyline will give you a warning about the fact that this file is not identical to what the the Audit Log expects it to be. You can safely ignore that warning.

Now that you are able to open your Skyline document, it would be very helpful to us if you could use the "File > Share" menu item to create a .zip file and send us that .zip file.

When you use the "File > Share" menu item, Skyline will create a .zip file containing the Skyline document and supporting files including the Audit Log.
That audit log will probably give me a good indication of where to look to find the Skyline bug that got you into this state.
-- Nick
 
alessandra tozzi1 responded:  2024-07-15 17:37
Many thanks Nick! The file works now :)
I attach to this e-mail the file you requested.
If there's something wrong, just let me know.
Have a good day!