Failure opening document - modification name error | joshuasmith | 2022-08-30 22:10 | |||||||||||||||||||||||
Hi all, We are doing untargeted PTM discovery and I have a document with a large number of modifications that I have manually entered and integrated. I saved the file and when I tried to reopen it, I got the message I have pasted below, and it won't open. I have just spent the better part of 16 hours manually QC'ing this document, and so I would be really, really disappointed if my file is now unusable. Is there any way to fix this? Thanks, Josh __ --------------------------- Skyline --------------------------- Failure opening C:\Users\Josh Smith\iCloudDrive\Documents\Projects\Adductomics\SHIELD\PAA_analysis\SHIELD_Pilot_PAA_072622_analysisinprogress_backup.sky. The file contains an error on line 5833 at column 9. No modification named Unknown 712.3934 (C) was found in this document. --------------------------- OK More Info --------------------------- System.Reflection.TargetInvocationException: There is an error in XML document (5833, 9). ---> System.InvalidOperationException: There is an error in XML document (5833, 9). ---> System.IO.InvalidDataException: No modification named Unknown 712.3934 (C) was found in this document. at pwiz.Skyline.Model.DocSettings.TransitionLosses.FromLossProtos(SrmSettings settings, IEnumerable`1 lossProtos) in C:\proj\skyline_21_2\pwiz_tools\Skyline\Model\DocSettings\Loss.cs:line 388 at pwiz.Skyline.Model.TransitionDocNode.FromTransitionProto(AnnotationScrubber scrubber, SrmSettings settings, TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist, ExplicitTransitionValues pre422ExplicitTransitionValues, CrosslinkBuilder crosslinkBuilder, Transition transitionProto) in C:\proj\skyline_21_2\pwiz_tools\Skyline\Model\TransitionDocNode.cs:line 719 at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionListXml(XmlReader reader, TransitionGroupDocNode nodeGroup, ExplicitMods mods, ExplicitTransitionValues pre422ExplicitTransitionValues) in C:\proj\skyline_21_2\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1457 at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupXml(XmlReader reader, Peptide peptide, ExplicitMods mods) in C:\proj\skyline_21_2\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1332 at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupListXml(XmlReader reader, Peptide peptide, ExplicitMods mods) in C:\proj\skyline_21_2\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1258 at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideXml(XmlReader reader, PeptideGroup group, Boolean isCustomMolecule) in C:\proj\skyline_21_2\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 905 at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideListXml(XmlReader reader, PeptideGroup group) in C:\proj\skyline_21_2\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 840 at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupXml(XmlReader reader) in C:\proj\skyline_21_2\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 810 at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupListXml(XmlReader reader) in C:\proj\skyline_21_2\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 651 at pwiz.Skyline.Model.Serialization.DocumentReader.ReadXml(XmlReader reader) in C:\proj\skyline_21_2\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 616 at pwiz.Skyline.Model.SrmDocument.ReadXml(XmlReader reader) in C:\proj\skyline_21_2\pwiz_tools\Skyline\Model\SrmDocument.cs:line 2074 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__DisplayClass744_0.<OpenFile>b__0(IProgressMonitor progressMonitor) in C:\proj\skyline_21_2\pwiz_tools\Skyline\SkylineFiles.cs:line 328 at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\skyline_21_2\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_2\pwiz_tools\Skyline\Util\Util.cs:line 1941 at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_21_2\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_2\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 140 at pwiz.Skyline.SkylineWindow.OpenFile(String path, FormEx parentWindow) in C:\proj\skyline_21_2\pwiz_tools\Skyline\SkylineFiles.cs:line 345 --------------------------- |
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