Error in skyline for small molecules

2020-12-01

Hello!  I just updated my skyline line for small molecules and I seeing this error.  What does this mean?  Thank you!

 

 

---------------------------
Skyline
---------------------------
Failure opening S:\Departments\Analytics\BioAnalytics\Chia-Wei\QQQ-Demo\skyline_data analysis\troubleshooting skyline_falcon QQQ\032420_Troubleshooting_skyline_QQQ_falcon.sky.
The file contains an error on line 652 at column 9.
---------------------------
OK More Info
---------------------------
System.Reflection.TargetInvocationException: There is an error in XML document (652, 9). ---> System.InvalidOperationException: There is an error in XML document (652, 9). ---> pwiz.Skyline.Util.AssumptionException: error reading mz values - declared mz value 88.02 does not match calculated value 148.1
at pwiz.Skyline.Util.Assume.Fail(String error) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Util\Util.cs:line 1973
at pwiz.Skyline.Util.Assume.IsTrue(Boolean condition, String error) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Util\Util.cs:line 1932
at pwiz.Skyline.Model.Serialization.DocumentReader.ValidateSerializedVsCalculatedProductMz(Nullable`1 declaredProductMz, TransitionDocNode node) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1396
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionXml(XmlReader reader, TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist, ExplicitTransitionValues pre422ExplicitTransitionValues) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1382
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionListXml(XmlReader reader, TransitionGroupDocNode nodeGroup, ExplicitMods mods, ExplicitTransitionValues pre422ExplicitTransitionValues) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1271
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupXml(XmlReader reader, Peptide peptide, ExplicitMods mods) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1140
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupListXml(XmlReader reader, Peptide peptide, ExplicitMods mods) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1066
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideXml(XmlReader reader, PeptideGroup group, Boolean isCustomMolecule) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 898
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideListXml(XmlReader reader, PeptideGroup group) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 767
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupXml(XmlReader reader) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 738
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupListXml(XmlReader reader) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 579
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadXml(XmlReader reader) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 545
at pwiz.Skyline.Model.SrmDocument.ReadXml(XmlReader reader) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 1960
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 System.Xml.Serialization.XmlSerializer.Deserialize(TextReader textReader)
at pwiz.Skyline.SkylineWindow.<>c__DisplayClass979_0.<OpenFile>b__0(IProgressMonitor progressMonitor) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 322
at pwiz.Skyline.Util.ProgressWaitBroker.PerformWork(ILongWaitBroker broker) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Util\UtilUI.cs:line 125
at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 246
--- End of inner exception stack trace ---
at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Util\Util.cs:line 1909
at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 194
at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 131
at pwiz.Skyline.SkylineWindow.OpenFile(String path, FormEx parentWindow) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 316
---------------------------