line 6675 column 10 error

line 6675 column 10 error landerson  2021-06-23
I am receiving an error when I try to reopen a skyline doc I was working on the other day. I receive an error per below and attached. This is not the first time I have received the error when trying to re-open a previously saved skyline doc with results. There is no work in the document, it is completely empty. How can I recover my data that I already spend hours on QCing?


System.Reflection.TargetInvocationException: There is an error in XML document (6675, 10). ---> System.InvalidOperationException: There is an error in XML document (6675, 10). ---> pwiz.Skyline.Util.AssumptionException: error reading mz values - declared mz value 148.060434 does not match calculated value 147.07641824
   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
Nick Shulman responded:  2021-06-23
If you send us your .sky file, I can fix it for you and send it back.

If that .sky file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here:

You might also be able to fix this error yourself by opening the .sky file in a text editor.
You should replace all instances of:

(those numbers come from that error message).

The error is saying that the m/z of a transition in the .sky file is different than what Skyline gets when it calculates that m/z from scratch. This is always caused by a bug in Skyline, but the actual nature of the bug can vary. A different user recently got into this state because they changed the definition of a neutral loss which was being used by transitions in the document. You can read about that support request is here:

Even if you manage to fix this yourself you should also send us your .sky file so that we can try to figure out what Skyline bug allowed you to get in this state.
-- Nick
landerson responded:  2021-06-25
Thanks Nick. I attempted to replaced the m/z as you suggested in a text editor but am still getting an error when I try to open the file. Can you give it a shot?
I had replaced the precursor mass (by formula) from the template document I started with so it seems like the error you are referring to.

Nick Shulman responded:  2021-06-25
Here is a fixed version of that file.
The number "147.07641824" appeared many times in that file, but the only one that was supposed to be replaced with 148.060433835 was the one in the "<product_mz>" tag.