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File from previous version does not open in Skyline 4.1

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File from previous version does not open in Skyline 4.1 afmpinto  2018-02-07 15:08
 
After updating to version 4.1, files from the previous version do not open.
This is the error one of those files gave me.

Failure opening file
The file contains an error on line 233 at column 10.
unable to locate precursor calculator for isotope label type heavy and mods (null)

System.Reflection.TargetInvocationException: There is an error in XML document (233, 10). ---> System.InvalidOperationException: There is an error in XML document (233, 10). ---> System.IO.InvalidDataException: unable to locate precursor calculator for isotope label type heavy and mods (null)
   at pwiz.Skyline.Model.DocSettings.SrmSettings.GetPrecursorCalc(IsotopeLabelType labelType, ExplicitMods mods) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\DocSettings\SrmSettings.cs:line 249
   at pwiz.Skyline.Model.TransitionGroupDocNode.CalcPrecursorMZ(SrmSettings settings, ExplicitMods mods, IsotopeDistInfo& isotopeDist, TypedMass& mass) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\TransitionGroupDocNode.cs:line 724
   at pwiz.Skyline.Model.TransitionGroupDocNode..ctor(TransitionGroup id, Annotations annotations, SrmSettings settings, ExplicitMods mods, SpectrumHeaderInfo libInfo, ExplicitTransitionGroupValues explicitValues, Results`1 results, TransitionDocNode[] children, Boolean autoManageChildren) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\TransitionGroupDocNode.cs:line 78
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupXml(XmlReader reader, Peptide peptide, ExplicitMods mods, Double deltaMass) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1237
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupListXml(XmlReader reader, Peptide peptide, ExplicitMods mods, Double deltaMass) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1042
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideXml(XmlReader reader, PeptideGroup group, Boolean isCustomMolecule) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 873
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideListXml(XmlReader reader, PeptideGroup group) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 756
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupXml(XmlReader reader) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 726
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupListXml(XmlReader reader) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 568
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadXml(XmlReader reader) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 536
   at pwiz.Skyline.Model.SrmDocument.ReadXml(XmlReader reader) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 1947
   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__DisplayClass12b.<OpenFile>b__129(IProgressMonitor progressMonitor) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 258
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 228
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Util\Util.cs:line 1837
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 176
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 131
   at pwiz.Skyline.SkylineWindow.OpenFile(String path, FormEx parentWindow) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 262
 
 
Brian Pratt responded:  2018-02-07 15:22
Hi Antonio,

It is likely that we have already addressed this for the upcoming 4.1 patch release, but if you can provide the Skyline document that is giving you this error I would be very happy to make sure that this is handled.

You can upload to http://skyline.ms/files.url .

Thanks,

Brian Pratt
 
afmpinto responded:  2018-02-07 15:30
Hello Brian

Thanks for your answer.

I am attaching the files.
They are two templates. The template_neg.sky opens and I can see there was a change in the structure of how heavy atoms are described for each molecule.

When is the patch going to be released?

Thanks again
 
Brian Pratt responded:  2018-02-07 16:15
I'm not sure exactly when we'll be releasing it. Brendan handles the release process and he is away at the moment.

I will make sure that the problem in loading your Template_pos.sky file is corrected in time for the patch release.

Thanks for reporting the problem.

>> I can see there was a change in the structure of how heavy atoms are described for each molecule.

That is correct - Skyline is now much more rigorous in modeling molecules as a neutral formula with an adduct, where the adduct may include isotopic labeling information. This makes it much easier for Skyline to understand heavy/light relationships and multiple ionizations, which allows us to apply quant logic and other features already developed for peptides which Skyline already models as a neutral molecule with modifications. As you have found, we did not get the backward compatibility completely right the first time, but we do think it is very important to be able to read previous version files and will get this done.

Brian
 
afmpinto responded:  2018-02-07 16:33
Thanks again. I will wait for the next release.

Until then, is it possible to have access to a previous version of skyline do I can continue working with my file until the backward compatibility is fixed?

Thanks
 
Brian Pratt responded:  2018-02-07 17:04
You can download an "unplugged" version here:

https://skyline.ms/labkey/_webdav/home/software/Skyline/%40files/installers/Skyline-64_3_7_0_11317.zip
 
Brendan MacLean responded:  2018-02-07 17:12
A simpler way to rollback to your previous installation than installing the unplugged version is to go to "Add or remove programs" in your system settings and remove Skyline. You will be asked whether you want to remove it completely or just rollback to the previously installed version. If they previous version was working for you, just rollback and you should be fine.

Thanks for reporting the issue before rolling back!

--Brendan
 
afmpinto responded:  2018-02-08 07:26
Brian and Brendan

Thank you very much for your help.
As soon as the new patch is released, I'll test again and report any issues.

Thank you