Error matching m/z values in older documents

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Error matching m/z values in older documents liisa arike  2018-11-30
 
Hi!

I am getting a following error when opening older processed Skyline files:
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Skyline
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Failure opening C:\Users\xarili\Google Drive\Projects\CR crosslinking\MS562_CR Chymotrp human\MS562_01_25\Crosslinking_human chymotrp_MS562_01_25.sky.
The file contains an error on line 1897 at column 7.
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OK More Info
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System.Reflection.TargetInvocationException: There is an error in XML document (1897, 7). ---> System.InvalidOperationException: There is an error in XML document (1897, 7). ---> pwiz.Skyline.Util.AssumptionException: error reading mz values - declared mz value 756.338 does not match calculated value 757.34582457991
   at pwiz.Skyline.Util.Assume.Fail(String error) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Util\Util.cs:line 1918
   at pwiz.Skyline.Util.Assume.IsTrue(Boolean condition, String error) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Util\Util.cs:line 1877
   at pwiz.Skyline.Model.Serialization.DocumentReader.ValidateSerializedVsCalculatedProductMz(Nullable`1 declaredProductMz, TransitionDocNode node) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1371
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionXml(XmlReader reader, TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1357
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionListXml(XmlReader reader, TransitionGroupDocNode nodeGroup, ExplicitMods mods) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1247
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupXml(XmlReader reader, Peptide peptide, ExplicitMods mods) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1117
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupListXml(XmlReader reader, Peptide peptide, ExplicitMods mods) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1043
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideXml(XmlReader reader, PeptideGroup group, Boolean isCustomMolecule) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 877
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideListXml(XmlReader reader, PeptideGroup group) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 761
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupXml(XmlReader reader) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 732
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupListXml(XmlReader reader) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 573
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadXml(XmlReader reader) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 539
   at pwiz.Skyline.Model.SrmDocument.ReadXml(XmlReader reader) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 2022
   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__DisplayClass925_0.<OpenFile>b__0(IProgressMonitor progressMonitor) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 301
   at pwiz.Skyline.Util.ProgressWaitBroker.PerformWork(ILongWaitBroker broker) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Util\UtilUI.cs:line 123
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 232
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Util\Util.cs:line 1854
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 180
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 132
   at pwiz.Skyline.SkylineWindow.OpenFile(String path, FormEx parentWindow) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 295
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Best,
Liisa
 
 
Nick Shulman responded:  2018-11-30
Title: Errror
Can you send us the file "Crosslinking_human chymotrp_MS562_01_25.sky"?
The file that you attached is the .sky.view file, which is not the file that we need to fix. You should send us the .sky file.

I believe that many errors like this are caused by bugs that we had in older versions of Skyline in terms of calculating the mass of molecules or fragments. When those bugs were fixed in the current version of Skyline it sometimes resulted in errors like this when you tried to open older documents.
That error also might indicate a bug in the current version of Skyline.
If you send us that .sky file, we will be able to either fix the .sky file or figure out whether there is a current bug in Skyline.
-- Nick
 
liisa arike responded:  2018-11-30
I'm sorry, I thought I sent everything. Thank you very much for responding so fast.

Best,
Liisa
 
Brendan MacLean responded:  2018-11-30
No problem, Lisa. Our file naming can be confusing on systems that don't show file extensions. On such a system our names come out looking like:

filename
filename.sky
filename

When the full extension view would be:

filename.sky
filename.sky.view
filename.skyd

Because we usually work on systems where we show extensions (one of the first things I change in a default Windows installation), I think we often forget this. Maybe we should be thinking about ways of improving this.

Thanks for reporting your issue.
 
Nick Shulman responded:  2018-12-03
Hi, Liisa,

When the current version of Skyline tries to open a document that was created in version 3.7, Skyline tries to guess whether the transition m/z values refer to the ion mass with or without protons. We have a bug in this code, and the logic does not work correctly for transitions whose charge is not 1.

We will try to fix this soon.
I have attached a modified version of the .sky file that you gave me, which should fix this problem.

If you have other Skyline documents that you need fixed, you can fix them by opening them in a text editor (such as Notepad) and doing a search and replace.
You need to replace every occurrence of:
product_charge="2"
with
product_charge="2" ion_formula="[M+2]"

I hope this works for you, and let us know if you have any more troubles with your Skyline documents.
-- Nick
 
liisa arike responded:  2018-12-10
Thanks a lot, this solved the problem.