Dear Skyline support,

Our lab has encountered an issue in regards to some small molecule skyline assays from 3.7 and earlier. I believe it originates from our method of describing small molecules for import with Skyline in which we give the bare minimum for transition list import (molecule list name, precursor name, product name, precursor m/z, product m/z, precursor charge and product charge). Please find the error at the bottom of this text.

We already have a workaround (importing our transition list to feature the adduct form) so it's not essential for our work to continue but it does mean that we can't open some of our assays built in 3.7 and earlier. Curiously, some of the assays I've made for 3.7 do work in 4.1 so I'm still trying to work that bit out (likely I used additional transition list import columns). Reading into the error below, the calculated value is 0.577550289955 less than the declared mz value (which is my observed m/z) but the theoretical value of my small molecule is 819.2533 which is still 0.410850289955 greater than the calculated value. Is there something weird going on with adduct calculation for assay files from 3.7 and earlier?

This error has also occurred with a colleague's skyline assay with a different small molecule but funnily enough, the deviation between calculated and declared is different than what I observed? Sorry I can't be of much more help.

Please find one error below, I can provide the Skyline assay file in sharing format (.zip) via email if requested:
 System.Reflection.TargetInvocationException: There is an error in XML document (189, 9). ---> System.InvalidOperationException: There is an error in XML document (189, 9). ---> pwiz.Skyline.Util.AssumptionException: error reading mz values - declared mz value 819.42 does not match calculated value 818.842449710045
   at pwiz.Skyline.Util.Assume.Fail(String error) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Util\Util.cs:line 1901
   at pwiz.Skyline.Model.Serialization.DocumentReader.ValidateSerializedVsCalculatedProductMz(Nullable`1 declaredProductMz, TransitionDocNode node) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1484
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionXml(XmlReader reader, TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1476
   at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionListXml(XmlReader reader, TransitionGroupDocNode nodeGroup, ExplicitMods mods) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\Serialization\DocumentReader.cs:line 1365
   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

Cheers,
Chris