Cross-link Transition Calculator - Problem/input

support
Cross-link Transition Calculator - Problem/input tatianibl  2020-06-10
 
Dear Skyline Team,
How are you?

I tried to use cross-link transition calculator tool and I am having a problem during the input process (error message below).

System.Reflection.TargetInvocationException: Exception has been thrown by the target of an invocation. ---> System.Exception: System.Runtime.Serialization.SerializationException: Type 'pwiz.Skyline.Model.LineColNumberedIoException' in Assembly 'Skyline, Version=20.1.0.155, Culture=neutral, PublicKeyToken=null' is not marked as serializable.
   at System.Runtime.Serialization.Formatters.Binary.WriteObjectInfo.InitSerialize(Object obj, ISurrogateSelector surrogateSelector, StreamingContext context, SerObjectInfoInit serObjectInfoInit, IFormatterConverter converter, ObjectWriter objectWriter, SerializationBinder binder)
   at System.Runtime.Serialization.Formatters.Binary.ObjectWriter.Write(WriteObjectInfo objectInfo, NameInfo memberNameInfo, NameInfo typeNameInfo)
   at System.Runtime.Serialization.Formatters.Binary.ObjectWriter.Serialize(Object graph, Header[] inHeaders, __BinaryWriter serWriter, Boolean fCheck)
   at System.Runtime.Serialization.Formatters.Binary.BinaryFormatter.Serialize(Stream serializationStream, Object graph, Header[] headers, Boolean fCheck)
   at SkylineTool.RemoteBase.SerializeObject(Object o) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\SkylineTool\RemoteBase.cs:line 60
   at SkylineTool.RemoteService.ProcessClientThread(Object streamArg) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\SkylineTool\RemoteService.cs:line 104
   --- End of inner exception stack trace ---
   at SkylineTool.RemoteClient.RemoteCallName(String methodName, Object[] arguments)
   at SkylineIntegration.Program.Main(String[] args) in c:\Users\Yuval\Documents\Skyline\3-27-17-tool\pwiz_tools\Skyline\Executables\Tools\PRMCalc\c#\SkylineIntegration\Program.cs:line 50

I am using as input:

0.0 0.0
NVVHQLSVTLEDLYNGATRKLALQK KLALQK 837.532@7,156.079@20 3103.692@1 2
GGKKGAVECCPNCR CKSCNGR 1018.4325@3,156.0786@4,57.0215@9,57.0215@10,57.0215@13    57.0215@1,1885.8485@2,57.0215@4    2
GGKKGAVECCPNCR ISPKDRCKSCNGR 1870.903@3,156.0786@4 156.0786@4,57.0215@7,1885.8485@8,57.0215@10 2
GGKKGAVECCPNCR KLALQKNVICDK 1665.9375@3,156.0786@4 156.0786@1,1885.8485@6,57.0215@10 2
GKNVVHQLSVTLEDLYNGATR CKSCNGR 1018.4325@2 57.0215@1,2451.2758@2,57.0215@4 2

Thank you!
Best wishes,
Tatiani.
 
 
Nick Shulman responded:  2020-06-10
The most recent version of Skyline-Daily has native support for crosslinked peptides. We would appreciate your feedback on this new feature. You can find out more about this in this PowerPoint:
https://skyline.ms/announcements/home/software/Skyline/daily/download.view?entityId=3016000e-80d8-1038-8aae-e465a393ee52&name=CrosslinkingInSkylineDaily.pptx

I am not very familiar with the Crosslink Transition Calculator tool. Questions about external tools should usually be asked on the support page for the individual tool:
https://skyline.ms/project/home/software/Skyline/tools/Support/Cross-link%20Transition%20Calculator/begin.view?

In this case, it looks like your input is causing an error in Skyline itself, and because of a coding mistake in Skyline, the error message is being prevented from making it back to the external tool (this is what the "not marked as serializable" error is saying).

I am not familiar with this tool at all, but if you send me your Skyline document and that input file, I can take a look.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files. (I need your Skyline document in order to know which modifications you have defined).
You should also attach your input file. I am not sure exactly how your input file was formatted in terms of tabs and spaces.

If those files are less than 50MB, you can attach them to this support request.
Otherwise, you can upload them here:
https://skyline.ms/files.url

-- Nick
 
tatianibl responded:  2020-06-10
Dear Nick,

Thank you for your fast reply. Attached please find the documents that you have requested. I have no modifications in my skyline.
I'll also ask in the support page for the individual tool as you mentioned.

Thank you!
Best wishes,
Tati.
 
Nick Shulman responded:  2020-06-10
Thanks for sending those files.

I can tell you that the error message that Skyline is trying to give you is:
Error on line 96, column2: The precursor m/z 2020.093986 is not measureable with your current instrument settings.

It looks like you can work around this problem in Skyline by going to:
Settings > Transition Settings > Instrument
and change "Max m/z" to a larger number such as 2500.
-- Nick
 
tatianibl responded:  2020-06-10
Dear Nick,

Thank you very much for your help. I didn't pay attention to that detail.
Sorry to bother you with that kind of detail

Thank you very much.
Best wishes.
Tati