"resolving protein details" problem AND lost library problem upon install of newer Skyline version

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"resolving protein details" problem AND lost library problem upon install of newer Skyline version cabarnescabarnes  2020-12-05
 

Hi all,
Thanks for the great software. I am using the EncyclopeDIA work flow to get DIA data into Skyline. I imported an .elib library out of EncyclopeDIA that seemed to be working and everything was working great until one day I got the "resolving protein details" problem. I was using Skyline 20.1.0.31, so I uninstalled that and then downloaded Skyline 20.2.0.286 and installed that. Now, I'm getting a library problem. Everything else seems to be working. Here's the error code:

Skyline version: 20.2.0.286-59e53e849 (64-bit)
Installation ID: 5b133551-e4fe-4406-b30c-a9e78485df9a
Exception type: Exception
Error message: Failed loading library 'C:\TPP\data\smORF_Experiments\Mouse_plasma_inflammation_young_old_smORF\Mouse_plasma_inflammation_young_old_smORF_spectral_library_w_plasma_fractionations_Joan_chromolib_quant_report.elib'.
SQL logic error or missing database
no such table: LibInfo
Format: BiblioSpec
FileRevision: 0
SchemaVersion: 0


System.Exception: Failed loading library 'C:\TPP\data\smORF_Experiments\Mouse_plasma_inflammation_young_old_smORF\Mouse_plasma_inflammation_young_old_smORF_spectral_library_w_plasma_fractionations_Joan_chromolib_quant_report.elib'.
SQL logic error or missing database
no such table: LibInfo
Format: BiblioSpec
FileRevision: 0
SchemaVersion: 0 ---> System.Data.SQLite.SQLiteException: SQL logic error or missing database
no such table: LibInfo
at System.Data.SQLite.SQLite3.Prepare(SQLiteConnection cnn, String strSql, SQLiteStatement previous, UInt32 timeoutMS, String& strRemain)
at System.Data.SQLite.SQLiteCommand.BuildNextCommand()
at System.Data.SQLite.SQLiteDataReader.NextResult()
at System.Data.SQLite.SQLiteDataReader..ctor(SQLiteCommand cmd, CommandBehavior behave)
at System.Data.SQLite.SQLiteCommand.ExecuteReader(CommandBehavior behavior)
at pwiz.Skyline.Model.Lib.BiblioSpecLiteLibrary.CreateCache(ILoadMonitor loader, IProgressStatus status, Int32 percent) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLite.cs:line 605
at pwiz.Skyline.Model.Lib.BiblioSpecLiteLibrary.Load(ILoadMonitor loader, IProgressStatus status, Boolean cached, Exception& failureException) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLite.cs:line 949
--- End of inner exception stack trace ---
at pwiz.Skyline.Model.Lib.BiblioSpecLiteLibrary.Load(ILoadMonitor loader) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLite.cs:line 927
at pwiz.Skyline.Model.Lib.BiblioSpecLiteLibrary.Load(BiblioSpecLiteSpec spec, ILoadMonitor loader) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLite.cs:line 150
at pwiz.Skyline.Model.Lib.LibraryManager.LoadLibrary(LibrarySpec spec, Func`1 getMonitor) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Lib\Library.cs:line 295
at pwiz.Skyline.Model.Lib.LibraryManager.LoadBackground(IDocumentContainer container, SrmDocument document, SrmDocument docCurrent) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Lib\Library.cs:line 124
at pwiz.Skyline.Model.BackgroundLoader.OnLoadBackground(IDocumentContainer container, SrmDocument document) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\BackgroundLoader.cs:line 130
Exception caught at:
at pwiz.Skyline.Model.BackgroundLoader.OnLoadBackground(IDocumentContainer container, SrmDocument document) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\BackgroundLoader.cs:line 130
at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)
at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)
at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)
at System.Threading.ThreadHelper.ThreadStart()

 
 
Nick Shulman responded:  2020-12-05
It looks like the problem is that Skyline is trying to read that EncycopeDIA .elib file as if it were a BiblioSpec .blib file, which is not going to work.

I have not seen this error before, but it turns out that this can happen if you point Skyline at the wrong type of library when Skyline asks you where to find a missing library.

That is, when you open up a Skyline document, Skyline tries to find all of the libraries that are being used by the document, but which Skyline cannot find on disk. If any libraries cannot be found, Skyline asks you if you want to browse the file system and find them. If you browse and find a .elib when the file that you were supposed to be looking for was a .blib, you will get this error.

What you should do to correct this is go to:
Settings > Peptide Settings > Libraries > Edit List
and remove the library that is causing troubles.

You can then add that library using the "Add" button from the Edit Libraries dialog, and Skyline will correctly figure out what type of library it is based on its filename.

We should definitely fix the problem where Skyline misinterprets libraries when you browse for them when opening a document.

-- Nick
 
cabarnescabarnes responded:  2020-12-05
Hi Nick,

Thanks for the quick turn around on your answer. I think I'm more at fault than I implied. I had actually been unsure as to whether or not the EncyclopeDIA .elib would work or not, so I had imported it. It seemed to have more information than the blib in the final document although my memory of this is not great at this point. I've been using the .elib import method for a while and it has been fine. Then, recently, I got the "resolving protein details" error and could not fix it. I uninstalled Skyline and installed the newest version and reopened the same Skyline document that pointed to the .elib file that was previously working with no problems. So, I don't think you need to go fix that based on this post because it's probably my fault. However, do you think that the "resolving protein details" problem is associated with this .elib vs. .blib situation?

Thanks again for the fast response!!

Best,

chris
 
Brian Pratt responded:  2020-12-07
Hi Chris,

Can you elaborate on this "resolving protein details" issue? A screenshot is always helpful.

Thanks,

Brian Pratt