Issue with Library creation using DIA-NN based 'report-lib.tsv' file (SPECLIB file type)

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Issue with Library creation using DIA-NN based 'report-lib.tsv' file (SPECLIB file type) abhinav bioc1213  2021-05-13
 

Hi, I am not able to create a library using the DIA-NN generated library (report-lib.tsv' ). I get the attached error message, I have been trying this for many times now and still get the same message. The DIA-NN data shows about 4500 proteins IDs at 1% FDR.

Can you please suggest if I am doing it in wrong way?

Regards
Abhinav

 
 
matt.chambers42 responded:  2021-05-13

Hi Abhinav,

The DIA-NN import uses the .speclib file, not the .tsv file. The latter is trying to masquerade (or conform) to an OpenSWATH assay TSV, which BiblioSpec also supports (and indeed I don't think it can even tell the difference). I suspect it's not working because the conformance is not 100%.

 
abhinav bioc1213 responded:  2021-05-13

Hi Matt,

I cannot see any file as .speclib from DIA-NN. Do you suggest to re-process the data on DIA-NN. when I use other .tsv file (generated last year) it work in Skyline. I have attached the lists of files generated from DIA-NN output.

Regards
Abhinav

 
matt.chambers42 responded:  2021-05-13

You have "show file extensions" turned off. But in the details view you're in, you can see the file type in the column on the right. There are 2 speclib files. You want the non-predicted one. It has the .tsv part added on the end of its name despite not being a TSV file.

 
abhinav bioc1213 responded:  2021-05-13

Hi Matt,
Yes I want non predicted one so used the last file ending with .tsv (but it is a specblib file type) and it is not working. I hat should I then?

Regards

 
matt.chambers42 responded:  2021-05-13

Hmm, then I may need to see the speclib file to see what's going wrong. Can you upload it to https://skyline.ms/project/home/support/file sharing/begin.view ?

Thanks.

 
abhinav bioc1213 responded:  2021-05-14

Hi Matt,

I just uploaded the file (report-lib.tsv).

Regards
Abhinav

 
matt.chambers42 responded:  2021-05-14

I was able to create a library from that file without a problem. Are you sure you selected that file from Skyline, and not the report-lib.tsv file (without the .speclib extension)?

 
abhinav bioc1213 responded:  2021-05-17

Hi Matt,

I could not understand you. I tried creating the lib as follows:

Setting>peptide setting>Library>Build>Named the lib> selected the output path to designated folder> Next>Add files>selected file titled 'report-lib.tsv' (which is SPECLIB)>FINISH>OK

and then I get the error message after sometime which I have shared with you earlier.

Am I trying to create the lib in correct way or is there any other things in Settings I need to be careful of?

Regards
Abhinav

 
abhinav bioc1213 responded:  2021-05-17

I get follwoing error when I tried building the lib again:

Skyline version: 20.2.0.343-a7a9e8c4f (64-bit)
Installation ID: 297fe0c5-5990-4c8d-9d87-76d86543a109
Exception type: Exception
Error message: Failed loading library '\10.0.0.8\proteome\Abhinav\Absolute Quant-PRM\DIA_NN_Lib.blib'.
Specified argument was out of the range of valid values.
Parameter name: capacity
Format: BiblioSpec
LSID: urn:lsid:proteome.gs.washington.edu:spectral_library:bibliospec:nr:DIA_NN_Lib
FileRevision: 0
SchemaVersion: 10


System.Exception: Failed loading library '\10.0.0.8\proteome\Abhinav\Absolute Quant-PRMDIA_NN_Lib.blib'.
Specified argument was out of the range of valid values.
Parameter name: capacity
Format: BiblioSpec
LSID: urn:lsid:proteome.gs.washington.edu:spectral_library:bibliospec:nr:DIA_NN_Lib
FileRevision: 0
SchemaVersion: 10 ---> System.ArgumentOutOfRangeException: Specified argument was out of the range of valid values.
Parameter name: capacity
at System.Collections.Generic.HashSet1..ctor(Int32 capacity, IEqualityComparer1 comparer)
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 677
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()

 
matt.chambers42 responded:  2021-05-17

Try in the latest Skyline-daily. I think Skyline 20.2 only supports an older version of the speclib format and won't give a proper error if the format is updated in the future. Skyline-daily and 21.1 will work with the current format (AFAIK) and will give an error if the format is updated (as long as DIA-NN updates the file's version number, at least).