Library Building Failure Tomson  2021-06-29
 

Dear Skyline Team:

Recently I'm going to build a glycoproteome library from Byonic's DDA searching result. I have put files of .mzid and .MGF in same place. However, when I added the file and started the building, the message of error came out.

Here's the message:
System.IO.IOException: ERROR: No spectra were found for the new library.
Command-line: C:\Users\張崑皓\AppData\Local\Apps\2.0\LK9XBYRP.8XT\EGDNLVVT.38L\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\BlibBuild -s -A -H -o -c 0.95 -i stepHCD_stHp_20210629 -S "C:\Users\張崑皓\AppData\Local\Temp\tmpA3BF.tmp" "C:\Users\張崑皓\Desktop\skyline\Library\stepHCD_stHp_20210629.redundant.blib"
Working directory: C:\Users\張崑皓\Desktop\實驗室\實驗\20210529_stHP_HCD_EThcD_DIA\stepHCD
於 pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) 於 C:\proj\skyline_21_1_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs: 行 65
於 pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) 於 C:\proj\skyline_21_1_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs: 行 201
於 pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) 於 C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs: 行 157

Please let me know if there's anything should be refined.
Best
Tomson

 
 
Kaipo responded:  2021-07-06

Hi Tomson,
Would you mind uploading the mzid and mgf files here: https://skyline.ms/files.url

Thanks,
Kaipo

 
Tomson responded:  2021-07-06

Dear Kaipo,
I have uploaded the files. Thanks for your help.

Best
Tomson

 
Kaipo responded:  2021-07-12

Hi Tomson,
Do you have any information about how the mgf file was generated? Normally we expect the "spectrum title" fields in the Byonic mzid output to match the title field of the corresponding spectrum in the mgf file. However the formats look different between the files you've provided, so when building the library Skyline is not able to match the search results to the spectra.

For example:
The first result in the mzid file has spectrum title yjc_20210529_sthp_dda_stephcd_01.ScanId;v=1;d1=3.3.2_INDEX0
but the spectra in the mgf file have titles like File: "E:\Biosignature\Hp\20210529_stHP_HCD_EThcD_DIA\YJC_20210529_stHP_DDA_stepHCD_01.raw"; SpectrumID: "1"; PrecursorID: "0"; scans: "3"

Thanks,
Kaipo

 
Tomson responded:  2021-07-12

Hi Kaipo,

Thanks for your response. Actually the mgf file is from Proteome Discoverer rather than Byonic, and I think that is the reason why the formats of two files are different. If I obtain both file from Byonic, the problem will be solved?

Thanks,
Tomson

 
Tomson responded:  2021-07-13

Hi Kaipo,

This time I used mgf and mzid files from Byonic, and it worked. Now I can build the library very well. Thanks a lot for your help.

Best,
Tomson