System.IO.IOException: ERROR: No spectra were found for the new library Pavan Kumar Dappili  2020-02-12
 

Hi all

I am trying to DDA search by importing to the library from msmsscans.txt file generated after Maxquant analysis. But the skyline is showing the following error.

System.IO.IOException: ERROR: No spectra were found for the new library.

Command-line: C:\Users\admin\AppData\Local\Apps\2.0\1QE2T2VZ.QYZ\8XBYAZMR.OMP\skyl..tion_e4141a2a22107248_0014.0001_bc11b87fcb56f175\BlibBuild -s -A -H -o -c 0.99 -i Four_cell_lines_trial -S "C:\Users\admin\AppData\Local\Temp\tmp82BA.tmp" "D:\Important Information\Pavan\Skyline Protein Analaysis\Four cell lines_trial.redundant.blib"
Working directory: D:\Important Information\Pavan\Protein Analysis\Agilent Raw data\Cell analysis_Trials\200201\combined\txt
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in C:\proj\skyline_20_1_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 62
at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_20_1_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 201
at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 160

Please suggest how to resolve this issue.

I have used the latest version of the skyline and maxquant for this analysis.

Thanks and Regards
Pavan Kumar Dappili

 
 
Nick Shulman responded:  2020-02-13
Can you send us the files that you are using to build your library? We will try to figure out what is going wrong.

For MaxQuant, I believe the files are "msms.txt" and maybe a "mqpar.xml" and maybe a "modification.xml".
(I might be mistaken about exactly what those files are called).

If those files are less than 50MB you can attach them to this support request.
Otherwise, you can put them in a zip file and post them here:
https://skyline.ms/files.url

-- Nick
 
Pavan Kumar Dappili responded:  2020-02-13
Hi Nick

Thank you for your response.

Through MaxQuant analysis, we will get msms.txt file to build the library.

Actually now it worked after removing the already built-in spectral library in the skyline.

Please give me suggestions on how to create a separate spectral library for different experimentation, to avoid this kind of issue in the future? or what is the best practice in the creation of spectral libraries the first time.

-
Thanks and Regards
Pavan Kumar Dappili
 
Nick Shulman responded:  2020-02-13
Can you give me your mqpar.xml? Skyline won't let me try to build a library with the msms.txt file that you gave me unless I have the mqpar.xml.

I am not sure I understand your question. Are you saying that the msms.txt that you attached earlier does not work but you have a different msms.txt which does work? I certainly can try to figure out what is going wrong with the file that does not work.
-- Nick
 
Pavan Kumar Dappili responded:  2020-02-16
Hi Nick

The msms.txt I shared with you is the same one which earlier didn't work to generate the spectral library and now it worked. I just cleared the already present spectral library information in the skyline and then started the DDA peptide search with this msms.txt file.

I can share with you the Maxquant parameters file, but to do spectral library along with msms.txt file raw data files are also needed. If you want the raw data files, I can share them through a link.

I started using the skyline very recently and don't know many things in it. My query is what is the best practice to build a spectral library? What to do to get a separate library with every new experiment and the data generated with one experiment will not be shared or compared with other experiments.

-
Thanks and regards
Pavan Kumar Dappili
 
Pavan Kumar Dappili responded:  2020-02-16
Hi Nick

The msms.txt I shared with you is the same one which earlier didn't work to generate the spectral library and now it worked. I just cleared the already present spectral library information in the skyline and then started the DDA peptide search with this msms.txt file.

I can share with you the Maxquant parameters file, but to do spectral library along with msms.txt file raw data files are also needed. If you want the raw data files, I can share them through a link.

I started using the skyline very recently and don't know many things in it. My query is what is the best practice to build a spectral library? What to do to get a separate library with every new experiment and the data generated with one experiment will not be shared or compared with other experiments.

-
Thanks and regards
Pavan Kumar Dappili
 
Nick Shulman responded:  2020-02-17
Pavan,

I believe the .raw files are not necessary for building a spectra library from MaxQuant results. The spectra are actually stored in the msms.txt file.
By the way, this page has the list of which files are necessary for building spectral libraries from various types of peptide search results:
https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild

I know that .raw files are necessary for extracting chromatograms in Skyline, and also when building libraries from other types of peptide search results it it is necessary for Skyline to have access to the .raw files or the .mzML files.

Spectral libraries are used for two different purposes in Skyline. One is like a traditional spectral library where Skyline looks at the spectra in order to decide which transitions are most likely to be present so that you can decide which chromatograms to extract in an SRM, DIA, or PRM experiment. For these sorts of spectral libraries you would create them from one set of data, and then use the library to design future experiments.

The other thing that you can use spectral libraries for is as a way of converting peptide search results into something that Skyline understands, but all that Skyline is actually interested in are the retention times of the peptides in the particular .raw files that were searched.

You might find it helpful to look at the MS1 Full Scan filtering tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_ms1_filtering

I believe that tutorial shows you how to create a spectral library from DDA search results and use those results to decide what MS1 chromatograms to extract and at which retention times to find the peptides.
-- Nick