Hi Brandon,
Hope you are well. Thanks for all you great work. I am trying to generate a library with data that I exported from a PEAKS search. The PEAKS data is a EColi database search of Q-Exactive data, on samples digested with chymo, exported as a pep.xml file.
I am using the most recent release of Skyline for this (not the Daily release) and every time I try to build my library, I get an error indicating NO spectra were found for the new library.
This is the error message I see:
System.IO.IOException: ERROR: No spectra were found for the new library.
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, ProgressStatus& status, TextWriter writer) in c:\proj\skyline_3_5_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 109
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, ProgressStatus& status) in c:\proj\skyline_3_5_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 53
at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, ProgressStatus& status, String[]& ambiguous) in c:\proj\skyline_3_5_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 166
at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in c:\proj\skyline_3_5_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 128
I have attached the pep.xml file as well as the mzxml file in case that is useful. I am using a cutoff score of 0 as a test to try and pull in everything.
I am not sure if this is an issue with Skyline, or the PEAKS export, but any advice/suggestions you can offer would be great. This worked quite well yesterday with the Skyline Daily version, and a Trypsin export of PEAKS data.
Thanks,
Jonathan |
| |
| derock j responded: |
2018-09-11 |
Hello,
I get the same error message, do you solve your problem ? I'm realy interested !
Thanks,
Jeremy |
| |
| Nick Shulman responded: |
2018-09-11 |
|
| |
| derock j responded: |
2018-09-12 |
Nick,
Thanks a lot for your answer.
I just upload the results (named : Peaks Studio to Skyline). They are 1 .pep.xml file and 4 .mzxml files (because I performed Peaks search on 4 différent MS2 analysis and combined them together, the same problem arise with a single search). MS2 analysis were performed on Impact II from Bruker and peptide search was performed with Peaks studio. I export .pep.xml and .mzxml files. I was not able to created a library from those files, I got this error message :
System.IO.IOException: ERROR: No spectra were found for the new library.
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in c:\Users\nicksh\svn\skyline_3_6_installer2\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 59
at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String[]& ambiguous) in c:\Users\nicksh\svn\skyline_3_6_installer2\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 171
at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in c:\Users\nicksh\svn\skyline_3_6_installer2\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 121
I tried to set cut-off score to 0 when creating library but it didn't work. I don't know what else to do.
Skyline version : 3.6.0.10167 or 4.1.0.11796
Peaks version : 8.5
Thank you in advance
Kind regards |
| |
| Nick Shulman responded: |
2018-09-12 |
Jeremy, Thank you for sending those files. The problem is that the scans in your .mzxml files are not in the right order. BiblioSpec expects the scans to appear in the mzXML ordered by scan number. For this reason, BiblioSpec is unable to find any of the scans that it is looking for. You can work around this problem by using "msconvert.exe" to reorder the scans in your .mzxml file.
You can install msconvert.exe from here (it's part of ProteoWizard):
http://proteowizard.sourceforge.net/download.html The "--filter sortByScanTime" option is not available in the MSConvert Graphical User Interface (msconvertgui.exe), so you have to use msconvert.exe on the command line. The commandline would be something like:
msconvert.exe myoldfolder\ProteinAnalysisResults_Impact2_U7_DoE_PT_030918_15_RB4_01_3795.mzxml --filter sortByScanTime mynewfolder\ProteinAnalysisResults_Impact2_U7_DoE_PT_030918_15_RB4_01_3795.mzxml -- Nick |
| |
| derock j responded: |
2018-09-13 |
Thank you very much !
It works just fine ! Jérémy |
| |
| kristina marx responded: |
2023-05-23 |
Hi,
some time ago that the error occurred. I never had problems with Peaks X pro but now I am using PEAKS 11.
And I get the error mentioned above: System.IO.IOException: ERROR: No spectra were found for the new library. It is a db.pep.xml exported from PEAKS 11. Is there any known issue with the current PEAKS version? Best wishes
Kristina |
| |
| Nick Shulman responded: |
2023-05-23 |
There are several things that could be causing that "No spectra were found for the new library" message.
Sometimes the problem is that there really were no peptide spectrum matches whose q-value was good enough to be included in the library, but, more often, the problem is that BiblioSpec did not understand the spectrum identifiers in the search results and so was not able to find any spectra to put into the spectral library.
If you send us your files we can figure out what is going wrong.
I think for peaks we need your pepxml and mzML files, but if you have other files that you think we might need you can send those too.
You can package everything up in a .zip file and upload it here:
https://skyline.ms/files.url
-- Nick |
| |
| kristina marx responded: |
2023-05-26 |
Hi Nick,
I uploaded the files you requested (2023-05-26_Kristina.rar)
Hope you can help me :-) |
| |
| Nick Shulman responded: |
2023-05-26 |
Thank you for uploading that .rar file containing "db.pep.xml".
Could you also send me the file "EndoIS_ISonly_DDAsetup_2_S3-A9_1_6732.d"?
You can zip that .d folder up and upload it to the same place.
-- Nick |
| |
| kristina marx responded: |
2023-05-26 |
file is uploaded |
| |
| Nick Shulman responded: |
2023-05-26 |
Kristina, Thank you for uploading that .d folder. I believe the reason that you are getting the "No spectra were found for the new library" message is that BiblioSpec does not understand the spectrum identifiers in the pep.xml file and therefore is unable to find any of the spectra in the .d folder. The way that I determined that BiblioSpec was not able to understand the spectrum identifiers is that I ran the command line executable BlibBuild.exe with with "-v warn" command line arguments.
If you want to run BlibBuild.exe form the commandline you can use the Skyline administrator installer to install Skyline in C:\Program Files\Skyline. After you have done that you would be able to run BlibBuild.exe: > "C:\Program Files\Skyline\BlibBuild.exe" -v warn -o db.pep.xml mylibrary.blib
Reading results from db.pep.xml.
Loading .\EndoIS_ISonly_DDAsetup_2_S3-A9_1_6732.d.
Reading spectra from .\EndoIS_ISonly_DDAsetup_2_S3-A9_1_6732.d.
WARNING: Did not find spectrum '791926' in '.\EndoIS_ISonly_DDAsetup_2_S3-A9_1_6732.d'.
WARNING: Did not find spectrum '801303' in '.\EndoIS_ISonly_DDAsetup_2_S3-A9_1_6732.d'.
WARNING: Did not find spectrum '1428283' in '.\EndoIS_ISonly_DDAsetup_2_S3-A9_1_6732.d'.
...
WARNING: Did not find spectrum '2970673' in '.\EndoIS_ISonly_DDAsetup_2_S3-A9_1_6732.d'.
ERROR: No spectra were found for the new library.
I will ask my coworkers and find out what you can do about this.
-- Nick |
| |
|
|