• Sign In
  1. Requests

Error building Spectral library from mzid generated by Peptide Shaker

support

View Request

view list print
Error building Spectral library from mzid generated by Peptide Shaker sstoychev  2018-07-17 09:26
 

Hi guys,

I'm getting the following error whilst buiding a spectral library from an mzid file generated by Peptide Shaker:

System.IO.IOException: ERROR: Could not find spectrum file HILIC_50mM 0X0.007FEDP-1022BC-HILIC[.MGF|.mzXML|.mzML] in current directory,.
ERROR:

at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in c:\proj\pwiz_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 59
at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String[]& ambiguous) in c:\proj\pwiz_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 171
at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 128

The spectra file "HILIC_50mM.mzml is stored in the same folder as the mzid file so not sure what "current directory" means in this case
 
 
Brendan MacLean responded:  2018-07-17 10:32

Hi Stoyan,
You can see from the message that Skyline is not expecting the file to be named simply "HILIC_50mM.mzml" but it should find it if you rename the file to "HILIC_50mM 0X0.007FEDP-1022BC-HILIC.mzml" (or .mzML). That appears to be the name stored in the mzIdentML file. Could you have renamed it after performing your search? If you feel the file has always had the same short name, then you should start looking at your search pipeline to understand how the longer name got into the mzIdentML file.

Anyway, for now, renaming the file should prove an acceptable workaround.

Thanks for the clear posting of your issue to the Skyline support board.

--Brendan
 
sstoychev responded:  2018-07-18 01:49

Thanks Brendan,

I think search GUI converts the mzML file to mgf and puts some time stamp on it which than appears in the mzid export from Pepetide Shaker. Will see if this can be avoided.

Regards,

Stoyan
 
Brendan MacLean responded:  2018-07-18 09:47

Note from the error message that the spectral library builder will accept .MGF or .mzMXL or .mzML. So, if you can get the .MGF that Peptide Shaker used into the same folder as the (more concisely named) mzML that should also allow you to create the spectral library without this error.

Any thoughts on how we could improve this error message to be more easily understood by our users?

Could not find spectrum file HILIC_50mM 0X0.007FEDP-1022BC-HILIC[.MGF|.mzXML|.mzML] in current directory,.

Maybe:

Could not find a spectrum file with base name "HILIC_50mM 0X0.007FEDP-1022BC-HILIC" and one of the extensions .MGF, .mzXML, or .mzML in the current directory...

Would that have made more sense? I see now that "[.MGF|.mzXML|.mzML]" is a very programmer way of stating "one of these 3 options".
 
sstoychev responded:  2018-07-18 10:03

Yes that second option is much easier to understand by someone with lack of programming experience such as me :)

The mgf file is there, search gui saves it in same folder as the original mzML but in the "concise" format i.e. without the " 0X0.007FEDP-1022BC-" part which is only in the mzid file. Have emailed the guys from Lennart's lab about this. For now will rename the mgf (or mzML) with the 0X0.007FEDP-1022BC so can see if can complete the library in Skyline