Hi Kaipo,
Here is the messages I got when trying to import the pep.xml from comet, the mzml from msgf+ and the mzid from peptideshaker.
First the comet pep.xml file with the mzML together in one directory and gives this error below.
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Skyline
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ERROR: Invalid cvParam accession "1003145".
ERROR: PwizReader could not parse .\20210408_TSQALTIS_UM2_Graaf168_SA_SN10824024_PTA-013_MSMS.mzML
Command-line: C:\Users\ErikdeGraafPepscope\AppData\Local\Apps\2.0\2328QLZT.01Q\9LTA2RM4.Z08\skyl..tion_e4141a2a22107248_0014.0002_2f1cb11a037aa924\BlibBuild -s -A -H -o -c 0 -i comet -S "C:\Users\ErikdeGraafPepscope\AppData\Local\Temp\tmp7B64.tmp" "C:\Temp\SearchGUI\Comet-MSGFplus-Unimod\comet.redundant.blib"
Working directory: C:\Temp\SearchGUI\Comet-MSGFplus-Unimod
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OK More Info
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System.IO.IOException: ERROR: Invalid cvParam accession "1003145".
ERROR: PwizReader could not parse .\20210408_TSQALTIS_UM2_Graaf168_SA_SN10824024_PTA-013_MSMS.mzML
Command-line: C:\Users\ErikdeGraafPepscope\AppData\Local\Apps\2.0\2328QLZT.01Q\9LTA2RM4.Z08\skyl..tion_e4141a2a22107248_0014.0002_2f1cb11a037aa924\BlibBuild -s -A -H -o -c 0 -i comet -S "C:\Users\ErikdeGraafPepscope\AppData\Local\Temp\tmp7B64.tmp" "C:\Temp\SearchGUI\Comet-MSGFplus-Unimod\comet.redundant.blib"
Working directory: C:\Temp\SearchGUI\Comet-MSGFplus-Unimod
bij pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in C:\proj\skyline_20_2_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:regel 62
bij pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_20_2_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:regel 201
bij pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:regel 156
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Then below is an example of the msgf+ output created by search gui.
I have the msgf+ *.mzid file with the *.mzML together in one directory and gives this error below.
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Skyline
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ERROR: Invalid cvParam accession "1003145".
ERROR: PwizReader could not parse .\20210408_TSQALTIS_UM2_Graaf168_SA_SN10824024_PTA-013_MSMS.mzML
Command-line: C:\Users\ErikdeGraafPepscope\AppData\Local\Apps\2.0\2328QLZT.01Q\9LTA2RM4.Z08\skyl..tion_e4141a2a22107248_0014.0002_2f1cb11a037aa924\BlibBuild -s -A -H -o -c 0 -i msgfplus -S "C:\Users\ErikdeGraafPepscope\AppData\Local\Temp\tmpCB18.tmp" "C:\Temp\SearchGUI\Comet-MSGFplus-Unimod\msgfplus.redundant.blib"
Working directory: C:\Temp\SearchGUI\Comet-MSGFplus-Unimod
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OK More Info
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System.IO.IOException: ERROR: Invalid cvParam accession "1003145".
ERROR: PwizReader could not parse .\20210408_TSQALTIS_UM2_Graaf168_SA_SN10824024_PTA-013_MSMS.mzML
Command-line: C:\Users\ErikdeGraafPepscope\AppData\Local\Apps\2.0\2328QLZT.01Q\9LTA2RM4.Z08\skyl..tion_e4141a2a22107248_0014.0002_2f1cb11a037aa924\BlibBuild -s -A -H -o -c 0 -i msgfplus -S "C:\Users\ErikdeGraafPepscope\AppData\Local\Temp\tmpCB18.tmp" "C:\Temp\SearchGUI\Comet-MSGFplus-Unimod\msgfplus.redundant.blib"
Working directory: C:\Temp\SearchGUI\Comet-MSGFplus-Unimod
bij pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in C:\proj\skyline_20_2_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:regel 62
bij pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_20_2_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:regel 201
bij pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:regel 156
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Then there is the peptideshaker mzidentml output I tried to import with this error message:
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Skyline
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ERROR: Invalid cvParam accession "1003145".
ERROR: PwizReader could not parse .\20210408_TSQALTIS_UM2_Graaf168_SA_SN10824024_PTA-013_MSMS.mzML
Command-line: C:\Users\ErikdeGraafPepscope\AppData\Local\Apps\2.0\2328QLZT.01Q\9LTA2RM4.Z08\skyl..tion_e4141a2a22107248_0014.0002_2f1cb11a037aa924\BlibBuild -s -A -H -o -c 0 -i comet_msgfplus_mzidentml -S "C:\Users\ErikdeGraafPepscope\AppData\Local\Temp\tmpABFA.tmp" "C:\Temp\SearchGUI\Comet-MSGFplus-Unimod\comet_msgfplus_mzidentml.redundant.blib"
Working directory: C:\Temp\SearchGUI\Comet-MSGFplus-Unimod
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OK More Info
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System.IO.IOException: ERROR: Invalid cvParam accession "1003145".
ERROR: PwizReader could not parse .\20210408_TSQALTIS_UM2_Graaf168_SA_SN10824024_PTA-013_MSMS.mzML
Command-line: C:\Users\ErikdeGraafPepscope\AppData\Local\Apps\2.0\2328QLZT.01Q\9LTA2RM4.Z08\skyl..tion_e4141a2a22107248_0014.0002_2f1cb11a037aa924\BlibBuild -s -A -H -o -c 0 -i comet_msgfplus_mzidentml -S "C:\Users\ErikdeGraafPepscope\AppData\Local\Temp\tmpABFA.tmp" "C:\Temp\SearchGUI\Comet-MSGFplus-Unimod\comet_msgfplus_mzidentml.redundant.blib"
Working directory: C:\Temp\SearchGUI\Comet-MSGFplus-Unimod
bij pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in C:\proj\skyline_20_2_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:regel 62
bij pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_20_2_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:regel 201
bij pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:regel 156
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Could it be due to type of raw file that only contains targeted MS/MS scans on the Altis?
I actually prefer to use MSAmanda because it gives better phosphosite localisation as output. I can also generate some files for you for this as well.
Greetings,
Erik |