We want to use IonQuant alone, without the whole MSFragger pipeline. When I feed IonQuant our pepxml file like this:
java -jar IonQuant-1.5.5.jar --specdir /path/to/spectral-directory/ my.pepXML
It returns the following error:
Please specify the directory containing the spectral file corresponding to /path/to/my.pepXML
When I feed IonQuant a pepXML file generated by MSFragger on the same original spectral file, the same command works. This makes me think the problem is an incompatibility between IonQuant and my.pepXML, not the directory containing the spectral file fed to IonQuant, and not the IonQuant execution itself. I would appreciate any help with pointing out where that incompatibility may be. I have included a portion of the relevant header of my.pepXML here:
Hello,
We want to use IonQuant alone, without the whole MSFragger pipeline. When I feed IonQuant our pepxml file like this:
java -jar IonQuant-1.5.5.jar --specdir /path/to/spectral-directory/ my.pepXML
It returns the following error:Please specify the directory containing the spectral file corresponding to /path/to/my.pepXML
When I feed IonQuant a pepXML file generated by MSFragger on the same original spectral file, the same command works. This makes me think the problem is an incompatibility between IonQuant and my.pepXML, not the directory containing the spectral file fed to IonQuant, and not the IonQuant execution itself. I would appreciate any help with pointing out where that incompatibility may be. I have included a portion of the relevant header of my.pepXML here:
I have also included a portion of the relevant header for the MSFragger pepXML file here: