idconvert

idconvert is a command line tool for converting between various file formats.

• Read: pepXML, protXML, mzIdentML (ProteoWizard supported formats)
• Write: pepXML, mzIdentML

Examples:

• idconvert
  prints usage information

• idconvert sequest.pepXML
  creates sequest.mzid in current directory

• idconvert interact.protXML
  converts interact.protXML to interact.mzid. Also reads any pepXML file referenced in the protXML file if available. If the protXML file has been moved from its original location, the pepXML will still be found if it has also been moved to the same position relative to the protXML file. This relative position is determined by reading the protXML protein_summary:summary_xml and protein_summary_header:source_files values.

• idconvert mascot.mzid --pepXML
  converts mascot.mzid to mascot.pepXML

• idconvert omssa.pepXML -o my_output_dir
  puts output file in my_output_dir