In mzXML output file it is expected to put software name and version in dataProcessing element. Unfortunately converting RAW file to mzXML with ProteoWizard does not provide this information. This cause jrap parser failure.
Example:
<dataProcessing>
<software type="conversion" name="ReAdW" version="4.2.1(build Apr 7 2009 13:17:55)" />
</dataProcessing>
Thanks