[FIX] Convert  XTandem search results into .pepXML by IDFileConverter

Currently, converted pepXML in OpenMS only stores PeptideProphet results but not PeptideID information.
Fixes #809
Update for this required format. When the mz data file is not given, the scan_index (scan number) can be replaced by 00000. I tested "base_name.00000.00000.charge" is working well. This change doesn't make impact on the TPP analysis. If the correct scan_index is not needed, the changes of XTandemFile (a new metaValue "scan_index") can be thrown away.