X Tandem and Spectra from higher charge states

[tgreco]

I was wondering if anyone running X Tandem searches through TPP has been able to include spectra with > 3+ in the search output.  My mzXML files are from an Orbitrap analyses and I have verified that MS2 spectra were acquired for >3+ charge states.   I am specifying the following command in the X Tandem parameter file:

<note type="input" label="spectrum, maximum parent charge">5</note>

However, after the database search, when I inspect the resulting pep.xml, all the spectra with > 3+ are removed (about 5% of the total scans). Many of them meet the minimum required peak count threshold, so I'm not sure why they aren't being passed into the final output.  If anyone has encountered this issue and has found a solution, please let me know.

Thanks,

Todd