All low charge peptides being lost in peptide prophet?

[KMackay]

Hi.

I am running samples through the TPP (web interface) post Mascot searching by importing the .dat files for conversion to pep.xml.  I seem to be loosing all the low charge (<5) peptides between this file and the interact.pep.xml.  The pep.xml files are ~16000KB in size which is reduced to ~ 200KB, even when no filters are applied by myself.  When inspecting the files in notepad++ I can't see any peptides with an assumed charge under +5.  Does anyone know why this would be?  I am currently running using: filter out results below PeptideProphet probability 0.05 and min. peptide length of 7.  All other selections are left blank except that to run ProteinProphet afterwards.

Thanks.