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.
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