Thanks for your question and interest in the TPP.
The PepXMLViewer.cgi tool can be used to display, filter and export pepXML data, including PTMProphet processed results. PTMProphet computes several statistics for each PSM and for each PTM analyzed:
Mean Best Probability -- is the average PTMProphet probability of the top m modified sites of a given type in the peptide
Normalized Information Gain -- is the information gain based on the PTMProphet probabiliy of the top m modified sites of a given type in the peptide
Localized Modification Count -- is the expected number of correct modifications of a given type localized with certainty on this peptide
For more information about there metrics please refer to the PTMProphet publication.
The reason you might want to use the more conservative Info Gain metric to threshold your results is that site probabilities are not directly comparable between PSMs with different site and PTM counts, but Info Gains are directly comparable. E.g. a Mean Best PTM probability of 0.75 on a peptide with 4 sites and 3 PTMs of the a given type means there is zero information about the location of those 3 PTMs and it means a different thing from a Mean Best PTM probability of 0.75 on a peptide with 4 sites and 1 PTM where the information regarding the location of the PTM is greater than zero!
You can set thresholds for any of these metrics on the Filter page in PepXMLViewer.cgi. Make sure to set it for the correct PTM type.
I hope I have understood your question correctly, please let me know if you have any more.