I'm running PeptideProphetParser and ProteinProphet with MINPROB=0. In the ProtXML viewer under the peptide sequence list, there is a 'total' column for the number of spectra that peptide is included in. I've found that for spectra where that peptide has a reported 0 peptide probability, while the spectra is included in the list of spectra when you click on the sequence, the spectra is not counted in the total column. Since I'm manually setting the minprob to zero, I'd like to see those spectra counted in the total. How can I change it so they are counted? Thanks.
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