Hi,
 
I got the pepXML and protXML files with TPP software (V.4.3), and wanted to use CPAS (v.8.1) for comparing the results from different groups. However, I found many obvious errors that the number of unique peptides of a protein is more than that of total peptides. There were many proteins identified with even zero total peptide and without AAcoverage information, although might the unique peptide number is much larger. I checked the TPP output and didn't find these errors. Is this due to the incompatible of the two softwares?