The final prophet in the pantheon is ProteinProphet 5 , which takes as input the output from any tool that writes pepXML with probabilities (typically PeptideProphet, iProphet, with or without PTMProphet) and writes protXML as output, providing protein inference information based on the input PSMs and their probabilities. Corroborating information is again learned via Bayesian models to provide robust probabilities for each protein in the most parsimonious list of which have been truly detected in the sample.