pepXML is a common file format for storing the results of assigning peptides to MS/MS spectra and subsequent peptide-level analyses. IPP will use the pepXML file format to store peptide level data. Prior to IPP analysis search data must be converted to pepXML. pepXML converters are currently available for SEQUEST, Mascot, COMET and X!Tandem search results. The Mascot software contains a pepXML exporter.