Although the TPP does not use the Proteomics Standards Initiative (PSI) (and Deutsch et al., submitted, this issue) standard format mzIdentML internally, the final output of a TPP analysis may be exported to mzIdentML 1.2 via the TPP tool tpp2mzid for deposition to ProteomeXchange repositories or for use with other mzIdentML-supporting tools. In the other direction, users may use the ProteoWizard idconvert tool (bundled with TPP) to convert externally acquired mzIdentML files to pepXML for further TPP processing.