Status of support for mzIdentML in proteome informatics software
| Tool | Status | IMPORT/EXPORT |
| Mascot | mzIdentML Version 1.0 available in Mascot version 2.3, mzid stable version 1.1 available in Mascot version 2.4 | EXPORT |
| OMSSA | http://code.google.com/p/mzidentml-lib/ from the U.Liverpool group | EXPORT |
| MSGF+ | Full support for results into mzid 1.1 | EXPORT |
| Peaks | Native export of mzIdentML version 1.1 | EXPORT |
| Phenyx | Exporter to mzIdentML v1.1 now available - contact GeneBio for details. | EXPORT |
| PLGS | ||
| ProCon | - conversion of SEQUEST *.out files/folder information into mzIdentML (SpectrumIdentificationResults only) - conversion of ProteomeDiscoverer 1.2 + 1.3 (Thermo) *.msf and *.prot.xml files into mzIdentML | EXPORT |
| ProteinPilot | Contact is Sean Seymour | |
| ProteinScape | Work in progress | |
| SEQUEST - Native | ProCon (see above) | |
| ProteoWizard | pepXML converter available now - impl. of C++ library for reading/writing MzIdentML / interface for importing other formats | IMPORT AND EXPORT |
| SEQUEST - BioWorks | Work in progress | |
| SEQUEST - Proteome Discoverer | Work in progress (exporters available from ProCon project) | |
| SpectraST | Proteowizard conversion from pepXML | EXPORT |
| Spectrum Mill | ||
| X!Tandem | http://code.google.com/p/mzidentml-lib/ from the U.Liverpool group. | EXPORT |
| OpenMS | Fully supported in release 1.9 | IMPORT AND EXPORT |
| Scaffold | Available now in Scaffold version 3.0 | EXPORT |
| Scaffold PTM | Scaffold PTM tool imports identifications in mzIdentML | IMPORT |
| TPP | pepXML to mzIdentML converter available from ProteoWizard | IMPORT AND EXPORT |
| Mascot Integra | Scheduled | |
| MIAPE MSI Extractor | Tool available from the ProteoRed team: latest version available here. | IMPORT |
CSV exporter | mzIdentML2CSV in http://code.google.com/p/mzidentml-lib/ converter written by U.Liverpool group | IMPORT |
| PAnalyzer | The PAnalyzer tool developed by the University of the Basque Country also imports and exports mzIdentML (v1.0.0 and v1.1.0) | IMPORT AND EXPORT |
| Myrimatch | Identifications exported in mzIdentML | EXPORT |
| TagRecon | Identifications exported in mzIdentML | EXPORT |
| Pepitome | Identifications exported in mzIdentML | EXPORT |
| IDPicker | Version 3.x implements mzIdentML import | IMPORT |
| jmzIdentML | Java API for reading and writing mzIdentML | IMPORT AND EXPORT |
| mzidLibrary | Library of routines for post-processing mzIdentML (setting thresholds, FDR, protein inference, CSV export) | IMPORT AND EXPORT |
| ProteoIDViewer | Open source viewer | IMPORT |