Tools implementing mzIdentML

Status of support for mzIdentML in proteome informatics software


MascotmzIdentML Version 1.0 available in Mascot version 2.3, mzid stable version 1.1 available in Mascot version 2.4EXPORT
OMSSA from the U.Liverpool groupEXPORT
MSGF+Full support for results into mzid 1.1EXPORT
PeaksNative export of mzIdentML version 1.1EXPORT
PhenyxExporter to mzIdentML v1.1 now available - contact GeneBio for details.EXPORT

- conversion of SEQUEST resp. Comet *.out files/folder information into mzIdentML 1.0 / 1.1 (SpectrumIdentificationResults only)

- conversion of ProteinScape 1.3 results into mzIdentML

- conversion of ProteinScape2.1 results into mzIdentML 1.1

- conversion of ProteomeDiscoverer 1.1 + 1.2 *.msf and *.prot.xml files (Thermo) resp. ProteomeDiscoverer 1.3 + 1.4 *.msf files (Thermo) into mzIdentML 1.1

ProteinPilotContact is Sean Seymour 
ProteinScapeWork in progress 
SEQUEST - NativeProCon (see above) 
ProteoWizardpepXML converter available now - impl. of C++ library for reading/writing MzIdentML / interface for importing other formatsIMPORT AND EXPORT
SEQUEST - BioWorksWork in progress 
SEQUEST - Proteome DiscovererWork in progress (exporters available from ProCon project) 
SpectraSTProteowizard conversion from pepXMLEXPORT
Spectrum Mill  
X!Tandem from the U.Liverpool group.EXPORT
OpenMSFully supported in release 1.9IMPORT AND EXPORT

Available now in Scaffold version 3.0 (export only); Scaffold 4.0 supports IMPORT AND EXPORT

Scaffold PTMScaffold PTM tool imports identifications in mzIdentMLIMPORT
Scaffold perSPECtivesSupports import of mzIdentML (as long as a ProteinDetectionList is present)IMPORT
TPPpepXML to mzIdentML converter available from ProteoWizardIMPORT AND EXPORT
Mascot IntegraScheduled
MIAPE MSI ExtractorTool available from the ProteoRed team: latest version available here.IMPORT

CSV exporter

mzIdentML2CSV in converter written by U.Liverpool group

PAnalyzerThe 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
MyrimatchIdentifications exported in mzIdentMLEXPORT
TagRecon Identifications exported in mzIdentMLEXPORT
PepitomeIdentifications exported in mzIdentMLEXPORT
IDPicker Version 3.x implements mzIdentML importIMPORT
jmzIdentMLJava API for reading and writing mzIdentMLIMPORT AND EXPORT
mzidLibraryLibrary of routines for post-processing mzIdentML (setting thresholds, FDR, protein inference, CSV export)IMPORT AND EXPORT
ProteoIDViewerOpen source viewerIMPORT

mzID package

 R package available throgh BioconductorIMPORT


Java standalone tool for the analysis and post-processing of MS proteomics experimentsIMPORT AND EXPORT


Software toolkit for tandem mass spectrometry analysis. PMID: 18505281.IMPORT AND EXPORT 


PIA is a toolbox for MS based protein inference and identification analysis. PMID: 25938255.IMPORT AND EXPORT 


Integrated Proteomics Pipeline (from Integrated Proteomics Applications)EXPORT


IPeak is a peptide identification pipeline that is designed to combine a post-processing algorithm and multi-search strategy to enhance the sensitivity of peptide identifications without comprimising accuracy. PMID: 25951428.IMPORT AND EXPORT
IQuantIQuant is an automated pipeline for quantitative proteomics based upon isobaric tags. PMID: 25069810.IMPORT
PGAPGA provides functions for construction of customized protein databases based on RNA-Seq data with/without genome guided, database searching, post-processing (accept mzid) and report generation.  IMPORT