Tools implementing mzIdentML

Status of support for mzIdentML in proteome informatics software

 

ToolStatusIMPORT/EXPORT
MascotmzIdentML Version 1.0 available in Mascot version 2.3, mzid stable version 1.1 available in Mascot version 2.4EXPORT
OMSSAhttps://github.com/fghali/mzidlib from the U.Liverpool groupEXPORT
MSGF+Full support for results into mzid 1.1EXPORT
PeaksNative export of mzIdentML version 1.1EXPORT
EasyProtExporter to mzIdentML v1.1 now available - contact GeneBio for details.EXPORT
PLGSVersion 3.0.3EXPORT 
ProCon

- 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

EXPORT
ProteinPilotThe ProteinPilot software now exports search results in mzIDentML version 1.2 candidate format. PMID: 25092112.EXPORT
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!Tandemhttps://github.com/fghali/mzidlib from the U.Liverpool group.EXPORT
OpenMSFully supported in release 1.9IMPORT AND EXPORT
ScaffoldAvailable now in Scaffold version 3.0 (export only); Scaffold 4.0 supports IMPORT AND EXPORTIMPORT AND EXPORT (In 4.0)
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 exportermzIdentML2CSV in https://github.com/fghali/mzidlib converter written by U.Liverpool groupIMPORT
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 packageR package available throgh Bioconductor.IMPORT
PeptideShakerJava standalone tool for the analysis and post-processing of MS proteomics experiments. PMID: 25574629.IMPORT AND EXPORT
CruxSoftware toolkit for tandem mass spectrometry analysis. PMID: 18505281.IMPORT AND EXPORT 
PIAPIA is a toolbox for MS based protein inference and identification analysis. PMID: 25938255.IMPORT AND EXPORT 
IP2Integrated Proteomics Pipeline (from Integrated Proteomics Applications)EXPORT
IPeakIPeak 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

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