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Tools implementing mzIdentML

Status of support for mzIdentML in proteome informatics software


Status / Description
Byonic (Protein Metrics Inc.)SearchByonic search engine supports mzIdentML 1.1 as an output format
CruxSearchSupports mzIdentML 1.1 as an output format and reads mzIdentML 1.1 to generate spectral count data & EF
IDPickerGroupingVersion 3.x implements mzIdentML 1.1 import
IP2Search & QuantIntegrated Proteomics Pipeline supports export of results into mzIdentML 1.1
IquantQuantAutomated pipeline for quantification by using isobaric tags; identification results are imported via mzIdentML 1.1
jmzIdentMLIOJava API for reading and writing mzIdentML 1.1 & EF
jPOSTDatabaseidentification result files can be uploaded in mzIdentML 1.1
Mascot (Matrix Science)Search & QuantmzIdentML version 1.1 available in Mascot version 2.4+
MassIVEDatabaseidentification files can be uploaded in mzIdentML 1.1https://massive.ucsd.eduIF
ms-data-core-apiIOJava API that supports reading of PSI standard and open formats e.g. mzML, mzIdentML, mzTab, mgf and others.
MS-GF+SearchFull support for exporting identification results into mzIdentML 1.1
MyriMatchSearchIdentifications exported in mzIdentML 1.1
mzID packageIOR package available through Bioconductor supporting v 1.1
mzidLibraryPost-processingRoutines and viewer (stats, protein inference, CSV import/export, proteogenomics) supporting v1.1 and 1.2 & EF
OMSSA [mzidLib]SearchConverter from OMSSA .omx files to v1.1 or 1.2 in mzidLibrary.
OpenMSPipelinemzIdentML 1.1 fully supported in release 1.9 + & EF
PAnalyzerGroupingUsed for protein grouping; it imports and exports mzIdentML (v1.1 and 1.2) & EF
PEAKS (Bioinformatics Solutions Inc.)Search & QuantNative export of mzIdentML version 1.1
PeptideShakerPost-processingJava stand-alone tool for the analysis and post-processing of proteomics experiments; it support mzIdentML 1.1 & 1.2 & EF
PGAProteogenomicsSoftware for creating RNA-Seq based databases; it supports v1.1 as an input format for post-processing.
PIAGroupingToolbox for protein inference and identification analysis; it supports mzIdentML 1.1. & EF
ProteinLynx Global ServerSearch & QuantPeptide/protein identification and quantification software; it supports export to mzIdentML in version 3.0.3+
PRIDEDatabasemzIdentML 1.1 fully supported as an import format as part of the “complete” dataset submission pipeline
PRIDE InspectorVisualisationJava stand-alone tool that can be used to visualise mzIdentML 1.1 files, independently or together with the corresponding mass spectra files (available in any open formats e.g. mzML, mzXML, mgf, dta, pkl, and apl).
Progenesis QI for proteomics (Waters Corp.)QuantLabel-free quantification software can read identifications from Byonic in mzIdentML 1.1
ProteinPilotSearch & QuantProteinPilot 5.0+ exports search results in mzIdentML version 1.2.
ProteinScape (Bruker)Search & QuantIt imports search engine results other than Mascot in mzIdentML 1.1
SEQUEST / Proteome Discoverer (Thermo) [m2Lite / ProCon]Search & QuantConversion of msf files from Proteome Discoverer to mzIdentML 1.1 via m2Lite or ProCon (ProCon also supports ProteinScape and Comet conversions).

ProteoAnnotatorProteogenomicsProteogenomics software that uses mzIdentML 1.1 as its internal file format
ProteoWizardIOpepXML converter available and support for reading/writing mzIdentML 1.1 & EF
ScaffoldSearch & QuantScaffold 4.0+ supports reading and writing of mzIdentML 1.1 & EC
Spectrum Identification Machine for Cross-Linked Peptides (SIM-XL)SearchSpectrum Identification Machine for cross-linked Peptides. PMID: 25638023
SkylineQuantSRM/MRM/PRM, DIA and targeted DDA software can import mzIdentML 1.1 for spectral library constructionhttps://skyline.msIF
Trans Proteomic Pipeline [ProteoWizard]PipelinepepXML to mzIdentML 1.1 converter available from ProteoWizard & EF
X!Tandem [mzidLib]SearchConverter from X!Tandem XML files to mzIdentML 1.1 or 1.2 as part of the mzidLibrary.
PACom (Proteomics Assay Comparator)Integration, visualisation and comparisonTool for the integration, visualization and comparison of multiple datasets. It supports mzIdentML 1.1 and 1.2. 
DTASelect2MzIdIOConverter from DTASelect output files to mzIdentML 1.2. 
Proteome DiscovererAnalysis softwareThe software offers a full suite of analysis tools. Flexible to address multiple research workflows and an easy-to-use interface. 
xiFDRAnalysis softwareCrosslinking / Mass Spectrometry error control software which exports mzIdentML 1.2 
xiVIEWVisualisation softwareWeb-based Crosslinking / Mass Spectrometry visualisation software which reads mzIdentML 1.2