Status of support for mzIdentML in proteome informatics software
| Tool | Type | Status / Description | URL | I/E | F/C |
| Byonic (Protein Metrics Inc.) | Search | Byonic search engine supports mzIdentML 1.1 as an output format | http://www.proteinmetrics.com/products/byonic/ | E | C |
| Crux | Search | Supports mzIdentML 1.1 as an output format and reads mzIdentML 1.1 to generate spectral count data | http://crux.ms/ | I & E | F |
| IDPicker | Grouping | Version 3.x implements mzIdentML 1.1 import | https://medschool.vanderbilt.edu/msrc-bioinformatics/software | I | F |
| IP2 | Search & Quant | Integrated Proteomics Pipeline supports export of results into mzIdentML 1.1 | http://www.integratedproteomics.com/ | E | C |
| Iquant | Quant | Automated pipeline for quantification by using isobaric tags; identification results are imported via mzIdentML 1.1 | https://sourceforge.net/projects/iquant/ | I | F |
| jmzIdentML | IO | Java API for reading and writing mzIdentML 1.1 | https://github.com/PRIDE-Utilities/jmzIdentML | I & E | F |
| jPOST | Database | identification result files can be uploaded in mzIdentML 1.1 | http://jpostdb.org/ | I | F |
| Mascot (Matrix Science) | Search & Quant | mzIdentML version 1.1 available in Mascot version 2.4+ | http://www.matrixscience.com/ | E | C |
| MassIVE | Database | identification files can be uploaded in mzIdentML 1.1 | https://massive.ucsd.edu | I | F |
| ms-data-core-api | IO | Java API that supports reading of PSI standard and open formats e.g. mzML, mzIdentML, mzTab, mgf and others. | https://github.com/PRIDE-Utilities/ms-data-core-api | I | F |
| MS-GF+ | Search | Full support for exporting identification results into mzIdentML 1.1 | https://omics.pnl.gov/software/ms-gf | E | F |
| MyriMatch | Search | Identifications exported in mzIdentML 1.1 | https://medschool.vanderbilt.edu/msrc-bioinformatics/software | E | F |
| mzID package | IO | R package available through Bioconductor supporting v 1.1 | http://www.bioconductor.org/packages/release/bioc/html/mzID.html | I | F |
| mzidLibrary | Post-processing | Routines and viewer (stats, protein inference, CSV import/export, proteogenomics) supporting v1.1 and 1.2 | https://github.com/PGB-LIV/mzidlib | I & E | F |
| OMSSA [mzidLib] | Search | Converter from OMSSA .omx files to v1.1 or 1.2 in mzidLibrary. | https://github.com/PGB-LIV/mzidlib | E | F |
| OpenMS | Pipeline | mzIdentML 1.1 fully supported in release 1.9 + | https://www.openms.de/ | I & E | F |
| PAnalyzer | Grouping | Used for protein grouping; it imports and exports mzIdentML (v1.1 and 1.2) | https://github.com/akrogp/EhuBio/wiki/Panalyzer | I & E | F |
| PEAKS (Bioinformatics Solutions Inc.) | Search & Quant | Native export of mzIdentML version 1.1 | http://www.bioinfor.com/ | E | C |
| PeptideShaker | Post-processing | Java stand-alone tool for the analysis and post-processing of proteomics experiments; it support mzIdentML 1.1 & 1.2 | http://compomics.github.io/projects/peptide-shaker.html | I & E | F |
| PGA | Proteogenomics | Software for creating RNA-Seq based databases; it supports v1.1 as an input format for post-processing. | http://www.bioconductor.org/packages/devel/bioc/html/PGA.html | I | F |
| PIA | Grouping | Toolbox for protein inference and identification analysis; it supports mzIdentML 1.1. | https://github.com/mpc-bioinformatics/pia | I & E | F |
| ProteinLynx Global Server | Search & Quant | Peptide/protein identification and quantification software; it supports export to mzIdentML in version 3.0.3+ | http://www.waters.com/waters/en_GB/ProteinLynx-Global-SERVER-%28PLGS%29/nav.htm?cid=513821&locale=en_GB | E | C |
| PRIDE | Database | mzIdentML 1.1 fully supported as an import format as part of the “complete” dataset submission pipeline | https://www.ebi.ac.uk/pride/archive/ | I | F |
| PRIDE Inspector | Visualisation | Java 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). | https://github.com/PRIDE-Toolsuite/pride-inspector | I | F |
| Progenesis QI for proteomics (Waters Corp.) | Quant | Label-free quantification software can read identifications from Byonic in mzIdentML 1.1 | http://www.nonlinear.com/progenesis/qi-for-proteomics/ | I | C |
| ProteinPilot | Search & Quant | ProteinPilot 5.0+ exports search results in mzIdentML version 1.2. | https://sciex.com/products/software/proteinpilot-software | E | C |
| ProteinScape (Bruker) | Search & Quant | It imports search engine results other than Mascot in mzIdentML 1.1 | https://www.bruker.com/products/mass-spectrometry-and-separations/ms-software/proteinscape/overview.html | I | C |
| SEQUEST / Proteome Discoverer (Thermo) [m2Lite / ProCon] | Search & Quant | Conversion of msf files from Proteome Discoverer to mzIdentML 1.1 via m2Lite or ProCon (ProCon also supports ProteinScape and Comet conversions). |
https://bitbucket.org/paiyetan/m2lite/downloads/ http://www.ruhr-uni-bochum.de/mpc/software/ProCon/index.html.en |
E | F* |
| ProteoAnnotator | Proteogenomics | Proteogenomics software that uses mzIdentML 1.1 as its internal file format | http://www.proteoannotator.org/ | E | F |
| ProteoWizard | IO | pepXML converter available and support for reading/writing mzIdentML 1.1 | http://proteowizard.sourceforge.net/ | I & E | F |
| Scaffold | Search & Quant | Scaffold 4.0+ supports reading and writing of mzIdentML 1.1 | http://www.proteomesoftware.com/products/scaffold/ | I & E | C |
| Spectrum Identification Machine for Cross-Linked Peptides (SIM-XL) | Search | Spectrum Identification Machine for cross-linked Peptides. PMID: 25638023 | http://patternlabforproteomics.org/sim-xl/ | E | F |
| Skyline | Quant | SRM/MRM/PRM, DIA and targeted DDA software can import mzIdentML 1.1 for spectral library construction | https://skyline.ms | I | F |
| Trans Proteomic Pipeline [ProteoWizard] | Pipeline | pepXML to mzIdentML 1.1 converter available from ProteoWizard | http://proteowizard.sourceforge.net/ | I & E | F |
| X!Tandem [mzidLib] | Search | Converter from X!Tandem XML files to mzIdentML 1.1 or 1.2 as part of the mzidLibrary. | https://github.com/PGB-LIV/mzidlib | E | F |
| PACom (Proteomics Assay Comparator) | Integration, visualisation and comparison | Tool for the integration, visualization and comparison of multiple datasets. It supports mzIdentML 1.1 and 1.2. | https://github.com/smdb21/PACOM/wiki | I | |
| DTASelect2MzId | IO | Converter from DTASelect output files to mzIdentML 1.2. | https://github.com/proteomicsyates/DTASelect2MzId | E |
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| Proteome Discoverer | Analysis software | The software offers a full suite of analysis tools. Flexible to address multiple research workflows and an easy-to-use interface. | https://www.thermofisher.com/uk/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/multi-omics-data-analysis/proteome-discoverer-software.html | E |
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| xiFDR | Analysis software | Crosslinking / Mass Spectrometry error control software which exports mzIdentML 1.2 | https://www.rappsilberlab.org/software/xifdr/ | E |
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| xiVIEW | Visualisation software | Web-based Crosslinking / Mass Spectrometry visualisation software which reads mzIdentML 1.2 | https://www.rappsilberlab.org/software/xiview/ | I |
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