Tools implementing mzIdentML

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