jmzML statistics

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Associated diseases

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jmzML specifications


Unique identifier OMICS_03340
Name jmzML
Software type Framework/Library, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License Apache License version 2.0
Computer skills Advanced
Version 1.6.7
Stability Stable
Maintained Yes


  • mzML Viewer Application


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  • person_outline Lennart Martens <>

Additional information

Publication for jmzML

jmzML in publications

PMCID: 4416046
PMID: 25927999
DOI: 10.1371/journal.pone.0125108

[…] support for multiple standard formats. some of the more popular tools that strive towards standard-compliant implementation of (one or more) psi formats are the proteowizard library [, ], mspire [], jmzml [] mzr [], the pride toolsuite [], jmzreader [] and the openms library [] (see also perez-riverol et al. [] for a recent discussion of different open source software libraries in mass […]

PMCID: 4457114
PMID: 25726569
DOI: 10.1093/jamia/ocv001

[…] to promote adoption and to provide developers to include support for the standards in tools. these software libraries provide reading/writing functionality and other extra features. they are jmzml, jtraml, jmzidentml, jmzquantml, mzidlibrary, and jmztab. many open-source software tools implement the standards. some of them were developed in java making use of these libraries, […]

PMCID: 3013463
PMID: 20716697
DOI: 10.1074/mcp.R110.000133

[…] this functionality of openms was used to implement an off-line tool for validation of mzml files which is part of topp - the openms proteomics pipeline (). similarly, the ncbi c++ toolkit and the jmzml java toolkit () provide libraries for reading and writing mzml. because these libraries are already available to simplify addition of mzml support, several software applications are already […]

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jmzML institution(s)
EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK; Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
jmzML funding source(s)
Supported by the "ProDaC" grant LSHGCT-2006-036814 of the European Union.

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