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jTraML specifications


Unique identifier OMICS_10416
Name jTraML
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Lennart Martens

Publication for jTraML

jTraML citations


Development of data representation standards by the human proteome organization proteomics standards initiative

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

[…] l 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, but other programmi […]


A tutorial for software development in quantitative proteomics using PSI standard formats☆

Biochim Biophys Acta
PMCID: 4008935
PMID: 23584085
DOI: 10.1016/j.bbapap.2013.04.004

[…] s to create tools without requiring an underlying knowledge of the source data format. Various groups have also collaborated to build APIs in Java for processing each of the standards, called jmzML , jTraML , jmzIdentML , jmzQuantML and jmzTab . The Java APIs have read/write capabilities and implement random-access strategies allowing files of any size to be processed without requiring the whole […]


Controlled vocabularies and ontologies in proteomics: Overview, principles and practice☆

Biochim Biophys Acta
PMCID: 3898906
PMID: 23429179
DOI: 10.1016/j.bbapap.2013.02.017

[…] s developed by the HUPO-PSI working group, which developed several Java libraries for the memory-efficient reading and writing of the information contained in the respective standard formats: jmzML , jTraML , jmzIdentML , jmzReader and jmzQuantML . The mzML format is the successor of the merged formats mzData and mzXML . In addition, the alternative de facto standard formats pepXML and protXML […]


Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective☆

Biochim Biophys Acta
PMCID: 3898926
PMID: 23467006
DOI: 10.1016/j.bbapap.2013.02.032

[…] cs framework provides different Java-based parsers for well-known search engines: MascotDatfile , OMSSA Parser , XTandem Parser , and Thermo-MSF-Parser , for Proteome Discoverer. It also provides the jTraML library for the TraML standard file format. Also, PeptideShaker supports the creation of a well-annotated PRIDE XML file from the combined search result files from Mascot, OMSSA and X!Tandem. […]


File Formats Commonly Used in Mass Spectrometry Proteomics*

PMCID: 3518119
PMID: 22956731
DOI: 10.1074/mcp.R112.019695

[…] ilar to SRM target lists. TraML is not yet supported by instrument vendor software, although most vendors have affirmed a plan to support it. Several open-source packages such as Anubis (), ATAQS (), jTraML (), OpenMS (), PeptideAtlas (), and Proteios () support TraML. The Skyline software program () has become a popular desktop application for the design and analysis of SRM experiments, and its o […]


TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists*

PMCID: 3322582
PMID: 22159873
DOI: 10.1074/mcp.R111.015040

[…] yeast experiment generated by ATAQS and a yeast inclusion list generated by the Proteios system (, ), which supports TraML for inclusion/exclusion lists, as well as a transition list converted by the jTraML toolkit. […]


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jTraML institution(s)
Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium; Computational Biology, Institute for Systems Biology, Seattle, WA, USA

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