jTraML statistics

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Citations per year

Number of citations per year for the bioinformatics software tool jTraML

Tool usage distribution map

This map represents all the scientific publications referring to jTraML per scientific context
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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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