JTraML: An open source java API for TraML, the PSI standard for sharing SRM transitions

Kenny Helsens; Mi Youn Brusniak; Eric Deutsch; Robert L. Moritz; Lennart Martens

doi:10.1021/pr200664h

JTraML: An open source java API for TraML, the PSI standard for sharing SRM transitions

Kenny Helsens, Mi Youn Brusniak, Eric Deutsch, Robert L. Moritz, Lennart Martens

Research output: Contribution to journal › Article › peer-review

18 Citations (Scopus)

Abstract

We here present jTraML, a Java API for the Proteomics Standards Initiative TraML data standard. The library provides fully functional classes for all elements specified in the TraML XSD document, as well as convenient methods to construct controlled vocabulary-based instances required to define SRM transitions. The use of jTraML is demonstrated via a two-way conversion tool between TraML documents and vendor specific files, facilitating the adoption process of this new community standard. The library is released as open source under the permissive Apache2 license and can be downloaded from http://jtraml.googlecode.com. TraML files can also be converted online at http://iomics.ugent.be/jtraml.

Original language	English
Pages (from-to)	5260-5263
Number of pages	4
Journal	Journal of Proteome Research
Volume	10
Issue number	11
DOIs	https://doi.org/10.1021/pr200664h
Publication status	Published - 4 Nov 2011
Externally published	Yes

Keywords

bioinformatics
mass spectrometry
proteomics
selection reaction monitoring
standards

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10.1021/pr200664h

Cite this

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abstract = "We here present jTraML, a Java API for the Proteomics Standards Initiative TraML data standard. The library provides fully functional classes for all elements specified in the TraML XSD document, as well as convenient methods to construct controlled vocabulary-based instances required to define SRM transitions. The use of jTraML is demonstrated via a two-way conversion tool between TraML documents and vendor specific files, facilitating the adoption process of this new community standard. The library is released as open source under the permissive Apache2 license and can be downloaded from http://jtraml.googlecode.com. TraML files can also be converted online at http://iomics.ugent.be/jtraml.",

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AU - Martens, Lennart

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AB - We here present jTraML, a Java API for the Proteomics Standards Initiative TraML data standard. The library provides fully functional classes for all elements specified in the TraML XSD document, as well as convenient methods to construct controlled vocabulary-based instances required to define SRM transitions. The use of jTraML is demonstrated via a two-way conversion tool between TraML documents and vendor specific files, facilitating the adoption process of this new community standard. The library is released as open source under the permissive Apache2 license and can be downloaded from http://jtraml.googlecode.com. TraML files can also be converted online at http://iomics.ugent.be/jtraml.

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KW - proteomics

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KW - standards

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JTraML: An open source java API for TraML, the PSI standard for sharing SRM transitions

Abstract

Keywords

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