jTraML: An Open Source Java API for TraML, the PSI Standard for Sharing SRM Transitions

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...

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Bibliographic Details
Published inJournal of proteome research Vol. 10; no. 11; pp. 5260 - 5263
Main Authors Helsens, Kenny, Brusniak, Mi-Youn, Deutsch, Eric, Moritz, Robert L, Martens, Lennart
Format Journal Article
LanguageEnglish
Published United States American Chemical Society 04.11.2011
Subjects
Automatic Data Processing - standards
Database Management Systems - standards
Mass Spectrometry - standards
Programming Languages
Reference Standards
Technical Note
Terminology as Topic
User-Computer Interface
standards
mass spectrometry
proteomics
selection reaction monitoring
bioinformatics
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ISSN1535-3893
1535-3907
1535-3907
DOI10.1021/pr200664h

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Summary: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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ISSN:1535-3893
1535-3907
1535-3907
DOI:10.1021/pr200664h