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J Proteome Res. 2011 Nov 4;10(11):5260-3. doi: 10.1021/pr200664h. Epub 2011 Oct 13.

jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions.

Author information

1
Department of Medical Protein Research, VIB , Ghent, Belgium.

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 .

PMID:
21967198
PMCID:
PMC3208355
DOI:
10.1021/pr200664h
[Indexed for MEDLINE]
Free PMC Article

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