title: jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions.
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 .
authors.affiliation: Department of Medical Protein Research,  VIB , Ghent, Belgium.
authors.forename: Kenny
authors.initials: K
authors.lastname: Helsens
authors.forename: Mi-Youn
authors.initials: MY
authors.lastname: Brusniak
authors.forename: Eric
authors.initials: E
authors.lastname: Deutsch
authors.forename: Robert L
authors.initials: RL
authors.lastname: Moritz
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
mesh_terms: D003628:Database Management Systems / Q000592:standards*; D001330:Electronic Data Processing / Q000592:standards*; D013058:Mass Spectrometry / Q000592:standards*; D011381:Programming Languages; D012015:Reference Standards; D009626:Terminology as Topic; D014584:User-Computer Interface