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

被引：16

作者：

Helsens, Kenny ^{[1
,2
]}

Brusniak, Mi-Youn ^{[3
]}

Deutsch, Eric ^{[3
]}

Moritz, Robert L. ^{[3
]}

Martens, Lennart ^{[1
,2
]}

机构：

[1] Univ Ghent VIB, Dept Med Prot Res, Ghent, Belgium

[2] Univ Ghent, Dept Biochem, B-9000 Ghent, Belgium

[3] Inst Syst Biol, Seattle, WA USA

来源：

JOURNAL OF PROTEOME RESEARCH | 2011年 / 10卷 / 11期

基金：

美国国家卫生研究院;

关键词：

proteomics; bioinformatics; mass spectrometry; standards; selection reaction monitoring; MASS-SPECTROMETRY; PLASMA-PROTEINS; PROTEOMICS; ASSAYS; VALIDATION; DATABASE;

D O I：

10.1021/pr200664h

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：5260 / 5263

页数：4

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