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jmzTab: A Java interface to the mzTab data standard
Article first published online: 29 APR 2014
© 2014 The Authors PROTEOMICS Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Volume 14, Issue 11, pages 1328–1332, June 2014
How to Cite
Xu, Q.-W., Griss, J., Wang, R., Jones, A. R., Hermjakob, H. and Vizcaíno, J. A. (2014), jmzTab: A Java interface to the mzTab data standard. Proteomics, 14: 1328–1332. doi: 10.1002/pmic.201300560
- Issue published online: 5 JUN 2014
- Article first published online: 29 APR 2014
- Accepted manuscript online: 22 MAR 2014 07:01PM EST
- Manuscript Accepted: 18 MAR 2014
- Manuscript Revised: 26 FEB 2014
- Manuscript Received: 19 DEC 2013
- EU FP7 grant ‘‘ProteomeXchange’’. Grant Number: 260558
- BBSRC. Grant Numbers: BB/I00095X/1, BB/K01997X/1
- Natural Science Foundation of the Hubei Province (China)
- Wellcome Trust. Grant Number: WT085949MA]
- Vienna Science and Technology Fund (WWTF). Grant Number: LS11_045
- Data standard;
- Java application programming interface;
- Proteomics Standards Initiative
mzTab is the most recent standard format developed by the Proteomics Standards Initiative. mzTab is a flexible tab-delimited file that can capture identification and quantification results coming from MS-based proteomics and metabolomics approaches. We here present an open-source Java application programming interface for mzTab called jmzTab. The software allows the efficient processing of mzTab files, providing read and write capabilities, and is designed to be embedded in other software packages. The second key feature of the jmzTab model is that it provides a flexible framework to maintain the logical integrity between the metadata and the table-based sections in the mzTab files. In this article, as two example implementations, we also describe two stand-alone tools that can be used to validate mzTab files and to convert PRIDE XML files to mzTab. The library is freely available at http://mztab.googlecode.com.