These authors contributed equally to the manuscript.
jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data
Article first published online: 26 APR 2012
© 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Volume 12, Issue 6, pages 790–794, March 2012
How to Cite
Reisinger, F., Krishna, R., Ghali, F., Ríos, D., Hermjakob, H., Antonio Vizcaíno, J. and Jones, A. R. (2012), jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data. Proteomics, 12: 790–794. doi: 10.1002/pmic.201100577
Colour Online: See the article online to view Figs. 2 and 3 in colour.
- Issue published online: 26 APR 2012
- Article first published online: 26 APR 2012
- Manuscript Accepted: 15 DEC 2011
- Manuscript Revised: 14 DEC 2011
- Manuscript Received: 4 NOV 2011
- BBSRC. Grant Numbers: BB/H024654/1, BB/G010781/1
- Wellcome Trust. Grant Number: WT085949MA
- EU FP7 grants LipidomicNet. Grant Number: 202272
- ProteomeXchange. Grant Number: 260558
- Java API;
- Proteomics standards initiative (PSI);
We present a Java application programming interface (API), jmzIdentML, for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. The API combines the power of Java Architecture of XML Binding (JAXB) and an XPath-based random-access indexer to allow a fast and efficient mapping of extensible markup language (XML) elements to Java objects. The internal references in the mzIdentML files are resolved in an on-demand manner, where the whole file is accessed as a random-access swap file, and only the relevant piece of XMLis selected for mapping to its corresponding Java object. The APIis highly efficient in its memory usage and can handle files of arbitrary sizes. The APIfollows the official release of the mzIdentML (version 1.1) specifications and is available in the public domain under a permissive licence at http://www.code.google.com/p/jmzidentml/.