jmzML, an open-source Java API for mzML, the PSI standard for MS data

We here present jmzML, a Java API for the Proteomics Standards Initiative mzML data standard. Based on the Java Architecture for XML Binding and XPath-based XML indexer random-access XML parser, jmzML can handle arbitrarily large files in minimal memory, allowing easy and efficient processing of mzM...

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Bibliographic Details
Published in:Proteomics (Weinheim) Vol. 10; no. 7; pp. 1332 - 1335
Main Authors: Côté, Richard G, Reisinger, Florian, Martens, Lennart
Format: Journal Article
Language:English
Published: Weinheim Wiley-VCH Verlag 01.04.2010
WILEY-VCH Verlag
WILEY‐VCH Verlag
Wiley-VCH
Subjects:
Analytical, structural and metabolic biochemistry
Bioinformatics
Biological and medical sciences
Databases, Protein
Fundamental and applied biological sciences. Psychology
Java API
Mass Spectrometry
Miscellaneous
Programming Languages
Proteins
Proteomics - methods
Proteomics Standards Initiative MS standard
Software
XML processing
Proteomics
Proteomics Standards Initiative MS standard
Java API
Standard
Bioinformatics
Standards
XML processing
ISSN:1615-9853, 1615-9861, 1615-9861
Online Access:Get full text
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Summary:We here present jmzML, a Java API for the Proteomics Standards Initiative mzML data standard. Based on the Java Architecture for XML Binding and XPath-based XML indexer random-access XML parser, jmzML can handle arbitrarily large files in minimal memory, allowing easy and efficient processing of mzML files using the Java programming language. jmzML also automatically resolves internal XML references on-the-fly. The library (which includes a viewer) can be downloaded from http://jmzml.googlecode.com.
Bibliography:http://dx.doi.org/10.1002/pmic.200900719
ArticleID:PMIC200900719
istex:D1FDF740B955789A3B8995BB609FBAAAF09BB5BA
European Union - No. LSHG-CT-2006-036814
ark:/67375/WNG-4ZFLQFK8-Q
These authors contributed equally to this work.
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ISSN:1615-9853
1615-9861
1615-9861
DOI:10.1002/pmic.200900719