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. 2012 Mar;12(6):795-8.
doi: 10.1002/pmic.201100578.

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats

Johannes Griss  1 , Florian Reisinger, Henning Hermjakob, Juan Antonio Vizcaíno
Affiliations
Free PMC article

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats

Johannes Griss et al. Proteomics. 2012 Mar.
Free PMC article

Abstract

We here present the jmzReader library: a collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML (based on the already existing API jmzML). The library is optimized to be used in conjunction with mzIdentML, the recently released standard data format for reporting protein and peptide identifications, developed by the HUPO proteomics standards initiative (PSI). mzIdentML files do not contain spectra data but contain references to different kinds of external MS data files. As a key functionality, all parsers implement a common interface that supports the various methods used by mzIdentML to reference external spectra. Thus, when developing software for mzIdentML, programmers no longer have to support multiple MS data file formats but only this one interface. The library (which includes a viewer) is open source and, together with detailed documentation, can be downloaded from http://code.google.com/p/jmzreader/.

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Figures

Figure 1
Figure 1
Simplified schema of the jmzReader library's structure displaying its main components and their dependencies. All parsers implement the common jmzReader interface and, in addition, provide a file-format specific Java object model to access a file format's specific information. Thereby, each parser can be used independently of the rest of the jmzReader library. If this detailed information is not required, programmers can process all seven supported file formats using a single, easy-to-use Java interface.
Figure 2
Figure 2
Screenshot of the jmzReader GUI after opening a mzXML file. The selected spectrum is displayed using the mzGraphBrowser library (http://code.google.com/p/pride-toolsuite/wiki/PRIDEmzGraphBrowser). This library allows the user to manually annotate a spectrum and export the loaded file into MGF format. The jmzReader GUI is built using the jmzReader interface and, thus, supports all file formats supported by the jmzReader library.
See this image and copyright information in PMC

References

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