A common open representation of mass spectrometry data and its application to proteomics research

Patrick G A Pedrioli, Jimmy K. Eng, Robert Hubley, Mathijs Vogelzang, Eric W. Deutsch, Brian Raught, Brian Pratt, Erik Nilsson, Ruth H. Angeletti, Rolf Apweiler, Kei Cheung, Catherine E. Costello, Henning Hermjakob, Sequin Huang, Randall K. Julian, Eugene Kapp, Mark E. McComb, Stephen G. Oliver, Gilbert Omenn, Norman W. PatonRichard Simpson, Richard Smith, Chris F. Taylor, Weimin Zhu, Ruedi Aebersold

    Research output: Contribution to journalArticlepeer-review


    A broad range of mass spectrometers are used in mass spectrometry (MS)-based proteomics research. Each type of instrument possesses a unique design, data system and performance specifications, resulting in strengths and weaknesses for different types of experiments. Unfortunately, the native binary data formats produced by each type of mass spectrometer also differ and are usually proprietary. The diverse, nontransparent nature of the data structure complicates the integration of new instruments into preexisting infrastructure, impedes the analysis, exchange, comparison and publication of results from different experiments and laboratories, and prevents the bioinformatics community from accessing data sets required for software development. Here, we introduce the 'mzXML' format, an open, generic XML (extensible markup language) representation of MS data. We have also developed an accompanying suite of supporting programs. We expect that this format will facilitate data management, interpretation and dissemination in proteomics research.
    Original languageEnglish
    Pages (from-to)1459-1466
    Number of pages7
    JournalNature biotechnology
    Issue number11
    Publication statusPublished - Nov 2004

    Research Beacons, Institutes and Platforms

    • Manchester Institute of Biotechnology


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