mzML—a Community Standard for Mass Spectrometry Data

Abstract

Mass spectrometry is a fundamental tool for discovery and analysis in the life sciences. With the rapid advances in mass spectrometry technology and methods, it has become imperative to provide a standard output format for mass spectrometry data that will facilitate data sharing and analysis. Initially, the efforts to develop a standard format for mass spectrometry data resulted in multiple formats, each designed with a different underlying philosophy. To resolve the issues associated with having multiple formats, vendors, researchers, and software developers convened under the banner of the HUPO PSI to develop a single standard. The new data format incorporated many of the desirable technical attributes from the previous data formats, while adding a number of improvements, including features such as a controlled vocabulary with validation tools to ensure consistent usage of the format, improved support for selected reaction monitoring data, and immediately available implementations to facilitate rapid adoption by the community. The resulting standard data format, mzML, is a well tested open-source format for mass spectrometer output files that can be readily utilized by the community and easily adapted for incremental advances in mass spectrometry technology.

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Affiliated Institutions

• Ghent University BE
• Leibniz Institute of Plant Biochemistry DE
• University of Tübingen DE
• European Bioinformatics Institute GB
• SIB Swiss Institute of Bioinformatics CH
• Institute for Systems Biology US
• University of California, Los Angeles US
• VIB-UGent Center for Medical Biotechnology BE
• Justus-Liebig-Universität Gießen DE
• Insilicos (United States) US
• Agilent Technologies (United States) US
• Vanderbilt University US
• Wellcome Trust GB
• University of Southern California US
• Lund University SE
• University of Pennsylvania US
• Stowers Institute for Medical Research US
• Thermo Fisher Scientific (United States) US

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