mzML—a Community Standard for Mass Spectrometry Data

TLDR

Mass spectrometry is a fundamental life‑science tool, and rapid technological advances have produced multiple competing formats, underscoring the need for a unified standard to enable data sharing and analysis. The HUPO PSI convened to create a single standard that resolves the fragmentation caused by multiple mass‑spectrometry data formats. The format combines prior desirable attributes with enhancements such as a controlled vocabulary with validation tools, improved support for selected reaction monitoring, and ready‑made implementations to promote rapid community adoption. mzML is a well‑tested open‑source format that the community can readily use and that can be easily extended to accommodate future technological advances.

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.