mzML for Metabolomics Initiative

Background

mzML (Mass Spectrometry Markup Language) is an XML-based vendor-neutral data format for storage and exchange of mass spectrometry data developed by an international proteomics consortium, including Human Proteome Organisation (HUPO) and Proteomics Standards Initiative (PSI). The mzML format has replaced two previous formats with the same purpose developed by the proteomics community (mzXML and mzData). mzML combines the best features of mzXML and mzData with the specific purpose to provide a unified standard data format for mass spectrometry based proteomics. Metabolomics community currently lacks standard data format for the storage and exchange of mass spectrometry data. The mzML format specification provides a unique opportunity to address this challenge by building on the experience of the proteomics community, and the success of mzML.

Challenges

The mass spectrometry techniques used in metabolomics includes techniques closely related to those used in proteomics (eg. LC-MS and SRM/MRMs), and those that are more distantly related ie. gas chromatography--mass spectrometry (GC-MS) and capillary electrophoresis--mass spectrometry (CE-MS). The purpose of testing and validation is to evaluate suitability of the current mzML format specification to efficiently store data for the full range of mass spectrometry-based metabolomic techniques. It is possible that the current mzML format specification lacks features to effectively support certain needs or mass spectrometry techniques used in metabolomics; if any such instances are identified, they will be documented, and the PSI/mzML working group will be approached for consultations.

Aims

The aims of this initiative are to (1) test, (2) validate, (3) recommend, and in the long-term (4) promote the use of mzML format as a standard vendor-neutral format for mass spectrometry-based metabolomics.

Outcomes

It is envisioned that the collaborative work on this initiative may produce mzML-related software tools and documentation. A specific objectives of this initiative are to achieve a consensus view on the suitability mzML for mass spectrometry based metabolomics after testing and validation; and an agreed recommendation for the use of mzML as a standard data format for storage and exchange of metabolomic mass spectrometry data.

Participants

• Sean O'Callaghan, University of Melbourne (Australia)
• Steffen Neumann, IPB Halle (Germany)
• Nils Hoffmann, Bielefeld University (Germany)
• Eric Deutsch, Institute for Systems Biology (USA)
• Wade Hines, Australian Wine Research Institute (Australia)
• Vladimir Likic, University of Melbourne (Australia)

If interested to collaborate/contribute to this initiative please contact us [vlikic(at)unimelb.edu.au].

Advisors