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Anal Chem. 2019 Mar 5;91(5):3302-3310. doi: 10.1021/acs.analchem.8b04310. Epub 2019 Feb 13.

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics.

Author information

1
Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V. , Otto-Hahn-Straße 6b , 44227 Dortmund , Germany.
2
Wellcome Sanger Institute , Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA , United Kingdom.
3
Applied Bioinformatics Group, Center for Bioinformatics , University of Tübingen , Sand 14 , 72076 Tübingen , Germany.
4
Institute of Computational Biotechnology , Graz University of Technology , Petersgasse 14 , 8010 Graz , Austria.
5
Center for Explorative Lipidomics , BioTechMed-Graz , 8010 Graz , Austria.
6
European Molecular Biology Laboratory , European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD , United Kingdom.
7
Medizinisches Proteom Center (MPC) , Ruhr-Universität Bochum , Universitätsstraße 150 , D-44801 Bochum , Germany.
8
Metabolomics Australia , The University of Melbourne , Parkville , Victoria 3010 , Australia.
9
MRC-NIHR National Phenome Centre, Department of Surgery & Cancer , Imperial College London , London SW7 2AZ , United Kingdom.
10
University of Oxford , e-Research Centre , 7 Keble Road , Oxford OX1 3QG , United Kingdom.
11
BGI-Shenzhen , Shenzhen , 518083 , People's Republic of China.
12
Institute of Integrative Biology, University of Liverpool , Liverpool L69 7ZB , United Kingdom.
13
International Agency for Research on Cancer , 150 cours Albert Thomas , 69008 Lyon , France.
14
Department of Stress and Developmental Biology , Leibniz Institute of Plant Biochemistry , 06120 Halle , Germany.
15
German Centre for Integrative Biodiversity Research (iDiv) , Halle-Jena-Leipzig Deutscher, Platz 5e , 04103 Leipzig , Germany.

Abstract

Mass spectrometry (MS) is one of the primary techniques used for large-scale analysis of small molecules in metabolomics studies. To date, there has been little data format standardization in this field, as different software packages export results in different formats represented in XML or plain text, making data sharing, database deposition, and reanalysis highly challenging. Working within the consortia of the Metabolomics Standards Initiative, Proteomics Standards Initiative, and the Metabolomics Society, we have created mzTab-M to act as a common output format from analytical approaches using MS on small molecules. The format has been developed over several years, with input from a wide range of stakeholders. mzTab-M is a simple tab-separated text format, but importantly, the structure is highly standardized through the design of a detailed specification document, tightly coupled to validation software, and a mandatory controlled vocabulary of terms to populate it. The format is able to represent final quantification values from analyses, as well as the evidence trail in terms of features measured directly from MS (e.g., LC-MS, GC-MS, DIMS, etc.) and different types of approaches used to identify molecules. mzTab-M allows for ambiguity in the identification of molecules to be communicated clearly to readers of the files (both people and software). There are several implementations of the format available, and we anticipate widespread adoption in the field.

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