The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

Johannes Griss¹, Andrew R Jones², Timo Sachsenberg³, Mathias Walzer³, Laurent Gatto⁴, Jürgen Hartler⁵, Gerhard G Thallinger⁵, Reza M Salek⁶, Christoph Steinbeck⁶, Nadin Neuhauser⁷, Jürgen Cox⁷, Steffen Neumann⁸, Jun Fan⁹, Florian Reisinger⁶, Qing-Wei Xu¹⁰, Noemi Del Toro⁶, Yasset Pérez-Riverol⁶, Fawaz Ghali², Nuno Bandeira¹¹, Ioannis Xenarios¹², Oliver Kohlbacher¹³, Juan Antonio Vizcaíno¹⁴, Henning Hermjakob⁶

Affiliations

¹ From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK; §Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Vienna, Austria;
² ‖Institute of Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK;
³ **Center for Bioinformatics and Department of Computer Science, University of Tübingen, D-72076 Tübingen, Germany;
⁴ ‡‡Computational Proteomics Unit and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, CB2 1QR, Cambridge, UK;
⁵ §§Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria; ¶¶Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14/V, 8010 Graz, Austria;
⁶ From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK;
⁷ ‖‖Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany;
⁸ Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
⁹ School of Biological and Chemical Sciences, Queen Mary University of London, London, UK;
¹⁰ From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK; College of Computer, Hubei University of Education, Wuhan, China;
¹¹ Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA;
¹² Swiss-Prot group, SIB Swiss Institute of Bioinformatics, 1 Rue Michel Servet, 1211 Geneva, Switzerland; Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, Genopode 1015 Lausanne; Center of Integrative Genomics, University of Lausanne, Quartier Sorge Genopode, 1015 Lausanne;
¹³ **Center for Bioinformatics and Department of Computer Science, University of Tübingen, D-72076 Tübingen, Germany; Quantitative Biology Center, University of Tübingen, D-72076 Tübingen, Germany.
¹⁴ From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK; juan@ebi.ac.uk.

PMID: 24980485
PMCID: PMC4189001
DOI: 10.1074/mcp.O113.036681

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

Johannes Griss et al. Mol Cell Proteomics. 2014 Oct.

. 2014 Oct;13(10):2765-75.

doi: 10.1074/mcp.O113.036681. Epub 2014 Jun 30.

Authors

Affiliations

¹ From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK; §Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Vienna, Austria;
² ‖Institute of Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK;
³ **Center for Bioinformatics and Department of Computer Science, University of Tübingen, D-72076 Tübingen, Germany;
⁴ ‡‡Computational Proteomics Unit and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, CB2 1QR, Cambridge, UK;
⁵ §§Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria; ¶¶Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14/V, 8010 Graz, Austria;
⁶ From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK;
⁷ ‖‖Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany;
⁸ Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
⁹ School of Biological and Chemical Sciences, Queen Mary University of London, London, UK;
¹⁰ From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK; College of Computer, Hubei University of Education, Wuhan, China;
¹¹ Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA;
¹² Swiss-Prot group, SIB Swiss Institute of Bioinformatics, 1 Rue Michel Servet, 1211 Geneva, Switzerland; Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, Genopode 1015 Lausanne; Center of Integrative Genomics, University of Lausanne, Quartier Sorge Genopode, 1015 Lausanne;
¹³ **Center for Bioinformatics and Department of Computer Science, University of Tübingen, D-72076 Tübingen, Germany; Quantitative Biology Center, University of Tübingen, D-72076 Tübingen, Germany.
¹⁴ From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK; juan@ebi.ac.uk.

PMID: 24980485
PMCID: PMC4189001
DOI: 10.1074/mcp.O113.036681

Abstract

The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools such as Microsoft Excel or R. We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. These range from a simple summary of the final results to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found online.

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Figures

**Fig. 1.**
**A diagrammatic representation of the data model for mzTab.**

See this image and copyright information in PMC

References

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The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

Affiliations

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

Authors

Affiliations

Abstract

Figures

References

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MeSH terms

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Full Text Sources

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