title: The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.
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.
authors: 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;
authors: Johannes
authors: J
authors: Griss
authors: ‖Institute of Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK;
authors: Andrew R
authors: AR
authors: Jones
authors: **Center for Bioinformatics and Department of Computer Science, University of Tübingen, D-72076 Tübingen, Germany;
authors: Timo
authors: T
authors: Sachsenberg
authors: **Center for Bioinformatics and Department of Computer Science, University of Tübingen, D-72076 Tübingen, Germany;
authors: Mathias
authors: M
authors: Walzer
authors: ‡‡Computational Proteomics Unit and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, CB2 1QR, Cambridge, UK;
authors: Laurent
authors: L
authors: Gatto
authors: §§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;
authors: Jürgen
authors: J
authors: Hartler
authors: §§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;
authors: Gerhard G
authors: GG
authors: Thallinger
authors: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK;
authors: Reza M
authors: RM
authors: Salek
authors: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK;
authors: Christoph
authors: C
authors: Steinbeck
authors: ‖‖Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany;
authors: Nadin
authors: N
authors: Neuhauser
authors: ‖‖Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany;
authors: Jürgen
authors: J
authors: Cox
authors: Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
authors: Steffen
authors: S
authors: Neumann
authors: School of Biological and Chemical Sciences, Queen Mary University of London, London, UK;
authors: Jun
authors: J
authors: Fan
authors: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK;
authors: Florian
authors: F
authors: Reisinger
authors: 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;
authors: Qing-Wei
authors: QW
authors: Xu
authors: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK;
authors: Noemi
authors: N
authors: Del Toro
authors: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK;
authors: Yasset
authors: Y
authors: Pérez-Riverol
authors: ‖Institute of Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK;
authors: Fawaz
authors: F
authors: Ghali
authors: Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA;
authors: Nuno
authors: N
authors: Bandeira
authors: 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;
authors: Ioannis
authors: I
authors: Xenarios
authors: **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.
authors: Oliver
authors: O
authors: Kohlbacher
authors: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK; juan@ebi.ac.uk.
authors: Juan Antonio
authors: JA
authors: Vizcaíno
authors: From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK;
authors: Henning
authors: H
authors: Hermjakob
mesh_terms: D022126:Access to Information; D030562:Databases, Protein; D013058:Mass Spectrometry; D055432:Metabolomics; D040901:Proteomics; D012984:Software; D014584:User-Computer Interface