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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Griss, Johannes Jones, Andrew R. Sachsenberg, Timo Walzer, Mathias Gatto, Laurent Hartler, Jürgen Thallinger, Gerhard G. Salek, Reza M. Steinbeck, Christoph Neuhauser, Nadin Cox, Jürgen Neumann, Steffen Fan, Jun Reisinger, Florian Xu, Qing-Wei Del Toro, Noemi Pérez-Riverol, Yasset Ghali, Fawaz Bandeira, Nuno Xenarios, Ioannis Kohlbacher, Oliver Vizcaíno, Juan Antonio Hermjakob, Henning |
| Description | Author Affiliation: Griss J ( From the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK); Jones AR ( âInstitute of Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK); Sachsenberg T ( **Center for Bioinformatics and Department of Computer Science, University of Tübingen, D-72076 Tübingen, Germany); Walzer M ( **Center for Bioinformatics and Department of Computer Science, University of Tübingen, D-72076 Tübingen, Germany); Gatto L ( Computational Proteomics Unit and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, CB2 1QR, Cambridge, UK); Hartler J ( §§Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria); Thallinger GG ( §§Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria); Salek RM ( From the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK); Steinbeck C ( From the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK); Neuhauser N ( ââDepartment of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany); Cox J ( ââDepartment of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany); Neumann S ( Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany); Fan J ( School of Biological and Chemical Sciences, Queen Mary University of London, London, UK); Reisinger F ( From the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK); Xu QW ( From the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK); Del Toro N ( From the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK); Pérez-Riverol Y ( From the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK); Ghali F ( âInstitute of Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK); Bandeira N ( Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA); Xenarios I ( Swiss-Prot group, SIB Swiss Institute of Bioinformatics, 1 Rue Michel Servet, 1211 Geneva, Switzerland); Kohlbacher O ( **Center for Bioinformatics and Department of Computer Science, University of Tübingen, D-72076 Tübingen, Germany); Vizcaíno JA ( From the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK); Hermjakob H ( From the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK) |
| 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. |
| File Format | HTM / HTML |
| ISSN | 15359476 |
| e-ISSN | 15359484 |
| DOI | 10.1074/mcp.O113.036681 |
| Journal | Molecular & Cellular Proteomics |
| Issue Number | 10 |
| Volume Number | 13 |
| Language | English |
| Publisher | American Society for Biochemistry and Molecular Biology |
| Publisher Date | 2014-10-01 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | Discipline Proteomics Databases, Protein Access To Information Mass Spectrometry Metabolomics Proteomics User-computer Interface Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't |
| Content Type | Text |
| Resource Type | Article |
| Subject | Medicine Analytical Chemistry Molecular Biology Biochemistry |
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