mzTab for Metabolomics Workshop 6 March 2014

On 6h of March 2014 COSMOS members together with the PSI community are holding the first “mzTab for metabolomics” workshop in Tübingen, Germany. Our aim is to drive reporting of metabolomic results further using a standardized, open, easy accessible and human readable tabular format. MzTab (version 1.0) already provides basic support for reporting small molecules that we plan to extend and harmonize with the more advanced reporting scheme for proteins and peptides available in MzTab.

Gerenal information:

This will be a joint MSI and PSI workshop to improve the representation of Metabolomics and Small-Molecule Identification and Quantification in mzTab. The workshop is another step towards coordination of standards between the proteomics and metabolomics communities and we would like to invite the interested individuals to join in our effort.

  • mzTab can be used for reporting both metabolite identification and metabolomics quantification. After extensive research and discussions within the consortium and members of the MSI and PSI community, we are convinced that mzTab is the medium of choice for capturing and reporting such metabolomics results.
  • To test and evaluate the standard, the mzTab development is accompanied by early implementations, e.g., in development versions of the OpenMS (, or separate export functions for XCMS and CAMERA ( software tools.
  • In addition, the MetaboLights metabolomics database ( accepts the quantification and identification of metabolites in a subset of mzTab, soon to be updated to the full compatible version, once the final discussions on the mzTab format for small molecules are completed.

mzTab for metabolomics workshop

Location: University of Tübingen, Sand 1, on Maps

Official link and Agenda to meeting agenda 

For further travel information to “Sand” Area see

Programme: We will have a few short presentations about the mzTab background from proteomics and the UseCases in metabolomics and small molecules in general. The workshop participants will discuss/finalise the specification of mzTab for metabolomics, create examples and determine the required PSI-MS controlled vocabulary terms. 

Workshop dinner: We will have a workshop dinner for the evening before, on 5th of March at a local restaurant, sponsored by the EU FP7 project COSMOS. 

Accommodation: Self organised, check out the Tübingen tourist information for hotels.

Some recommendations (old city part of town but easily accessible by bus line 2 which stops at Neckarbrücke and Sand Drosselweg):
Hotel Hospiz (next to the castle - 7 min. walk to bus station at Neckarbrücke)
Hotel am Schloss (next to the castle - 7 min. walk to bus station at Neckarbrücke)
Hotel Domizil (next to the river Neckar - 1 min. walk to bus station at Neckarbrücke)
Hotel Krone (next to the river Neckar - 1 min. walk to bus station at Neckarbrücke)

More documentation is available in the mzTab Google code project at:

More information on mzTab:

  • mzTab specification document (docPDF)
  • A quick introduction to the mzTab format is the 20 minute guide to mzTab (PDFdocx).
  • Example documents (external page)

jmzTab API Tutorial

The main principle behind the design of the jmzTab core model is to provide an independent light-weight architecture for simplifying the integration of the library in different proteomics/metabolomics software applications. Users can integrate the model into their applications, without the need any other third-party packages. Especially, when users want to recode the model by using other programming languages, and migrates jmzTab API into other heterogeneous system.

We provide a tutorial document and a couple of demos to help you to create metadata and fill data by calling jmzTab API.

  • jmzTab can read, write and convert mzTab files. jmzTab is free, open-source software written in Java.

In addition, it is important to highlight that jmzTab is already integrated and used in external software such as the LipidDataAnalyzer