BACKGROUND


Many downstream analysis use final results of an experiment which require an easily accessible format, therefore HUPO-PSI has developed the mzTab file format for MS-based proteomics and metabolomics results to meet such need. The mzTab file format is intended as a lightweight supplement to the existing standard XML-based file formats (e.g. mzML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication to:

  1.  Facilitate the sharing of final experimental results, especially with researchers outside the field of metabolomics.
  2. Export of results to external software, including programs such as Microsoft Excel® and OpenOffice Spreadsheet and statistical software / coding languages such as R.
  3. Act as an output format of (web-) services that report MS-based results and thus can produce standardized result pages.
  4. Be able to link to the external experimental evidence e.g. by referencing back to mzML files.


 For details and publication  (Mol Cell Proteomics. 2014 Oct;13(10):2765-75. doi: 10.1074/mcp.O113.036681. Epub 2014 Jun 30.)


CURRENT WORK


mzTab has been designed to act as a lightweight, tab-delimited file format for mass spec-derived omics data. It was originally designed for proteomics with limited support for metabolomics (version 1.0). The metabolomics aspects are undergoing further development towards full support in a planned version 1.1 update.


For details:

https://github.com/HUPO-PSI/mzTab


mzTab-M: exchange format for metabolomics results

https://github.com/HUPO-PSI/mzTab/blob/master/specification_document/1_1_draft_specs/mzTab_format_specification_1_1-M_draft.adoc


Use Cases for mzTab


The following cases of usage have driven the development of the mzTab data model, and are used to define the scope of the format in version 1.0.

  1.  mzTab-M files should be simple enough to make metabolomics results accessible to people outside the respective fields. This should facilitate the sharing of data beyond the borders of the fields and make it accessible to non-experts.
  2. mzTab-M files should contain sufficient information to provide an electronic summary of all findings in a metabolomics study to permit its use as a standard documentation format for ‘supplementary material’ sections of publications in metabolomics. It should thus be able to replace PDF tables as a way of reporting small molecules make published identification and quantification information more accessible.
  3. mzTab-M files should enable reporting at different levels of detail: ranging from a simple summary of the final results to a detailed reporting including the experimental design.
  4. It should be possible to open mzTab-M files with “standard” software such as Microsoft Excel® or Open Office Spreadsheet. This should furthermore improve the usability of the format to people outside the fields of metabolomics.
  5. mzTab files should make MS derived results easily accessible to scripting languages allowing bioinformaticians to develop software without the overhead of developing sophisticated parsing code. Since mzTab files will be comparatively small, the data from multiple experiments can be processed at once without requiring special resource management techniques.
  6. It should be possible to contain the complete final results of an MS-based metabolomics experiment in a single file. This should furthermore reduce the complexity of sharing and processing an experiment’s final results. mzTab-M files should be able to store quantitative values for small molecule identifications.
  7. It should be useful as an output format by web-services that can then be readily accessed by tools supporting mzTab-M.
  8. It should be possible to directly link a given peptide / small molecule identification to its source spectrum in an external MS data file.