mzTab-M is a HUPO-PSI standard for the description of quantitative mass spectrometry analysis results of small molecules [Neumann, S. et al. mzTab-M: a data standard for sharing quantitative results in mass spectrometry metabolomics. Anal. Chem. (2019). doi:10.1021/acs.analchem.8b04310]. It has been implemented as an input format already by MetaboAnalyst and the GNPS repository and is produced by multiple softwares, such as LipidDataAnalyzer, MZmine 3 and MS-DIAL 4. However, authoring an mzTab-M file is still challenging due to the lack of a user-interface to produce a skeleton structure containing the experiment metadata and summary information.
Within the scope of the biohackathon, our main goals are to:
- Provide a first version of a user interface in lxPostman to define and create a study design and metadata, backed by controlled vocabularies, as a template mzTab-M and combine it with the output of LipidXplorer.
- Align information that is reported within the mzTab-M file with the recently published Lipidomics Checklist [Mcdonald, J. G. et al. Introducing the Lipidomics Minimal Reporting Checklist. doi:10.1038/s42255-022-00628-3]
- Verify interoperability of the generated mzTab-M with the data submission and import workflow of the LipidCompass quantitative lipidomics reference database and other tools that already support the format.
- Convert mzTab-M into the ISA-Tab format to allow easier submission of lipidomics mass spectrometry results to the EBI MetaboLights database.
We aim to prepare a manuscript on lxPostman + mzTab-M support within one year after the Biohackathon.
As stretch goals, depending on available support by co-hackers, we want to explore the possibility of generating an mzTab-M file from Skyline, another software that is often used to run targeted lipidomics experiments, and to improve support for mzTab-M within MZmine 3 to support different peak detection and identification workflows.