A searchable and exportable tab-separated table of the following metadata is now available.
| metadata | definition/examples | adapted from source |
|---|---|---|
| Project title | Name of the project | MetaboLights (Haug et al. (2020)), Metabolomics Workbench (Sud et al. (2016)), Metabolonote (Ara et al. (2015)), MSI (Fiehn et al. (2007)) |
| Project description | Overall description of the project | MetaboLights (Haug et al. (2020)), Metabolomics Workbench (Sud et al. (2016)), Metabolonote (Ara et al. (2015)), MSI (Fiehn et al. (2007)) |
| Contact information | Person(s) responsible for contact including their affiliation | MetaboLights (Haug et al. (2020)), Metabolomics Workbench (Sud et al. (2016)), Metabolonote (Ara et al. (2015)), MSI (Fiehn et al. (2007)) |
| Sample species | Species of the sample | MetaboLights (Haug et al. (2020)), Metabolomics Workbench (Sud et al. (2016)), Metabolonote (Ara et al. (2015)), MSI (Fiehn et al. (2007)) |
| Sample type | Whether the sample was experimental/blank/control/qc | MetaboLights (Haug et al. (2020)), Metabolomics Workbench (Sud et al. (2016)), Metabolonote (Ara et al. (2015)) |
| Instrument | Description of instrument used including manufacturer & mode | MetaboLights (Haug et al. (2020)), Metabolomics Workbench (Sud et al. (2016)), Metabolonote (Ara et al. (2015)), MSI (Fiehn et al. (2007)) |
| File type | Type of file uploaded (e.g. RAW, SEARCH, RESULT, etc.) | MetaboLights (Haug et al. (2020)), Metabolomics Workbench (Sud et al. (2016)), Metabolonote (Ara et al. (2015)), MSI (Fiehn et al. (2007)) |
| Comments/questions: |
|---|
| metadata | definition/examples | adapted from source |
|---|---|---|
| Sample collection protocol | Description of sampling procedure, origin of sample, time point of collection, storage, etc. | MetaboLights (Haug et al. (2020)), Metabolomics Workbench (Sud et al. (2016)), Metabolonote (Ara et al. (2015)), MSI (Fiehn et al. (2007)) |
| Extraction protocol | Protocol of extraction steps before analysis including control samples | MetaboLights (Haug et al. (2020)), Metabolomics Workbench (Sud et al. (2016)), Metabolonote (Ara et al. (2015)), MSI (Fiehn et al. (2007)) |
| Chromatography protocol | Description of instrument and column, mobile phase and gradient as well a settings used | MetaboLights (Haug et al. (2020)), Metabolonote (Ara et al. (2015)), MSI (Fiehn et al. (2007)) |
| Mass spectrometry protocol | Description of instrument, ion source, ionisation mode, mz range and settings | MetaboLights (Haug et al. (2020)), Metabolonote (Ara et al. (2015)), MSI (Fiehn et al. (2007)) |
| Data transformation protocol | Details of pipelines, methods and software used to transform the raw data | MetaboLights (Haug et al. (2020)), Metabolonote (Ara et al. (2015)), MSI (Fiehn et al. (2007)) |
| Metabolite identification protocol | Details of methods, pipelines, reference databases, and software used to identify and annotate | MetaboLights (Haug et al. (2020)), Metabolonote (Ara et al. (2015)), MSI (Fiehn et al. (2007)) |
| Comments/questions: |
|---|
We also highly encourage the readers of this GitHub to look for examples of submitted metabolomic samples and analyses in “MetabolomeXchange” that holds datasets from MetagoLights, Metabolic Repository Bordeaux, Metabolomics Workbench and Metabolonote. Publications MetaboLights: a resource evolving in response to the needs of its scientific community (Haug et al. (2020)), Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses (Ara et al. (2015)), Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools (Sud et al. (2016)) and The metabolomics standards initiative (MSI) (Fiehn et al. (2007)) in the ‘adapted from source’ section can be found online.
The MetaboLights submission portal offers light-weight and quick-start information on how to submit a study and what type of metadata to provide. A detailed overview of metadata fields is offered when you create your own study and start including detailed information on the types of assays used.
Ara, Takeshi, Mizuki Enomoto, Masanori Arita, Chisato Ikeda, Kenichiro Kera, Masanobu Yamada, Toshio Nishioka, et al. 2015. “Metabolonote: A Wiki-Based Database for Managing Hierarchical Metadata of Metabolome Analyses.” Front. Bioeng. Biotechnol. 3: 38. https://doi.org/10.3389/fbioe.2015.00038.
Fiehn, Oliver, Donald Robertson, Julian Griffin, Mariët J van der Werf, Basil Nikolau, Neil Morrison, Lloyd W Sumner, et al. 2007. “The Metabolomics Standards Initiative (MSI).” Metabolomics 3: 175–78. https://doi.org/10.1007/s11306-007-0070-6.
Haug, Kenneth, Keeva Cochrane, Venkata Chandrasekhar Nainala, Mark Williams, Jiakang Chang, Kalai Vanii Jayaseelan, and Claire O’Donovan. 2020. “MetaboLights: A Resource Evolving in Response to the Needs of Its Scientific Community.” Nucleic Acids Research. https://doi.org/10.1093/nar/gkz1019.
“MetabolomeXchange.” http://www.metabolomexchange.org/site/#/.
Sud, Manish, Eoin Fahy, Dawn Cotter, Kenan Azam, Ilango Vadivelu, Charles Burant, Arthur Edison, et al. 2016. “Metabolomics Workbench: An International Repository for Metabolomics Data and Metadata, Metabolite Standards, Protocols, Tutorials and Training, and Analysis Tools.” Nucleic Acids Res. 44 (D1): D463–70. https://doi.org/10.1093/nar/gkv1042.