Does anyone know of a publicly-available database storing metabolomics datasets, particularly containing datasets for plants? NCBI GEO is an Omnibus mostly containing Gene Expression datasets like microarray, RNA-seq, CHIP, etc. and not so much individual metabolomics datasets. Are published metabolomics data deposited online somewhere else?
Of course!!! Like NCBI/DDBJ- for Genes, Genomes, Transcriptomes and PRIDE for Proteomics/ Proteins, there are Major 3 such databases/ archives/ repositories for "metabolomics" data sets: MetaboLights, MetabolomicsWorkbench, and GNPS/Massive.
You have to search these for "plant names you are interested in" i.e., Arabidopsis, Brassica to get to the data sets and download them- typically in .mzML or .mzXML or such open source formats (some may be in mass-spec vendor formats as well!). More detailed information are here:
- UK-based MetaboLights (http://www.ebi.ac.uk/metabolights/) (Kale et al., 2016)
For example, 2 of my own published data sets on MetaboLights are here:
(a)http://www.ebi.ac.uk/metabolights/MTBLS309 (Brassica napus)
(b) http://www.ebi.ac.uk/metabolights/MTBLS311 (Arabidopsis thaliana)
USA-based MetabolomicsWorkbench (http://www.metabolomicsworkbench.org/) (Sud et al., 2015)
Also USA-based Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry based metabolomics data is gaining popularity through the Mass Spectrometry Interactive Virtual Environment (MassIVE) data repository (https://gnps.ucsd.edu/ProteoSAFe/index.jsp) hosted at computational infrastructure of the University of California San Diego (UCSD) Center for Computational Mass Spectrometry (CCMS; http://proteomics.ucsd.edu/) (Wang et al., 2016).
Some other minor data sets are also available from Japan-based MEKO@ PRIME DB:http://prime.psc.riken.jp/meko/downloads.html as well as in their DROP met DB: http://prime.psc.riken.jp/menta.cgi/prime/drop_index A lot of downloadable data there as well!
Thanks, Biswapriya B. Misra