Question: Publicly-available Metabolomics Data
2
gravatar for theobroma22
21 months ago by
theobroma221.1k
theobroma221.1k wrote:

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?

ADD COMMENTlink modified 21 months ago • written 21 months ago by theobroma221.1k

Thanks a lot! I also found MetabolomeXchange which has data as well. Here is the site: http://www.metabolomexchange.org/site/#/

ADD REPLYlink written 21 months ago by theobroma221.1k
3
gravatar for bbmisraccb
21 months ago by
bbmisraccb30
United States
bbmisraccb30 wrote:

Hello,

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:

  1. 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)

  1. USA-based MetabolomicsWorkbench (http://www.metabolomicsworkbench.org/) (Sud et al., 2015)

  2. 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).

  3. 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

ADD COMMENTlink written 21 months ago by bbmisraccb30

Hi, I went to the MetaboLights on EBI and the screen is blocked with a transparent white screen such that I can't interact with the webpage. Do you know how to resolve this?

ADD REPLYlink written 21 months ago by theobroma221.1k

Hello, I guess, it is functional- I see everything alright- may be a temporary glitch? Also, start with "search" box or for studies: http://www.ebi.ac.uk/metabolights/studies Another note: I did not mention MetabolomeXchange as it is a mirror site/ aggregator for MetaboLights, MetabolomicsWorkBench and another one.... Thanks, Biswa

ADD REPLYlink written 21 months ago by bbmisraccb30
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