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National Metabolomics Data Repository
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StudiesAs of 11/20/24 a total of 3501 studies have been processed by the National Metabolomics Data Repository (NMDR). There are 3120 publicly available studies and the remainder (381) will be made available subject to their embargo dates.
Recently released studies on NMDR
ST003340 - Effect of feeding and the mTORC1 activity on metabolism in Caenorhabditis elegans; Caenorhabditis elegans; Hiroshima University
ST003542 - Dysregulated Follicular Fluid Metabolism in Women with Unexplained Infertility; Homo sapiens; ICMR - National Institute for Research in Reproductive and Child Health
ST003562 - MULTIPLE, REDUNDANT CARBOXYLIC ACID TRANSPORTERS SUPPORT MITOCHONDRIAL METABOLISM IN PLASMODIUM FALCIPARUM; Plasmodium falciparum; Pennsylvania State University
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Focus on raw data inspection and reuse
Raw data file inspection and reuse (Aug 15, 2024)
NMDR contains approximately 500,000 individual raw files, about half of which are in open-source format and amenable to inspection, searching and reanalysis on the Metabolomics Workbench, GNPS and ADAP-KDB. Each NMDR study has links in the "Download data files" section to these resources. One can view TIC, MS1 and MS2 spectra, and search by neutral loss or product ion m/z without the need to download files. See study ST003038 tandem MS data for an example.
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Focus on sterol drawing tools and nomenclature
Sterol drawing tools (Feb 29, 2024)
This web-based sterol drawing tool contains a selection of 45 different cores (including bile acid amidates for proteogenic amino acids) and numerous functional group options. It generates downloadable structures in molfile or image formats, as well as systematic name, formula and exact mass, with an option to calculate m/z values for various ion-adducts. This tool is also available on LIPID MAPS. There is a new table of bile acid nomenclature covering RefMet names, systematic names and abbreviations.
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RefMet name harmonization combined with ion-adduct calculation
RefMet ion-adduct calculation (Nov 20, 2023)
The RefMet metabolite name harmonization resource leverages data from over 500,000 annotations obtained from MS and NMR studies in NMDR to provide a standardized reference nomenclature across 4 different levels of structural resolution. A new feature is the ability to map a list of metabolite names to RefMet and simultaneously perform an ion-adduct calculation to generate a list of m/z values.
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Core structures in RefMet classification
RefMet core structures (March 1, 2023)
Browse and search core structures associated with the RefMet classification system. For example, what are "Flavones", "Flavanols", "Flavonols" and "Flavanones" and what's the difference? The RefMet classification hierarchy has recently been updated to place more emphasis on biosynthetic considerations for Alkaloid, Polyketide and Prenol lipid super classes.
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Molecular structure similarity analysis
Create molecular structure similarity networks (February 3, 2023)
This Structure similarity network tool creates a network map from a list of metabolite names (up to 500) by selecting a fingerprint type (MACCSkeys, Chem.RDK, Topological, Morgan,MorganBitVector) and similarity method (Tanimoto, Dice) with a similarity coefficient cutoff. This feature is also implemented for each NMDR study containing named metabolites (in 'Perform statisctical analysis' section). This application uses the Python-based Rdkit.
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Searching untargeted LC-MS data
Searching untargeted LC-MS data on the Workbench (December 13, 2022)
This portal searches over 4.5 million m/z,retention time features from over 890 NMDR studies and over 1500 LC-MS analyses. Search with a m/z value and tolerance window and optionally specify a retention time value and tolerance window to restrict the search. Limit search to studies by sample source and/or species, and also by chromatography type, MS instrument and polarity. Features that have been identified by submitters will appear in the "Name" column in the results table.
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Correlated network graphs in NMDR
Correlated network graphs using Debiased Sparse Partial Correlation (DSPC)
The Metabolomics Workbench has released a new graphical tool for estimating and visualizing partial correlation networks in NMDR studies. It uses the Debiased Sparse Partial Correlation algorithm (DSPC) developed at U.Michigan. Nodes may be mapped to chemical classification or fold-change. Study example: See "Perform Network analysis on correlated metabolites" links here
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Lipid Notation in RefMet and lipid m/z calculation tools
View table of over 170 revised lipid abbreviations covered by RefMet, including structure examples and m/z calculation tools for a variety of adducts.
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Convert your metabolite name to standardized nomenclature via RefMet
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Exemplary Studies
A list of exemplary studies are listed here which adhere to the submission guidelines of Metabolomics Workbench. Specifically, publically available studies having all or most of the features below were identified as exemplary studies.
- Well-written study summary
- Detailed metadata for collection/treatment/chromatography/MS/NMR, etc.
- Post-processing details
- Presence of control samples
- Raw data availability for samples and controls
- One-to-one mapping of sample names to raw data file name
- Internal standards (with measurements)
- Clear and organized metabolite annotations
These include different analysis (GC-MS, LC-MS, NMR) and species type. We recommend looking at these studies as a model example before submitting to Metabolomics Workbench.
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NMDR studies and Jupyter Notebooks
Analyze Workbench studies via Python-based Jupyter Notebooks. Launch notebooks on Binder or download notebooks from GitHub and run them locally.
