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            title="Search the RefMet database by metabolite name, neutral mass, formula, InChIKey or PubChem compound ID, the metabolite database by name and the NMDR studies by metabolite name, project title or study title. Perform a regular expression search on names by using a 'grep:' prefix."
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  <strong>Enter name</strong>:<input type="text" value="N-Palmitoyl-Sphinganine" size="45" name="metabolite_name"><input type="submit" value="Standardize">&nbsp;&nbsp; <a href="/databases/refmet/name_to_refmet_form.php">Convert a metabolite list</a>
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 * Home
   *    Welcome to the UCSD Metabolomics Workbench, a resource sponsored by the
     Common Fund of the National Institutes of Health.
 * Data Repository
   Overview Upload / Manage Studies Browse / Search Studies Analyze Studies Data
   Sharing Policy Tutorials FAQ
 * Databases
   Overview Metabolite Database Human Metabolome Gene/Protein Database (MGP)
   RefMet: Reference List of Metabolite Names External Metabolomics Databases
   (Links)
 * Protocols
   Overview General Protocols Study-specific Protocols
 * Tools
   Overview Load and analyze your own dataset Analyze Studies MS Searches
   Structure drawing REST Service External Tools (Links)
 * About
   Overview Publishing Partners How to Cite How to Link Terms of Use Personnel
   Contact Sitemap
 * Search
   Keyword Search Advanced Searches


HOME


HOME


 * NATIONAL METABOLOMICS DATA REPOSITORY
   
   Upload and Manage
   Studies Browse and Search
   Studies Analyze
   Studies
   
   As of 11/06/24 a total of 3470 studies have been processed by the National
   Metabolomics Data Repository (NMDR). There are 3094 publicly available
   studies and the remainder (376) will be made available subject to their
   embargo dates.
   
   
   RECENTLY RELEASED STUDIES ON NMDR
   
   ST002742 - Differentiation of ayahuasca samples according to the origin,
   religious groups, and botanical varieties using multivariate statistical
   analysis of UHPLC-MS qualitative data; Psychotria viridis; Banisteriopsis
   caapi; University of Campinas
   
   ST003519 - Effect of insluin on metabolism of ex vivo ischemia heart; Rattus
   norvegicus; Mayo Clinic
   
   ST003529 - Measurement of itaconic acid in liver of male mice treated with
   TCDD; Mus musculus; Michigan State University

New!MetStat: View most frequently encountered metabolites in NMDR (mapped to
RefMet)




 * 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.
   
   
   
   
   
   Higlights/News archive


 * 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.
   
   
   
   
   
   Higlights/News archive


 * 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.
   
   
   
   
   
   Higlights/News archive


 * 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.
   
   
   
   
   
   Higlights/News archive


 * 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.
   
   
   
   
   
   Higlights/News archive


 * 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.
   
   
   
   
   
   Higlights/News archive


 * 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
   
   
   
   
   
   Higlights/News archive


 * 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.


 * CONVERT YOUR METABOLITE NAME TO STANDARDIZED NOMENCLATURE VIA REFMET
   
   Enter name:   Convert a metabolite list


 * 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.


 * 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.

Quick Links - Key Resources Upload / Manage Studies Browse / Search Studies
Analyze Studies Data Sharing Plan Tutorials FAQ Metabolite Database Human
Metabolome Gene/Protein Database (MGP) RefMet: Reference List of Metabolite
Names General Protocols Study-specific Protocols Load and analyze your own
dataset MS Searches REST Service --> How to Cite Site Map NMDR and NIH
Metabolomics Consortium Personnel








Gordon Research Conference The Gordon Research Conference on Metabolomics and
Human Health takes place in Ventura,CA on February 2 to 7, 2025. Click here for
additional information and registration.



NIH Common Fund Stage 2 Metabolomics Consortium Centers Metabolomics Consortium
Coordinating Center (M3C)
Richard Yost, U. of Florida Metabolomics Workbench/NMDR
Shankar Subramaniam, UC San Diego
(this website) Compound Identification Cores (CIDCs)
Arthur Edison, U. of Georgia
Alexey Nesvizhskii, U. of Michigan
Oliver Fiehn, UC Davis
Dean Paul Jones, Emory University
Thomas Metz, Pacific Northwest Nat. Lab. Data and Tools Cores (DTCs)
John Weinstein, MD Anderson Cancer C.
Jamey Young, Vanderbilt University
Xiuxia Du, U. of North Carolina Charlotte
Shuzhao Li, Emory University
Alla Karnovsky, U. of Michigan
Katerina Kechris, U. of Colorado, Denver
Gary Patti, Washington U. at St. Louis



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 * UCSD Metabolomics Workbench, a resource sponsored by the Common Fund of the
   National Institutes of Health

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