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Online compound database search

Module is currently removed and no longer maintained.

🚧 This module has known bugs and is being updated, which might affect its functionality

Description

Feature list methods → Annotation → Search precursor mass → Online compound database search

This module allows identification of peaks or whole peak lists using an on-line compound database. Databases are queried for the calculated neutral mass of the peak and matching compounds are returned.

If a user is interested in more comprehensive online compound database search, they can export their data to Sirius software.

Parameters

Database

On-line database to search (list of the available databases).

Ionization type

Type of ionization that produced the peak subjected to identification.

Number of results

Limit for the number of results to be retrieved from the on-line database.

m/z tolerance

Maximum allowed m/z difference to set an identification to a peak.

Isotope pattern filter

If selected, only results which fit the required isotope pattern similarity score will be returned.

Currently supported databases

Supported databases are listed below. Support for other databases may be implemented as additional plugins.

  • KEGG

    KEGG database (http://www.genome.jp/kegg/) contains metabolites and other biomolecules present in natural metabolic pathways.

  • PubChem

    PubChem database (http://pubchem.ncbi.nlm.nih.gov/) contains millions of chemical compound structures.

  • HMDB

    The Human Metabolome Database (HMDB) (http://www.hmdb.ca/) contains over 7,000 known metabolites found in human body.

  • YMDB

    The Yeast Metabolome Database (YMDB) (http://www.ymdb.ca) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast).

  • LipidMaps

    LipidMaps Structure Database (LMSD) (https://www.lipidmaps.org/databases/lmsd) is a database of structures and annotations of biologically relevant lipids, containing over 47000 different lipids.

  • MassBank.eu

    MassBank (https://massbank.eu/MassBank/) is an open source mass spectral library for the identification of small chemical molecules of metabolomics, exposomics and environmental relevance. The majority of MassBank contents now features high-resolution mass spectrometry data.

  • ChemSpider

    The ChemSpider database (http://www.chemspider.com/) contains over 67 million compounds. To search ChemSpider you must provide a "Security key" from your ChemSpider API account. If you don't have an account, please register at https://developer.rsc.org.

  • MetaCyc

    MetaCyc (https://metacyc.org/) is a curated database of experimentally elucidated metabolic pathways from all biological domains. MetaCyc currently contains 2937 pathways, 17,780 reactions and 18,124 metabolites.

Steffen Heuckeroth, omokshyna