Online compound database search¶
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.
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KEGG
KEGG database (http://www.genome.jp/kegg/) contains metabolites and other biomolecules present in natural metabolic pathways.
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PubChem
PubChem database (http://pubchem.ncbi.nlm.nih.gov/) contains millions of chemical compound structures.
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HMDB
The Human Metabolome Database (HMDB) (http://www.hmdb.ca/) contains over 7,000 known metabolites found in human body.
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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).
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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.
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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.
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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.
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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.