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ECMDB specifications


Unique identifier OMICS_02690
Alternative name EColi Metabolome DataBase
Restrictions to use None
Version 2.0
Maintained Yes


  • Bacteria
    • Escherichia coli


  • person_outline David Wishart

Publications for EColi Metabolome DataBase

ECMDB citations


Untargeted metabolomics reveals a new mode of action of pretomanid (PA 824)

Sci Rep
PMCID: 5865180
PMID: 29572459
DOI: 10.1038/s41598-018-23110-1
call_split See protocol

[…] nnotation was made using a 3 ppm tolerance on their accurate mass. Metabolomic annotation was made using MZedDB (, the E. coli Metabolome Database (ECMDB, and LipidMaps ( databases, considering the following possible adducts: [M + H] + , [2 M + H] + , [M + 2 H]2 + , [M + 3 H] + , [M + Na] + , [M + Na +  […]


Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy

J Cheminform
PMCID: 5445034
DOI: 10.1186/s13321-017-0219-x

[…] ucture rankings by its membership in the local database of MS-FINDER. This local compound database covers structures from the 13 most important metabolomic databases, including BMDB, CheBI, DrugBank, ECMDB, FoodDB, HMDB, KNApSack, PlantCyc, SMPDB, T3DB, UNPD, YMDB and STOFF-IDENT [], containing 220,213 entries sorted according to InChIKey, PubChem, exact mass, formula and SMILES.(2) Using database […]


Relationship between recombinant protein expression and host metabolome as determined by two dimensional NMR spectroscopy

PLoS One
PMCID: 5423636
PMID: 28486539
DOI: 10.1371/journal.pone.0177233

[…] pectively. The resulting spectra were visualized and analyzed by rNMR []. The peaklist generated by rNMR was sent to MMCD ( [], PRIMe ( [, ], and ECMDB ( [, ] to retrieve a list of candidate metabolites that might exist in the sample. Only the metabolites that could be confirmed with the actual HSQC spectra of standard compo […]


Shigatoxin encoding Bacteriophage ϕ24B modulates bacterial metabolism to raise antimicrobial tolerance

Sci Rep
PMCID: 5247750
PMID: 28106081
DOI: 10.1038/srep40424

[…] on accurate mass. Further multivariate analysis was performed using SIMCA-P. ID’s were obtained through the QI plugin ’Progenesis metascope’ and filtered through a range of databases using sdf files (ECMDB, HMDB, small molecules drugs, Biomolecules, analgesics mix, Lipid MBD, Basic lipids, and Yeast DB). A paired sample t test was used to determine statistically significant differences between int […]


The components of Huang Lian Jie Du Decoction act synergistically to exert protective effects in a rat ischemic stroke model

PMCID: 5348361
PMID: 27779107
DOI: 10.18632/oncotarget.12645
call_split See protocol

[…] he assignment of metabolites. The signals were assigned by querying publicly accessible metabolomics databases [], such as Madison (, MMCD (, ECMDB ( and HMDB (, aided by Chenomx NMR suite 7.5 (Chenomx Inc., Edmonton, Canada) and the statistical total correlation spectroscopy (STOCSY) analysis method […]


The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection

Nucleic Acids Res
PMCID: 4702933
PMID: 26740669
DOI: 10.1093/nar/gkv1356

[…] erstanding of kinase-ligand interactions.The next section includes updated resources on metabolic pathways, such as KEGG, MetaCyc, Reactome, WikiPathways and the Escherichia coli metabolism database (ECMDB), and databases of metabolic network modeling, such as BiGG Models and MNXref/MetaNetX. A new arrival here is the Metabolomics Workbench (), which strives to be a one-stop repository for all kin […]


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ECMDB institution(s)
Department of Computing Science, University of Alberta, Edmonton, AB, Canada
ECMDB funding source(s)
Canadian Institutes of Health Research (CIHR); Genome Alberta, a division of Genome Canada

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