In order for the MSEA server to accept a range of metabolite names, synonyms or ID as input, it was also necessary to develop a local metabolite dictionary that could be used to perform facile name conversion or ‘normalization’. Information contained in the HMDB was used to extract common names, synonyms, as well as ID used in nine major metabolomic databases [HMDB, PubChem (19 (link)), ChEBI (20 (link)), KEGG (21 (link)), BiGG (22 (link)), METLIN (23 (link)), BioCyc (24 (link)), Reactome (25 (link)), and Wikipedia]. Examples of MSEA’s supported IDs are listed in Table 2. In order for MSEA to perform single sample profiling (SSP) analysis, it was also critical to obtain reference concentrations for as many metabolites as possible. These concentration data were collected primarily from the HMDB with additional values being added through manual curation. MSEA’s reference concentrations are organized based on the biofluids in which they were measured. Concentrations are presented in the form of mean (minimum – maximum). For concentrations reported as mean and standard deviation (SD), their 95% confidence intervals (mean ± 2 SD) were used to define the concentration ranges. One compound may have multiple concentration values as reported from different studies.

Overview of compound labels currently supported by MSEA

Label typeExamples
Common NameAdenosine, acetic acid, adenine, creatine
HMDBHMDB00050, HMDB00042, HMDB00034, HMDB0006
PubChem60961, 176, 190, 586
ChEBI16335, 15366, 16708, 16919
KEGGC00212, C00033, C00147, C00300
BiGG34273, 33590, 34039, 34543
METLIN86, 3206, 85, 7
BioCycADENOSINE, ACET, ADENINE, CREATINE
Reactome114933, 114747, 114936, 114818
WikipediaAdenosine, acetic acid, adenine, creatine