The experimental identification of unknown metabolites is not a trivial process. Extensive work by individual labs and consortiums around the world have established independent databases that contain accurate information on hundreds to thousands of metabolites. The links listed here are the most inclusive and freely accessible databases that currently exist.

Metabolite Database Name Link
Metabolite Database Name Link
METLIN Metabolite & MS/MS Database
LIPID MAPS
KEGG
KNApSAcK
NIST
MassBank
HMP
ARM