Making accurate, precise metabolomic measurements can be extremely challenging. Please see the "42 Factors" Series of Articles as a primer on how to improve data quality in metabolomic and other types of multi-omic experiments.
The Human Metabolome Database
This database contains 220,945 metabolite entries with 130 data fields devoted to chemical/clinical data and enzymatic or biochemical data. This is the top database for information about metabolites.
This database contains all known biochemical reactions. It’s an excellent place to look for biochemical reactions that involve specified proteins or metabolites (see the REACTIONS tab within a particular protein or metabolite page).
This is the largest repository of metabolomic data in the world. During the process of publishing your manuscript, be sure to deposit your metabolomic data here.