Metabolon´s platform technology uses a combination of chromatography and mass spectrometry to separate and identify a wide range of biochemicals and metabolites including amino acids, carbohydrates, lipids, nucleic acids and cofactors. This analysis results in a very large number of biochemicals identified in a given sample. The analytical platform incorporates two separate UHPLC/MS/MS2 methods and a GC/MS method which increases the overall coverage of small molecules in a biological sample. The resulting MS and/or MS2 data are searched against an in-house generated authentic standard library which includes retention time, molecular mass to charge (m/z), preferred adducts and in-source fragment information as well as the associated MS fragmentation spectra for all biochemicals in the library. The library enables the rapid and accurate identification of the experimentally detected small molecules based on a multi-parameter match without need for the time consuming further analysis. This global approach allows researchers to measure system-wide changes in biochemistry due to disease, drug or diet. Here we will discuss the applications of Metabolons platform in the areas of biomarker discovery, drug mechanism of action and early indicators in toxicity.