Abstract: Techniques for identifying metabolites in a sample may utilize observed precursor and product ion data obtained by subjecting the sample to tandem mass spectrometry (MS/MS). The techniques may include first accessing a database of precursor ion data to identify one or more matching candidate metabolites in the database that match the observed precursor ion data. Each of the matching candidate metabolites may then be further validated by matching product ion data associated with the matching candidate metabolite and stored in a database of computationally generated product ion fragments with the observed product ion data comprising product ion fragments. A structure of a metabolite in the sample may be identified by selecting a candidate metabolite based on scores computed for the candidate metabolites based on the matching. Large volumes of metabolite precursor and product ion data may be analyzed in this way with improved speed and accuracy.