Abstract: A method of programmatically reducing a set of collected LC-MS or LC-MS/MS data such that true chromatographic and MS peaks are identified for use in Metabonomics is disclosed. The identified peaks are used to create a list of LC/MS, GC/MS, DIOS-MS or MALDI-MS signals and responses for a batch of samples which appear in a Master Entity List. The samples in the Master Entity List are then subjected to isotope de-clustering and adduct removal prior to chemometrics being applied to automatically identify biomarkers. An LC-MS/MS or LC/MS, GC/MS, DIOS-MS or MALDI-MS acquisition list is generated for the signals identified as responsible for the PLS-DA or PCA separation. The LC or GC retention time, exact mass and MS/MS spectrum may be compared to databases of known compounds and identified compounds associated with biological parameters may be stored in a new compound database.