A platform based on hydrophilic interaction chromatography in combination with Fourier transform mass spectrometry was developed in order to carry out metabonomics of Drosophilaâmelanogaster strains. The method was able to detect âŒâ230 metabolites, mainly in the positive ion mode, after checking to eliminate false positives caused by isotope peaks, adducts and fragment ions. Two wildâtype strains, CantonâS and OregonâR, were studied, plus two mutant strains, Maroon Like and Chocolate. In order to observe the differential expression of metabolites, liquid chromatographyâmass spectrometry analyses of the different strains were compared using sieveâ1.2 software to extract metabolic differences. The output from sieve was searched against a metabolite database using an Excelâbased macro written inâhouse. Metabolic differences were observed between the wildâtype strains, and also between both Chocolate and Maroon Like compared with OregonâR. It was established that a metabonomic approach could produce results leading to the generation of new hypotheses. In addition, the structure of a new class of lipid with a histidine head group, found in all of the strains of flies, but lower in Maroon Like, was elucidated.