Metabolomics facilitates the identification of numerous metabolites in a sample with mass less than 1 kD. The purpose of this study was to determine the effect of feed on the metabolites in raw goat milk samples obtained from two breeds namely Saanen and Shami that were collected from a farm in Selangor and Negeri Sembilan, Malaysia, respectively. The types of feed given to the goats were recorded. The fat in the samples were removed via centrifugation before analysis using liquid chromatography quadrupole time of flight mass spectrometry (LC-QToF-MS). From the chromatograms obtained the presence of veterinary drug residue, di- and tri-peptides, short and long-chain fatty acids, some components from plants, and insecticide residue were detected using HMP, KEGG, LMP, and METLIN databases identification. It is expected that through metabolomics study it may be possible to formulate the feed and determine the breed that give good quality milk.