Mass spectrometry is a high throughput technique widely used for metabolic fingerprinting of plant material. Among the diverse plant metabolites, pigments such as anthocyanins play a determinant role in plant defence mechanisms, protecting them from biotic and abiotic stresses. Anthocyanins are phenolic water-soluble glycosides or acyl-glycosides of anthocyanidins which could be accurately detected and quantified through mass spectrometry. This chapter describes how to extract anthocyanins from higher plant materials and quantify them through a liquid chromatography-mass spectrometry (LC-MS) based method.