Whole grain cereals are staple foods providing major sources of carbohydrates, proteins, vitamins and minerals for the world's population. The impact of food processing methodology on the chemical composition of whole grain foods can be investigated through metabolomics. Knowing the bioactive chemical content of grain or processed food products made of whole grains is a requirement for investigating the bioavailability and biochemical impact of any particular metabolite. Metabolomics experiments can be conducted using two basic approaches: untargeted and targeted. Processing is a prerequisite for the consumption of whole grains by humans. Baking is a common process used to increase nutritional value and acceptability of processed cereals. All processing steps alter nutritional properties of the grains and may be used to improve the nutrition value in food products.