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Inflammatory bowel disease (IBD) is a chronic, idiopathic and relapsing inflammation of the gastrointestinal tract (GIT) with an unknown etiology, which is characterized by diarrhea, electrolyte loss, bleeding and abdominal pain. Urine represents a convenient biofluid for metabolomic studies due to its noninvasive collection and richness in metabolites. Here, amino acids are valuable biomarkers for their ability to reflect imbalances of different biochemical pathways. An impact of amino acids on pathology, prognosis and therapy of various diseases, including inflammatory bowel disease (IBD), is therefore the subject of current clinical research. This service provides a capillary electrophoresis-tandem mass spectrometry (CE-MS/MS) method for the quantification of the 20 proteinogenic amino acids in human urine samples obtained from patients suffering from IBD and treated with thiopurines.