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Patulin (4-hydroxy-4H-furo[3,2-c]pyran-2(6H)-one) belongs to a class of toxic compounds known as mycotoxins, which is naturally produced by several species of fungi such as Aspergillus, Penicillium, and Byssochlamys. Patulin residues have been frequently found in apples and various apple-based food products in many countries. Taking into consideration the toxicity of patulin and the high risk of its pervasive occurence in fruit-based products, reliable and sensitive analytical methods for its assay in food are required. This service provides a simple and sensitive method for the determination of patulin at µg·kg−1 level in apple-based products. This method relies on the application of an in-line molecularly imprinted polymer solid-phase extraction microcartridge in capillary electrophoresis coupled with mass spectrometry.