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Untargeted mass spectrometry-based monitoring of samples is a rapidly growing field. It enables comprehensive analysis of chemical compounds present in a sample by measurement of the accurate mass of the analytes. Generally, the methodologies and types of instruments used for targeted analysis are different from those used for untargeted analysis, as the former requires optimal sensitivity and dynamic range, while the latter requires high-resolution and high-mass accuracy. The state of the art of analytical chemistry using high-resolution mass spectrometry permits accurate mass measurements in many fields of bioanalysis such as metabolite identification, structure elucidation and in the field of food analysis. The focus of this chapter has been put on ‘modified’ mycotoxins, a term that has been recently introduced, which encompass biologically modified and chemically modified mycotoxins. Conjugated mycotoxins in this matter consist of biologically modified mycotoxins generated in planta (masked mycotoxins), in animalia and in fungi. Their chemical structures and physicochemical characteristics cover a wide variability range, resulting in their escape during routine biomonitoring, leading to underestimation of the mycotoxin content of samples. In this chapter, the possibilities of high-resolution mass spectrometry will be clarified, and an overview of the current status of untargeted analysis of conjugated (Fusarium) mycotoxins in natural products and modified mycotoxins in human biological fluids will be pointed out.

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