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LC with MS detection was optimized for sensitive and selective analysis of main classes of natural dyes used in ancient times for dyeing textiles -- red anthraquinoids, yellow flavonoids, and known degradation products of flavonols -- hydroxybenzoic acids. Fragmentation patterns of both negative and positive molecular ions for the above mentioned compounds were investigated. Three acquisition modes of MS analysis: scanning, SIM, and multiple reaction monitoring (MRM) in both positive and negative ion modes were optimized and compared with each other and with the UV-Vis diode-array detection. Even though in the applied chromatographic system formic acid was used in the mobile phase, SIM in the negative ion mode was the most selective and sensitive detection for all the investigated compounds when both mixtures of standards and analysis of extracts from archeological samples were concerned, with one exception -- alizarin, for which MS detection in positive ion mode was more sensitive. Detection limits obtained with MS detection for all investigated compounds except quinizarin were lower than the ones obtained with the diode-array UV-Vis detection, making MS detection the most suitable tool for the analysis of natural dyes and their degradation products in extracts from archeological samples.

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