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Mass spectrometry (MS) and high performance liquid chromatography coupled to mass spectrometry (HPLC–MS) techniques were developed to characterize two surfactants, cetheareth-12 and sorbitan oleate, used to manufacture AF03, an emulsified oil-in-water (O/W) adjuvant. MS was first used to characterize the chemical structure and determine the composition of the two surfactants. The two surfactants appeared as complex products, in particular with respect to the nature of the fatty alcohols and the distribution of the number of ethylene oxides in cetheareth-12, and with respect to the different sorbitan-bound fatty acids (oleic, linoleic and palmitic acids) in sorbitan oleate. Subsequently, once the ions of interest were determined and selected, HPLC–MS was developed and optimized to quantify and to “quality control” the two surfactants as raw materials and as ingredients in the final O/W emulsion bulk and filled products.