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The chemical warfare agents hydrolyze rapidly in environmental waters to form polar products and most of them are acidic in nature. In case of sulfur mustard a gram-negative bacterium, Alcaligenes xylosoxydans ssp. xylosoxydans, transforms its hydrolysis product thiodiglycol to thiodiglycolic acid (TDGA). TDGA determination is also important for the analysis of waste waters of polymer plants and environmental monitoring of nearby areas. In present study a novel sensitive screening method based on “Dilute-and-Shoot” sample preparation and liquid chromatography–tandem mass spectrometry (LC–MS/MS) is shown. The feasibility of separation and detection of TDGA and other polar metabolites in aqueous samples is demonstrated. The LC in combination with electrospray ionization mass spectrometry provides a sensitive and direct approach for TDGA identification and quantification using non-extracted non-derivitised samples from aqueous solutions. Chromatographic separation of the TDGA was produced using a reverse phase LC column with gradient mobile phases consisting of 0.1% formic acid in water and acetonitrile. Identification and quantification of species were achieved using electrospray ionization tandem MS monitoring of two precursor-to-product ion transitions for TDGA. The method demonstrates linearity over at least two orders of magnitude and detection limit of 10 ng/mL in environmental water samples. With regard to matrix effects, all concentrations were between 96% and 102% of the nominal values in the conducted measurements suggesting there were no significant matrix effects for TDGA and that no co-eluting substance influenced the ionization of the analyte. The method shown good accuracy and reproducibility and was employed in the authors laboratory during the OPCW 30th official proficiency test.