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The analysis of phosphonic acids in a spiked tap water has been investigated by capillary electrophoresis-mass spectrometry (CE-MS) and liquid chromatography-mass spectrometry (LC-MS) as part of the Third Official Proficiency Test of the Organization for the Prohibition of Chemical Weapons. The use of a non-volatile electrolyte (5 mM sorbic acid/ammonia, pH 6.5) in CE and a volatile mobile phase (water/0.1 v/v trifluoroacetic acid/acetonitrile) in LC achieves the baseline resolution of studied phosphonic acids. Tandem-MS detection analysis allows an accurate identification of these solutes by screening their characteristic fragmentations.