Botulinum neurotoxins (BoNT) are divided into seven toxinotypes based on their immunological properties and each toxinotype contains several subtypes according to their amino acid sequences. Here, we designed a mass spectrometry method able to identify BoNT/A subtypes in complex matrices including crude culture supernatants, food, and environmental samples. Peptides from BoNT light chain (L) specific to the subtypes BoNT/A1 to A3 and BoNT/A5 to A8 were identified. The method consists of an immunocapture step with antibodies specific to BoNT/A L chains followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) on a triple quadrupole mass spectrometer (QqQ) in multiple reaction monitoring (MRM) mode. BoNT/A subtypes were correctly identified in culture supernatants and in tap water or orange juice samples with a limit of detection of 20 to 150 mouse lethal doses (MLD) and with a lower sensitivity in serum samples.

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