New method to detect a cyanobacterial toxin

β-N-Methylamino-l-alanine (BMAA), a neurotoxic nonproteinogenic amino acid implicated in the development of neurodegenerative diseases, has been broadly associated with cyanobacteria and bioaccumulation through the food web. Early high-level detections, from poorly selective high-performance liquid chromatography-fluorescence detection (HPLC–FLD) methods, have never been repeated using modern, selective tandem mass spectrometry methods. We developed a hydrophilic interaction liquid chromatography–tandem mass spectrometry (HILIC–MS/MS) method for total BMAA analysis, using an improved solid-phase extraction sample cleanup to reduce suppression. We identified oxidative degradation products of BMAA, formed during strong acid hydrolysis, due to residual nitrate in culture media and implemented a dewatering step to resolve this problem. The method was validated using Spirulina powder, environmental, and two cultured cyanobacterial samples, achieving a reporting limit of 0.3 mg/kg in dry cyanobacterial samples. The validated method was then applied to an additional 30 cyanobacteria cultures from Aotearoa New Zealand. BMAA was only detected in one strain, Planktothrix sp. CAWBG-35, at 2.3 mg/kg. These results indicate that BMAA is not produced at the high levels originally reported (e.g., g/kg) in freshwater cyanobacteria and suggest that BMAA production is not widespread among freshwater cyanobacteria from Aotearoa New Zealand. These results have broad implications for future risk-based environmental and public health monitoring.