Botulinum neurotoxin (BoNT) causes the disease known as botulism, which can be lethal. Rapid determination of exposure to BoNT is an important public health goal. Our laboratory has developed Endopep-MS, a mass spectrometry-based endopeptidase method for detecting and differentiating BoNT. Here, we demonstrate that this method is very sensitive, detecting as little as 0.5 mouse LD 50 of BoNT/A and as little as 0.05 mouse LD 50 of BoNT/B, /E, and /F spiked into human serum samples. Additionally, the ability to further differentiate BoNT as the subtype of BoNT/A spiked into milk using toxin proteomics and mass spectrometry has been demonstrated. This method does not require DNA and can be performed on the same sample as that used for Endopep-MS analysis. The combination of these techniques, all performed on the same sample, provides a sensitive and selective analysis of BoNT isolated from a food or clinical sample and measures the toxin's activity.