Identification of Unknown Biological Toxin Proteins Using Mass Spectrometry: A Case Study on De Novo Sequencing of Ricin

Background: The rapid and reliable identification of unknown or highly variable biological toxin proteins, such as the potent Ricin toxin, remains a critical challenge in biodefense and public security. Methods: To address this, we developed a Heuristic De Novo Sequencing (HDPS) strategy, which combines multiple enzymatic and microwave-assisted acid hydrolysis to generate diverse peptides, followed by a two-stage assembly process integrating de novo sequencing with homology-based database searching for robust error correction. Results: When applied to Ricin, this approach achieved 100% sequence coverage for both its A and B chains, with amino acid-level accuracies of 98.13% and 98.47%, respectively, and successfully corrected potential sequencing ambiguities. Conclusions: These results demonstrate that HDPS is a highly accurate and effective method for the de novo sequencing of full-length proteins, making it particularly valuable for characterizing unknown or mutated toxins in the absence of comprehensive reference databases.