LanthMS: A Computational Tool for the Structure Elucidation ofLanthipeptides from Tandem Mass Spectrometry Data

Introduction/Objective: Lanthipeptides are a class of ribosomally synthesized peptides with intricate ring structures, whose structural elucidation poses significant challenges. This study aimed to develop a computational tool named LanthMS to efficiently and accurately determine the topology of lanthipeptides directly from tandem Mass Spectrometry (MS/MS) data, thereby overcoming the limitations of conventional approaches in deciphering their dehydration and cyclization modifications. Methods: This study developed the specialized software LanthMS. The software exhaustively enumerates all possible lanthipeptide structures derived from given peptide sequences and assigns multidimensional scores by comprehensively comparing theoretical spectra against experimental MS/MS data, thereby predicting the most probable structures. Results: Using this approach, two novel lanthipeptides, amyA and amyC, were identified, from the Bacillus amyloliquefaciens WS-8 strain. Discussion: The LanthMS tool developed and validated in this study provides an automated solution for the structural elucidation of lanthipeptides. It not only significantly reduces the difficulty and subjectivity of manual interpretation but also deeply integrates computational structural prediction with experimental mass spectrometry data. This establishes a key technological framework for accelerating the discovery of lanthipeptides with novel activities and guiding their rational engineering. Conclusion: As a specialized in silico prediction tool, LanthMS substantially reduces the burden of manual interpretation, enhances the efficiency and accuracy of structural confirmation, and serves as a powerful engine for rapidly exploiting and engineering lanthipeptides with novel activities.