MassCCS: A High-Performance Collision Cross-Section Software for Large Macromolecular Assemblies

Ion mobility massspectrometry (IM-MS) techniques have become highlyvalued as a tool for structural characterization of biomolecular systemssince they yield accurate measurements of the rotationally averagedcollision cross-section (CCS) against a buffer gas. Despite its enormouspotential, IM-MS data interpretation is often challenging due to theconformational isomerism of metabolites, lipids, proteins, and otherbiomolecules in the gas phase. Therefore, reliable and fast CCS calculationsare needed to help interpret IM-MS data. In this work, we presentMassCCS, a parallelized open-source code for computing CCS of moleculesranging from small organic compounds to massive protein assembliesat the trajectory method level of description using atomic and molecularbuffer gas particles. The performance of the code is comparable toother available software for small molecules and proteins but is significantlyfaster for larger macromolecular assemblies. We performed extensivetests regarding accuracy, performance, and scalability with systemsize and number of CPU cores. MassCCS has proven highly accurate andefficient, with execution times under a few minutes, even for large(84.87 MDa) virus capsid assemblies with very modest computationalresources. MassCCS is freely available at https://github.com/cces-cepid/massccs.