Since the commercial introduction of Ion Mobility coupled with Mass Spectrometry (IM-MS) devices in 2003, a large number of research laboratories have embraced the technique. IM-MS is a fairly rapid experiment used as a molecular separation tool and to obtain structural information. The interpretation of IM-MS data is still challenging and relies heavily on theoretical calculations of the molecule's collision cross section (CCS) against a buffer gas. Here, a new software (HPCCS) is presented, which performs CCS calculations using high perfomance computing techniques. Based on the trajectory method, HPCCS can accurately calculate CCS for a great variety of molecules, ranging from small organic molecules to large protein complexes, using helium or nitrogen as buffer gas with considerable gains in computer time compared to publicly available codes under the same level of theory. HPCCS is available as free software under the Academic Use License at https://github.com/cepid-cces/hpccs. © 2018 Wiley Periodicals, Inc.

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Ion mobility mass spectrometry (IM-MS) techniques have become highly valued as a tool for structural characterization of biomolecular systems since they yield accurate measurements of the rotationally averaged collision cross-section (CCS) against a buffer gas. Despite its enormous potential, IM-MS data interpretation is often challenging due to the conformational isomerism of metabolites, lipids, proteins, and other biomolecules in the gas phase. Therefore, reliable and fast CCS calculations are needed to help interpret IM-MS data. In this work, we present MassCCS, a parallelized open-source code for computing CCS of molecules ranging from small organic compounds to massive protein assemblies at the trajectory method level of description using atomic and molecular buffer gas particles. The performance of the code is comparable to other available software for small molecules and proteins but is significantly faster for larger macromolecular assemblies. We performed extensive tests regarding accuracy, performance, and scalability with system size and number of CPU cores. MassCCS has proven highly accurate and efficient, with execution times under a few minutes, even for large (84.87 MDa) virus capsid assemblies with very modest computational resources. MassCCS is freely available at https://github.com/ cces-cepid/massccs.

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