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

Samuel Cajahuaringa1,2, Daniel L Z Caetano2,3, Leandro N Zanotto1,2

  • 1Institute of Computing, University of Campinas, Campinas, São Paulo 13083-852, Brazil.

Journal of Chemical Information and Modeling
|May 15, 2023
PubMed
Summary

MassCCS is a new open-source code that rapidly calculates the collision cross-section (CCS) for biomolecular structures. This tool aids in interpreting ion mobility mass spectrometry (IM-MS) data for various molecules, from small compounds to large protein assemblies.

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Area of Science:

  • Computational chemistry
  • Biophysics
  • Structural biology

Background:

  • Ion mobility mass spectrometry (IM-MS) is crucial for biomolecular structural characterization, providing collision cross-section (CCS) data.
  • Interpreting IM-MS data is complex due to the conformational isomerism of biomolecules in the gas phase.
  • Accurate and rapid CCS calculations are essential for effective IM-MS data interpretation.

Purpose of the Study:

  • To present MassCCS, a parallelized open-source software for calculating molecular CCS.
  • To enable efficient CCS computation for a wide range of molecules, including large macromolecular assemblies.
  • To provide a tool that aids in the interpretation of IM-MS experimental data.

Main Methods:

  • Development of MassCCS, a parallelized code utilizing the trajectory method for CCS calculations.
  • Employing atomic and molecular buffer gas particles in the simulations.
  • Extensive testing of accuracy, performance, and scalability with varying system sizes and CPU core counts.

Main Results:

  • MassCCS demonstrates performance comparable to existing software for small molecules and proteins.
  • Significantly enhanced speed for calculating CCS of large macromolecular assemblies.
  • Highly accurate and efficient computations, with execution times under a few minutes for large systems (e.g., virus capsids).

Conclusions:

  • MassCCS is a highly accurate and efficient tool for CCS calculations, suitable for diverse biomolecular systems.
  • The software's speed and scalability make it valuable for analyzing large assemblies, such as virus capsids.
  • MassCCS is freely available, promoting its use in structural biology and computational chemistry research.