title: Collidoscope: An Improved Tool for Computing Collisional Cross-Sections with the Trajectory Method.
abstract: Ion mobility-mass spectrometry (IM-MS) can be a powerful tool for determining structural information about ions in the gas phase, from small covalent analytes to large, native-like or denatured proteins and complexes. For large biomolecular ions, which may have a wide variety of possible gas-phase conformations and multiple charge sites, quantitative, physically explicit modeling of collisional cross sections (CCSs) for comparison to IMS data can be challenging and time-consuming. We present a "trajectory method" (TM) based CCS calculator, named "Collidoscope," which utilizes parallel processing and optimized trajectory sampling, and implements both He and N2as collision gas options. Also included is a charge-placement algorithm for determining probable charge site configurations for protonated protein ions given an input geometry in pdb file format. Results from Collidoscope are compared with those from the current state-of-the-art CCS simulation suite, IMoS. Collidoscope CCSs are within 4% of IMoS values for ions with masses from ~18 Da to ~800 kDa. Collidoscope CCSs using X-ray crystal geometries are typically within a few percent of IM-MS experimental values for ions with mass up to ~3.5 kDa (melittin), and discrepancies for larger ions up to ~800 kDa (GroEL) are attributed in large part to changes in ion structure during and after the electrospray process. Due to its physically explicit modeling of scattering, computational efficiency, and accuracy, Collidoscope can be a valuable tool for IM-MS research, especially for large biomolecular ions. Graphical Abstract ᅟ.
authors.affiliation: Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, OR, 97403-1253, USA.
authors.forename: Simon A
authors.initials: SA
authors.lastname: Ewing
authors.affiliation: Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, OR, 97403-1253, USA.
authors.forename: Micah T
authors.initials: MT
authors.lastname: Donor
authors.affiliation: Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, OR, 97403-1253, USA.
authors.forename: Jesse W
authors.initials: JW
authors.lastname: Wilson
authors.affiliation: Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, OR, 97403-1253, USA. jprell@uoregon.edu.|Materials Science Institute, University of Oregon, 1252 University of Oregon, Eugene, OR, 97403-1252, USA. jprell@uoregon.edu.
authors.forename: James S
authors.initials: JS
authors.lastname: Prell
mesh_terms: D000465:Algorithms; D005740:Gases / Q000737:chemistry; D000075663:Ion Mobility Spectrometry / Q000379:methods*; D007477:Ions / Q000737:chemistry; D013058:Mass Spectrometry / Q000379:methods*; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*
chemical_list: D005740:Gases; D007477:Ions; D011506:Proteins
keywords: Collisional cross-section; Computational theory; Ion mobility; Native IM-MS; Native mass spectrometry; Noncovalent complexes; Trajectory method