Department of Mechanical Engineering, IUPUI, Indianapolis, IN, 46202, USA.
Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.
J Am Soc Mass Spectrom. 2017 Aug;28(8):1540-1551. doi: 10.1007/s13361-017-1661-8. Epub 2017 May 5.
A benchmark comparison between two ion mobility and collision cross-section (CCS) calculators, MOBCAL and IMoS, is presented here as a standard to test the efficiency and performance of both programs. Utilizing 47 organic ions, results are in excellent agreement between IMoS and MOBCAL in He and N when both programs use identical input parameters. Due to a more efficiently written algorithm and to its parallelization, IMoS is able to calculate the same CCS (within 1%) with a speed around two orders of magnitude faster than its MOBCAL counterpart when seven cores are used. Due to the high computational cost of MOBCAL in N, reaching tens of thousands of seconds even for small ions, the comparison between IMoS and MOBCAL is stopped at 70 atoms. Large biomolecules (>10000 atoms) remain computationally expensive when IMoS is used in N (even when employing 16 cores). Approximations such as diffuse trajectory methods (DHSS, TDHSS) with and without partial charges and projected area approximation corrections can be used to reduce the total computational time by several folds without hurting the accuracy of the solution. These latter methods can in principle be used with coarse-grained model structures and should yield acceptable CCS results. Graphical Abstract ᅟ.
本文对两种离子淌度和碰撞截面（CCS）计算器 MOBCAL 和 IMoS 进行了基准比较，以此作为测试这两个程序效率和性能的标准。利用 47 种有机离子，当两个程序使用相同的输入参数时，IMoS 和 MOBCAL 在 He 和 N 中的结果非常吻合。由于 IMoS 算法编写效率更高且实现了并行化，因此在使用 7 个核时，IMoS 能够以比 MOBCAL 快两个数量级的速度计算相同的 CCS（误差在 1%以内）。由于 MOBCAL 在 N 中计算成本很高，即使对于小离子，计算时间也长达数万个秒，因此 IMoS 和 MOBCAL 的比较在 70 个原子时停止。当在 N 中使用 IMoS 时，即使使用 16 个核，大型生物分子（>10000 个原子）的计算仍然很昂贵。可以使用扩散轨迹方法（DHSS、TDHSS）及其带或不带部分电荷和投影面积近似校正的近似方法将总计算时间减少几个数量级，而不会影响解决方案的准确性。这些后一种方法原则上可以与粗粒度模型结构一起使用，并且应该可以得到可接受的 CCS 结果。图摘要 ᅟ。
