Collidoscope: An Improved Tool for Computing Collisional Cross-Sections with the Trajectory Method.
Collidoscope: An Improved Tool for Computing Collisional Cross-Sections with the Trajectory Method.
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DOI：
10.1007/s13361-017-1594-2
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发表时间：
2017-04
影响因子：
3.2
通讯作者：
Prell JS
中科院分区：
文献类型：
--
作者：
Ewing SA;Donor MT;Wilson JW;Prell JS
离子迁移率质谱（IM-MS）可以是用于确定气相中离子的结构信息的有力工具，从小的共价分析物到大的、未折叠的和/或变性的蛋白质和复合物。对于大的生物分子离子，其可能具有各种各样的可能的气相构象和多个电荷位点，用于与IMS数据进行比较的碰撞截面（CCS）的定量、物理明确的建模可能是具有挑战性和耗时的。我们提出了一个“轨迹法”（TM）的CCS计算器，命名为“碰撞镜”，它利用并行处理和优化的轨迹采样，并实现了He和N2作为碰撞气体的选项。还包括一个电荷布局算法，用于确定质子化蛋白质离子的可能电荷位点配置，给定PDB文件格式的输入几何形状。碰撞镜的结果进行了比较，从目前的国家的最先进的CCS模拟套件，IMoS。对于质量为~18 Da至~800 kDa的离子，碰撞镜CCS通常在IMoS值的4%以内。使用X射线晶体几何形状的碰撞仪CCS通常在质量高达~3.5 kDa的离子（蜂毒肽）的IM-MS实验值的百分之几内，并且高达~800 kDa的较大离子（GroEL）的差异在很大程度上归因于电喷雾过程期间和之后的离子结构变化。由于其物理明确的散射模型，计算效率和准确性，碰撞镜可以是一个有价值的工具，IM-MS研究，特别是对大的生物分子离子。
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, unfolded, and/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 N2 as 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 to those from the current state-of-the-art CCS simulation suite, IMoS. Collidoscope CCSs are typically 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.
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影响因子：
44.1
作者：
KIHARA, T
通讯作者：
KIHARA, T
影响因子：
--
作者：
BONDI, A
通讯作者：
BONDI, A
影响因子：
2.9
作者：
Alexeev, Yuri;Fedorov, Dmitri G.;Shvartsburg, Alexandre A.
通讯作者：
Shvartsburg, Alexandre A.
影响因子：
5.7
作者：
Marklund, Erik G.;Degiacomi, Matteo T.;Benesch, Justin L. P.
通讯作者：
Benesch, Justin L. P.
影响因子：
7.4
作者：
Morsa, Denis;Defize, Thomas;de Pauw, Edwin
通讯作者：
de Pauw, Edwin