NDLI: Benchmark Comparison for a Multi-Processing Ion Mobility Calculator in the Free Molecular Regime

Content Provider	Springer Nature Link
Author	Shrivastav, Vaibhav Nahin, Minal Hogan, Christopher J. Larriba Andaluz, Carlos
Copyright Year	2017
Abstract	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$_{2,}$ 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$_{2}$, 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$_{2}$ (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
Starting Page	1540
Ending Page	1551
Page Count	12
File Format	PDF
ISSN	10440305
Journal	Journal of The American Society for Mass Spectrometry
Volume Number	28
Issue Number	8
e-ISSN	18791123
Language	English
Publisher	Springer US
Publisher Date	2017-05-05
Publisher Institution	The American Society for Mass Spectrometry
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	MOBCAL IMoS Mobility CCS Benchmark Spectrometry Trajectory method EHSS DHSS TDHSS Collision cross-section Projection approximation Analytical Chemistry Biotechnology Organic Chemistry Proteomics Bioinformatics
Content Type	Text
Resource Type	Article
Subject	Spectroscopy Structural Biology

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