Optimization of Algorithms for Ion Mobility Calculations
Abstract
Ion mobility spectrometry (IMS) is increasingly employed to probe the structures of gasphase ions, particularly those of proteins and other biological macromolecules. This process involves comparing measured mobilities with those computed for potential geometries, which requires evaluation of orientationally averaged cross sections using some approximate treatment of ionbuffer gas collisions. Two common models are the Projection Approximation (PA) and Exact HardSpheres Scattering (EHSS) that represent ions as collections of hard spheres. Though calculations for large ions and/or conformer ensembles take significant time, no algorithmic optimization had been explored. Previous EHSS programs were dominated by ion rotation operations that allow orientational averaging. We have developed two new algorithms for PA and EHSS calculations: one simplifies those operations and greatly reduces their number, and the other disposes of them altogether by propagating trajectories from a random origin. The new algorithms were tested for a representative set of seven ion geometries including diverse sizes and shapes. While the best choice depends on the geometry in a nonobvious way, the difference between the two codes is generally modest. Both are much more efficient than the existing software, for example faster than the widely used Mobcal (implementing EHSS) ~10  30 fold.
 Authors:
 Publication Date:
 Research Org.:
 Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
 Sponsoring Org.:
 USDOE
 OSTI Identifier:
 902680
 Report Number(s):
 PNNLSA52282
400412000; TRN: US200717%%610
 DOE Contract Number:
 AC0576RL01830
 Resource Type:
 Journal Article
 Resource Relation:
 Journal Name: Journal of Physical Chemistry A, 111(10):20022010; Journal Volume: 111; Journal Issue: 10
 Country of Publication:
 United States
 Language:
 English
 Subject:
 59 BASIC BIOLOGICAL SCIENCES; ALGORITHMS; APPROXIMATIONS; CROSS SECTIONS; EVALUATION; GEOMETRY; ION MOBILITY; OPTIMIZATION; ORIGIN; PROBES; PROTEINS; ROTATION; SCATTERING; SPECTROSCOPY; TRAJECTORIES
Citation Formats
Shvartsburg, Alexandre A., Mashkevich, Stefan V., Baker, Erin Shammel, and Smith, Richard D.. Optimization of Algorithms for Ion Mobility Calculations. United States: N. p., 2007.
Web. doi:10.1021/jp066953m.
Shvartsburg, Alexandre A., Mashkevich, Stefan V., Baker, Erin Shammel, & Smith, Richard D.. Optimization of Algorithms for Ion Mobility Calculations. United States. doi:10.1021/jp066953m.
Shvartsburg, Alexandre A., Mashkevich, Stefan V., Baker, Erin Shammel, and Smith, Richard D.. Thu .
"Optimization of Algorithms for Ion Mobility Calculations". United States.
doi:10.1021/jp066953m.
@article{osti_902680,
title = {Optimization of Algorithms for Ion Mobility Calculations},
author = {Shvartsburg, Alexandre A. and Mashkevich, Stefan V. and Baker, Erin Shammel and Smith, Richard D.},
abstractNote = {Ion mobility spectrometry (IMS) is increasingly employed to probe the structures of gasphase ions, particularly those of proteins and other biological macromolecules. This process involves comparing measured mobilities with those computed for potential geometries, which requires evaluation of orientationally averaged cross sections using some approximate treatment of ionbuffer gas collisions. Two common models are the Projection Approximation (PA) and Exact HardSpheres Scattering (EHSS) that represent ions as collections of hard spheres. Though calculations for large ions and/or conformer ensembles take significant time, no algorithmic optimization had been explored. Previous EHSS programs were dominated by ion rotation operations that allow orientational averaging. We have developed two new algorithms for PA and EHSS calculations: one simplifies those operations and greatly reduces their number, and the other disposes of them altogether by propagating trajectories from a random origin. The new algorithms were tested for a representative set of seven ion geometries including diverse sizes and shapes. While the best choice depends on the geometry in a nonobvious way, the difference between the two codes is generally modest. Both are much more efficient than the existing software, for example faster than the widely used Mobcal (implementing EHSS) ~10  30 fold.},
doi = {10.1021/jp066953m},
journal = {Journal of Physical Chemistry A, 111(10):20022010},
number = 10,
volume = 111,
place = {United States},
year = {Thu Feb 15 00:00:00 EST 2007},
month = {Thu Feb 15 00:00:00 EST 2007}
}

Inverse boundary value problems for the radiative transport equation play an important role in opticsbased medical imaging techniques such as diffuse optical tomography (DOT) and fluorescence optical tomography (FOT). Despite the rapid progress in the mathematical theory and numerical computation of these inverse problems in recent years, developing robust and efficient reconstruction algorithms remains a challenging task and an active research topic. We propose here a robust reconstruction method that is based on subspace minimization techniques. The method splits the unknown transport solution (or a functional of it) into lowfrequency and highfrequency components, and uses singular value decomposition to analyticallymore »

Experimental Evaluation and Optimization of Structures for Lossless Ion Manipulations for Ion Mobility Spectrometry with TimeofFlight Mass Spectrometry
We report on the performance of Structures for Lossless Ion Manipulation (SLIM) devices as a means for transmitting ions and performing ion mobility separations (IMS). Ions were successfully transferred from an electrospray ionization (ESI) source to the TOF MS analyzer by means of a linear SLIM device and an alternative arrangement including a 90° turn. First, the linear geometry was optimized for radial confinement by tuning RF on the central ‘rung’ electrodes and potentials on the DConly guard electrodes. Selecting an appropriate DC guard bias (26 V) and RF amplitude (≥160 Vpp at 750 kHz) resulted in the greatest ionmore » 
Effective Ion Mobility Calculations for Macromolecules by Scattering off Electron Clouds
Broad commercialization and increasing resolving power of ion mobility spectrometry/mass spectrometry (IMS/MS) platforms has engendered an explosion of IMS applications to structural characterization of gasphase biomolecules. That has renewed interest in more accurate and rapid ion mobility calculations needed to elicit ion geometries from the measurements. An approach based on scattering off electron density isosurfaces (SEDI) that mirrors the physics of molecular collisions was proven superior to the common methods involving atomic coordinates a decade ago, but has remained impractical for large ions because of extreme computational demands. Here, we accelerate SEDI by up to ~500 times using the fragmentmore » 
Squeezing of Ion Populations and Peaks in Traveling Wave Ion Mobility Separations and Structures for Lossless Ion Manipulations using Compression Ratio Ion Mobility Programming
In this work, we report an approach for spatial and temporal gas phase ion population manipulation, and demonstrate its application for the collapse of the ion distributions in ion mobility (IM) separations into tighter packets providing higher sensitivity measurements in conjunction with mass spectrometry (MS). We do this for ions moving from a conventionally traveling wave (TW)driven region to a region where the TW is intermittently halted or ‘stuttered’. This approach causes the ion packets spanning a number of TWcreated traveling traps (TT) to be redistributed into fewer TT, resulting in spatial compression. The degree of spatial compression is controllablemore »