High performance collision cross section calculation—HPCCS

Since the commercial introduction of Ion Mobility coupled with Mass Spectrometry (IM‐MS) devices in 2003, a large number of research laboratories have embraced the technique. IM‐MS is a fairly rapid experiment used as a molecular separation tool and to obtain structural information. The interpretation of IM‐MS data is still challenging and relies heavily on theoretical calculations of the molecule's collision cross section (CCS) against a buffer gas. Here, a new software (HPCCS) is presented, which performs CCS calculations using high perfomance computing techniques. Based on the trajectory method, HPCCS can accurately calculate CCS for a great variety of molecules, ranging from small organic molecules to large protein complexes, using helium or nitrogen as buffer gas with considerable gains in computer time compared to publicly available codes under the same level of theory. HPCCS is available as free software under the Academic Use License at https://github.com/cepid-cces/hpccs. © 2018 Wiley Periodicals, Inc.

[1]  Morteza Marzjarani,et al.  Simulation and the Monte Carlo Method (3rd ed.) , 2019, Technometrics.

[2]  Boniek G. Vaz,et al.  Isomeric separation of cannabinoids by UPLC combined with ionic mobility mass spectrometry (TWIM-MS)—Part I , 2017 .

[3]  D. Pereira,et al.  W1cep Theory For Computational Thermochemistry , 2015 .

[4]  M. Porrini,et al.  Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure , 2015, Journal of mass spectrometry : JMS.

[5]  E. Marklund,et al.  Collision cross sections for structural proteomics. , 2015, Structure.

[6]  M. Eberlin,et al.  Are Benzoic Acids Always More Acidic Than Phenols? The Case of ortho-, meta-, and para-Hydroxybenzoic Acids† , 2015 .

[7]  Gert Vriend,et al.  New ways to boost molecular dynamics simulations , 2015, J. Comput. Chem..

[8]  I. Gràcia,et al.  Review on ion mobility spectrometry. Part 1: current instrumentation. , 2015, The Analyst.

[9]  M. Eberlin,et al.  Separation of glycosidic catiomers by TWIM-MS using CO2 as a drift gas. , 2015, Journal of mass spectrometry : JMS.

[10]  John A. McLean,et al.  Ion Mobility-Mass Spectrometry: Time-Dispersive Instrumentation , 2014, Analytical chemistry.

[11]  C. Eyers,et al.  The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics. , 2014, Nature chemistry.

[12]  M. Bowers,et al.  A novel projection approximation algorithm for the fast and accurate computation of molecular collision cross sections (IV). Application to polypeptides , 2013 .

[13]  B. Chowdhry,et al.  Can ion mobility mass spectrometry and density functional theory help elucidate protonation sites in 'small' molecules? , 2013, Rapid communications in mass spectrometry : RCM.

[14]  M. Bowers,et al.  A novel projection approximation algorithm for the fast and accurate computation of molecular collision cross sections (II). Model parameterization and definition of empirical shape factors for proteins , 2013 .

[15]  M. Eberlin,et al.  Structure-drift time relationships in ion mobility mass spectrometry , 2013, International Journal for Ion Mobility Spectrometry.

[16]  James Reinders,et al.  Intel Xeon Phi Coprocessor High Performance Programming , 2013 .

[17]  Michael T Bowers,et al.  Factors contributing to the collision cross section of polyatomic ions in the kilodalton to gigadalton range: application to ion mobility measurements. , 2013, Analytical chemistry.

[18]  N. Morgon,et al.  Theoretical study of thermochemical properties using composite methods adapted to ONIOM , 2012 .

[19]  Keith Richardson,et al.  Structural characterization of drug-like compounds by ion mobility mass spectrometry: comparison of theoretical and experimentally derived nitrogen collision cross sections. , 2012, Analytical chemistry.

[20]  T. Wyttenbach,et al.  A novel projection approximation algorithm for the fast and accurate computation of molecular collision cross sections (I). Method , 2011 .

[21]  Ami Marowka,et al.  On Performance Analysis of a Multithreaded Application Parallelized by Different Programming Models Using Intel VTune , 2011, PaCT.

[22]  J. Staymates,et al.  Reliability of ion mobility spectrometry for qualitative analysis of complex, multicomponent illicit drug samples. , 2011, Forensic science international.

[23]  Ewa Jurneczko,et al.  How useful is ion mobility mass spectrometry for structural biology? The relationship between protein crystal structures and their collision cross sections in the gas phase. , 2011, The Analyst.

[24]  C. Robinson,et al.  Residual counter ions can stabilise a large protein complex in the gas phase , 2010 .

[25]  Anthony J. Midey,et al.  Improved analysis of explosives samples with electrospray ionization-high resolution ion mobility spectrometry (ESI-HRIMS) , 2010 .

[26]  C. Robinson,et al.  Collision cross sections of proteins and their complexes: a calibration framework and database for gas-phase structural biology. , 2010, Analytical chemistry.

[27]  M. Sillanpää,et al.  Ion mobility spectrometry and its applications in detection of chemical warfare agents. , 2010, Analytical chemistry.

[28]  Richard D. Smith,et al.  Optimum waveforms for differential ion mobility spectrometry (FAIMS) , 2008, Journal of the American Society for Mass Spectrometry.

[29]  Brandon T Ruotolo,et al.  Ion mobility–mass spectrometry analysis of large protein complexes , 2008, Nature Protocols.

[30]  D. Truhlar,et al.  The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals , 2008 .

[31]  University , 2006, The Genealogical Imagination.

[32]  Joop H. van Lenthe,et al.  Software news and updates , 2001, J. Comput. Chem..

[33]  George C. Schatz,et al.  Mobilities of carbon cluster ions: Critical importance of the molecular attractive potential , 1998 .

[34]  T. Wyttenbach,et al.  Effect of the long-range potential on ion mobility measurements , 1997 .

[35]  A. Shvartsburg,et al.  An exact hard-spheres scattering model for the mobilities of polyatomic ions , 1996 .

[36]  George C. Schatz,et al.  Structural Information from Ion Mobility Measurements: Effects of the Long-Range Potential , 1996 .

[37]  Michael Wolfe,et al.  High performance compilers for parallel computing , 1995 .

[38]  F. James,et al.  RANLUX: A Fortran implementation of the high-quality pseudorandom number generator of Lüscher , 1994 .

[39]  Reuven Y. Rubinstein,et al.  Simulation and the Monte Carlo method , 1981, Wiley series in probability and mathematical statistics.

[40]  N. Morgon,et al.  Validação computacional de métodos compostos no estudo de propriedades moleculares , 2011 .

[41]  Prabha Dwivedi,et al.  Ion mobility-mass spectrometry. , 2008, Journal of mass spectrometry : JMS.

[42]  Takuji Nishimura,et al.  Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator , 1998, TOMC.

[43]  L. Dagum,et al.  OpenMP: an industry standard API for shared-memory programming , 1998 .

[44]  RJ Allan.  An introduction to parallel programming , 1993 .