Computational Modelling in Mass Spectrometry and Ion Mobility: Methods for Ion Structure and Reactivity Determination

January 25 - 28, 2018
St. Petersburg, FL


  • Iain Campuzano, Amgen
  • Frank Sobott, University of Antwerp
  • Michael van Stipdonk, Duquesne University

Keynote Lecture Speakers:

  • James Cheeseman, Gaussian, Inc.
  • Mark Johnson, Yale University
  • Perdita Barran, University of Manchester
  • Lars Konermann, University of Western Ontario

Thursday, January 25, 2018

6:00-7:00 pm, Registration

7:00-7:15 pm, Opening Remarks: Iain Campuzano, Michael van Stipdonk and Frank Sobott

7:15-8:00 pm, Plenary Lecture: James Cheeseman, Gaussian, Inc.; "Quantum Mechanical Calculations: From Small Molecules to Helical Peptides"

8:00-10:00 pm, Reception

Friday, January 26, 2018

8:30-10:00 am, Small Molecule and Protein Molecular Dynamics and Quantum Mechanics: The Basics

  • Romelia Salomon, Pfizer; "Using MD to Accurately Compute Protein Structure: Real-Life Protein Examples"
  • Michael Bartberger, Amgen Inc; "Applying MD and QM for Rational Drug Design"
  • Beibei Wang, University of Calgary; "The Course-Grain Martini Force Field and Its Application for Membrane Protein Systems"

10:00-10:15 am, Coffee Break

10:15-11:45 am, Small Molecule and Peptide Molecular Dynamics and Quantum Mechanics

  • Béla Paizs, Bangor University Wales; "Exploring Peptide Fragmentation Reactions Using Density Functional Theory Calculations"
  • William Hase, Texas Tech University; "Computer Simulations of Unimolecular and Intramolecular Dynamics"
  • Mary Rodgers, Wayne State University; "Synergistic Tandem MS and Theoretical Studies of Nucleic Acid Building Block Structure and Stability"

11:15-11:35 am, Hot Topic from contributed abstracts

11:35 am-1:00 pm, Lunch and Learn Workshop:  Small Molecule Geometry Optimisations and CCS Calculations, lunch provided by ASMS
Attendees will learn how to perform small molecule geometry optimization and charge fitting calculations using the Gaussian (commercial) and Firefly (free/academic) quantum mechanical programs, and how to use these results to calculate collisional cross section values using MOBCAL and IMoS.  
Attendees are welcome (but not required) to follow along using their own laptops.  If so, installation of the following programs is ahead of time are recommended:
•    Avogadro (  sketching and visualization program,  
•    Firefly  (  
•    or  Gaussian  ( quantum chemistry program (if the attendee has a license for the latter) ,  
•    MOBCAL and IMoS CCS programs.

1:00-2:40 pm, Computational Methods for Determination of Ion Structure by Tandem Mass Spectrometry, Ion Mobility and Ion Spectroscopy

  • Ryan Steele, University of Utah; "Vibrational Signatures of Electronic Properties in Molecules"
  • Anne McCoy, University of Washington; "Theoretical and Computational Approaches for Investigation of Molecules and Complexes that Undergo Large Amplitude Vibrational Motions"
  • Bert de Jong, Lawrence Berkeley National Laboratory; "Application of High-Level DFT and QM-MD to Studies of Metal Ion Complexes"
  • Steven Valentine, West Virginia University; "Advanced Protocols for Molecular Dynamics Simulations and Collision Cross-Section Calculation"
  • Keith Richardson, Waters Corporation, UK; "ETD Reagent Design for a Glow Discharge Source"

2:40-3:00 pm, Hot Topic Talk selected from contributed abstracts

3:00-7:00 pm, Free Time

7:00-8:00 pm, Keynote Lecture: Mark Johnson, Yale University; "Experimental and Theoretical Investigation of Shared Protons in Water"

8:00-8:30 pm, Six highlighted poster presentations (4 minute talks + 1 minute transition)

8:30-10:00 pm, Poster Session I

Saturday, January 27, 2018

8:30-10:00 am, Computational Methods for Studies of Ion Chemistry

  • Peter Armentrout, University of Utah; "Computational and Experimental Studies of Intrinsic Metal Ion Chemistry"
  • Lai-Sheng Wang, Brown University; "Probing the Electronic Structure of Metal Complexes and Redox Species Using DFT and anion Photoelectron Spectroscopy"
  • Robert Continetti, University of California-San Diego; "Studies of Transient Species Using Electronic Structure Calculations and Photoelectron-Photofragment Coincidence Techniques"

9:50-10:10 am, Hot Topic Talk selected from contributed abstracts

10:10-10:30 am, Coffee Break

10:30-12:15 pm, Gas-Phase Structure and Reactions of Nucleic Acids and Glycans

  • Dan Fabris, University at Albany, SUNY; "Implementation of Course-Grain MD and Ion Mobility for Nucleic Acid Gas-Phase Structure Determination"
  • Benjamin Bythell, University of Missouri at St. Louis; "DFT Study of Glycan Dissociation"
  • Valerie Gabelica, IECB, France; "All Atom MD and QM Calculations in Native Nucleic Acid MS and IM"

12:00-12:15 pm, Hot Topic Talk selected from contributed abstracts

12:15-1:45 pm, Lunch and Learn Workshop:  Macromolecular Modelling with Cross-Linking and Ion Mobility MS, lunch is available for purchase
In this workshop, attendees will learn how to source and prepare constituent subunits for modelling (MODELLER/PyMOL), generate topologies using cross-linking MS, prepare and submit protein complexes for gas phase simulation (GROMACS) and evaluate collision cross sections (IMPACT).  
 UNIX-based operating systems such as Linux and Mac OS are highly recommended for attendees wishing to follow the workshop on their own laptops. The following softwares are recommended for those wishing to participate in the tutorial (but are not essential as inputs and outputs of each section will be provided):
•    PyMOL (
•    GROMACS (
•    IMPACT (

1:45-3:45 pm, Protein-Ligand and Protein/Protein Complexes: Soluble and Membrane Proteins

  • Thanh D Do, University of Illinois at Urbana-Champaign; "The Application of MD and IM to Determine Structural Transitions from Solution to Gas-Phase"
  • Brandon Ruotolo, University of Michigan; "Using Course-Grain MD to Model Protein Sub-unit Behavior in the Gas-Phase"
  • Michael Marty, University of Arizona; "Pushing the Limits of Membrane Protein-Lipid Interactions with Nanodiscs, Native Mass Spectrometry, and MD"
  • Argyris Politis, Kings College, London, UK; "Modelling a Membrane Protein and its Interaction with Detergent Molecules in the Gas-Phase"

3:45-4:15 pm, 2 x 15 minute Hot Topic Talks selected from contributed abstracts

4:15-7:00 pm, Free Time

7:00-8:00 pm, Keynote Lecture: Perdita Barran, University of Manchester, UK; "Using MD, MD and IM to Further Understand Protein Collapse in the Gas-Phase"

8:00-8:30 pm, Six highlighted poster presentations (4 minute talks + 1 minute transition)

8:30-10:00 pm, Poster Session II

Sunday, January 28, 2018

8:30-9:30 am, Ion Mobility Separation Algorithms: Which One is Optimal?

  • Carlos Larriba-Andaluz, Indiana University-Purdue University; "Molecular Dynamics/Kinetic Theory Algorithm for Numerical Determination of Electrical Mobility"
  • Christian Bleiholder, Florida State University; "Collision Cross Section Design and Considerations"
  • Erik Marklund, Uppsala University, Sweden; "Computations for the Gas-Phase Study of Macromolecular Structure"

9.30-9.45 am, Coffee Break

9:45-10:45 am, Molecular Dynamics and Quantum Mechanics in Medicinal Chemistry: Real Therapeutic Case Studies

  • Brian Lanman, Amgen; "Application of MD, QM and SAR to Design a Peptide-Like Drug Targeting a Free Cysteine Residue"
  • Jens Meiler, Duquesne University; "Application of Molecular Dynamics Simulations to Studies of Protein Conformational Change"

10:45-11:15 am, 2 x 15 minute Hot Topics Talks selected from contributed abstracts

11:15-12:00 pm, Keynote Lecture: Lars Konermann, University of Western Ontario; "Modelling the Electrospray Processes by Molecular Dynamics"

12:00-12:15 pm, Closing Remarks: Iain Campuzano, Michael van Stipdonk and Frank Sobott