Beyond Mass Measurement: Using Mass Spectrometry to Probe Biomolecular Structure and Stability in the Gas Phase
Assistant Professor Varun Gadkari: Chemistry, University of Minnesota
Journal club discussion of https://doi.org/10.1021/jacs.5c07327. Tuesday, January 13, 2026, 9:00 – 10:00 am in BAG 192G. Discussion moderated by Addison Roush.
Seminar, followed by open discussion: Monday, January 26, 2026, 3:30 – 4:30 p.m. in BAG 260. Link
Rapid advancements in structural biology have enabled remarkable elucidation of three-dimensional biomolecular structures, providing valuable insights into structure-function relationships. However, current structure determination techniques impose stringent sample purity requirements, limiting characterization to “well-behaved” biomolecules that exhibit chemical and structural homogeneity. As a result, several essential biomolecular classes remain inaccessible due to their inherent heterogeneity. To bridge this gap, there is a critical need for bioanalytical tools capable of analyzing complex and intractable biomolecules while elucidating their structural properties. This seminar will highlight the Gadkari Research Group’s efforts to develop mass spectrometry-based methods for characterizing biomolecules that have long posed analytical challenges and remain elusive to conventional structural biology approaches. Building on expertise in native mass spectrometry, the group is advancing gas-phase unfolding methods and integrating them with machine learning models to detect stress-induced structural changes in biotherapeutic antibodies. Additionally, they are developing Orbitrap-based charge detection mass spectrometry to characterize biotherapeutic nucleic acids in the megadalton mass range. Through the development of innovative mass spectrometry techniques, the group’s research seeks to expand the reach of structural biology, enabling the characterization of biomolecules previously deemed intractable. Following the seminar, there was an open discussion on various ion mobility topics
Trapped Ion Mobility – Assisted Sequencing and Analysis of Protein Ions
Assistant Professor Nick Borotto, University of Nevada
Monday Jan 13, 2025, 3:30 in Bagley 260
The sequencing of intact proteins within a mass spectrometer enables the profiling of post-translational modification (PTM) crosstalk but is frequently hindered by convoluted spectra and the fact that tandem mass spectrometry (MS/MS) techniques often generate poor sequence coverages when applied to protein ions. Ion mobility spectrometry is a promising tool to overcome the complexity of these spectra by separating ions by their mass- and size-to-charge ratios. Here, we discuss the development of an activation method that when paired with trapped ion mobility spectrometry deconvolutes MS/MS spectra and improves the sequence information provided by intact protein focused workflows. Furthermore, we demonstrate the isolation and fragmentation of mobility separated product ions with the downstream quadrupole and collisional cell. This second activation step improves sequence coverage because many of the labile bonds have been depleted during the first dissociation and subsequent dissociation events are more evenly distributed throughout the product ion backbone. When these two activation steps are combined this technique generates 92% of the sequence coverage of the most effective MS/MS technique, but it accomplishes this feat in a fifth of the time and can be facilely integrated with liquid chromatographic separations. Lastly, we demonstrate that this activation technique can be utilized to elucidate the conformation of protein ions.
Following the seminar, there will be an open discussion on various ion mobility topics.
Following the seminar, there was an open discussion that spanned a variety ion mobility topics.
(Hopefully not) Too Hot to Handle: the Internal Energies of Ions During IM
February 19, 2019
Matt Bush will present a brief overview of the contemporary understanding of heating during ion mobility experiments.
Multiplexing of Time-Dispersive IM Measurements. We will then discuss efforts by the IM community to improve the duty cycle of IM measurements. Before the meeting, participants should read “Pseudorandom Sequence Modifications for Ion Mobility Orthogonal Time-of-Flight Mass Spectrometry” by Clowers and coworkers.
Dr. John C. Fjeldsted (Agilent Technologies)
December 12, 2018
John C. Fjeldsted is Agilent’s senior director of LC/MS Research and Development. He presented on the Agilent IM-MS platform and recent developments in IM-MS.
Prof. Chris Hogan (University of Minnesota)
September 21, 2018
We were delighted to host Prof. Hogan, who presented a seminar titled “Ion Mobility Spectrometry: Beyond Separation and Structural Characterization”.
Targeted Analysis of Ion Mobility Data
We were pleased to hear from Brian Pratt and Brendan MacLean about recent progress on the use of Skyline for the analysis ion mobility mass spectrometry data.
Skyline is a freely-available, open-source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), DIA/SWATH and targeted DDA quantitative methods and analyzing the resulting mass spectrometer data. Its flexible configuration supports All Molecules. It aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large-scale quantitative mass spectrometry studies in life sciences.
Originally developed for proteomics, Skyline has been extended by popular demand to work with generalized molecules. An important aspect of this work has been to enable the use of ion mobility separation equipment offered by the major mass spec vendors in support of experimental regimes where chromatography alone is often insufficient to distinguish molecules of nearly identical mass.
Ion Mobility of Proteins in Nitrogen Gas: Effects of Charge State, Charge Distribution, and Structure Characterized using Trajectory Method Calculations. (Daniele Canzani, Bush Lab)
Internal Exchange Standards Enable Cross-Platform Reproducibility in Measuring Gas-Phase Hydrogen/Deuterium Exchange Kinetics by Mass Spectrometry. (Sanjit S. Uppal (Sunny), Guttman Lab)
Collision-Induced Unfolding and Dissociation Reveal the Location of Ni(II) Binding in the Dimer of the Alpha-Crystallin Domain of HSPB5. (Cece Hong, Bush Lab)
Site-specific differentiation of sialic acid linkage isomers by ion mobility and gas-phase H/D exchange. (Mike Guttman)
Memory of the Condensed-Phase in the Gas-Phase: Effects of Solution, Charge, and Energy on Structures of Serum Albumin Ions. (Meagan Gadzuk-Shea, Bush Lab)
Lipidomics by HILIC-ion mobility-mass spectrometry
April 11, 2018
Seminar presented by Dr. Kelly Hines.
Discussion: Prediction of Collision Cross-Section Values with Machine Learning
MESS Member Talks
January 17, 2018
Using Ion Mobility Mass Spectrometry for Structural Elucidation of Glycans (Dr. Abhigya Mookherjee, Guttman Lab)
Determining Absolute Collision Cross Sections of Glycans (Daniele Canzani, Bush Lab)
