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SLIMPHONY: A SLIM-Based Instrument That Orchestrates Complex Ion Mobility–Mass Spectrometry Experiments. AnneClaire Wageman, Addison E. Roush, Yuan Feng, Matthew F. Bush. J. Am. Soc. Mass Spectrom. 2026, 37, 95–104 . (Link)

The inherent heterogeneity of biological macromolecules offers a unique challenge for analysis. The combination of ion mobility (IM) and mass spectrometry (MS) is sensitive to the size, shape, and dynamics of, for example, proteins and their complexes. Combining multiple dimensions of ion mobility and mass spectrometry (IM–IM–MS) while leveraging unique gas-phase manipulations between dimensions has great potential for increasing the information content for challenging analytes. Here, we introduce an instrument, SLIMPHONY, which was built using the Structures for Lossless Ion Manipulations (SLIM) architecture. SLIMPHONY is unique in that eight independently controlled traveling-wave regions work in concert to enable complex, multidimensional separations. Single-dimension IM–MS experiments were used to separate a mixture of protein and protein-complex ions and demonstrate that the peak-to-peak resolution increases roughly with the square root of the separation length for a pair of hexakis(fluoroalkoxy)phosphazine ions. Ion selection and trapping between dimensions was then used to probe the gas-phase unfolding of a subpopulation of ubiquitin ions. Finally, by varying the guard potential used to confine ions, we demonstrate tunable activation of ubiquitin subpopulations, which we analyzed using IM separations of various lengths. With the ability to select and activate ions in multiple regions, to vary the number of dimensions of IM, and to control the length of IM separation, SLIMPHONY is a flexible platform for characterizing protein ions.

Finding relevant chemicals in the vast (known) chemical space is a major challenge for environmental and exposomics studies leveraging nontarget high resolution mass spectrometry (NT-HRMS) methods. Chemical databases now contain hundreds of millions of chemicals, yet many are not relevant. This article details an extensive collaborative, open science effort to provide a dynamic collection of chemicals for environmental, metabolomics, and exposomics research, along with supporting information about their relevance to assist researchers in the interpretation of candidate hits. The PubChemLite for Exposomics collection is compiled from ten annotation categories within PubChem, enhanced with patent, literature and annotation counts, predicted partition coefficient (logP) values, as well as predicted collision cross section (CCS) values using CCSbase. Monthly versions are archived on Zenodo under a CC-BY license, supporting reproducible research, and a new interface has been developed, including historical trends of patent and literature data, for researchers to browse the collection. This article details how PubChemLite can support researchers in environmental and exposomics studies, describes efforts to increase the availability of experimental CCS values, and explores known limitations and potential for future developments. The data and code behind these efforts are openly available. PubChemLite can be browsed at https://pubchemlite.lcsb.uni.lu.

https://pubs.acs.org/doi/10.1021/acs.estlett.4c01003

Increasing the dimensionality of ion mobility (IM) presents an enticing opportunity to increase the information content and selectivity of many analyses. However, for implementations of IM that use constant electrostatic gradients to separate ions in a buffer gas, technical challenges have limited the adoption of the technique and number of dimensions within individual experiments. Here, we introduce a strategy to “reset” the potentials of ions between IM dimensions. To achieve this, mobility-selected ions are trapped between dimensions of IM, using a combination of RF and electrostatic fields, while the subsequent dimension of IM is devoid of any drift field. By applying an incremental voltage ramp, the potential of the trapping region is elevated, simultaneously establishing the drift field in the subsequent dimension of IM. The trapped ions are then released and separated. We measured similar arrival-time distributions of protein ions using this strategy and a method without potential resetting, suggesting that potential resetting can be performed without additional losses or activation of ions. The findings of those experiments were corroborated by ion trajectory simulations, which exhibited a very small changes in ion position and no significant changes in effective temperatures during potential resetting. Finally, we demonstrate that IM information can be preserved during potential resetting by selecting subpopulations of 9+ cytochromec ions, resetting their potential, subjecting them to a second-dimension IM separation, and observing the retention of conformers within each subpopulation. We anticipate that this strategy will be useful for advancing flexible, multidimensional experiments on electrostatic IM instruments.

Towards IMⁿ with Electrostatic Drift Fields: Resetting the Potential of Trapped Ions Between Dimensions of Tandem Ion Mobility. Benjamin P. Zercher, Yuan Feng, Matthew F. Bush. Int. J. Mass Spectrom. 2024, 495, 117163. (Link)

Antibody-based therapeutics continue to expand both in the number of products and in their use in patients. These heterogeneous proteins challenge traditional drug characterization strategies, but ion mobility (IM) and mass spectrometry (MS) approaches have eased the challenge of higher-order structural characterization. Energy-dependent IM-MS, e.g., collision-induced unfolding (CIU), has been demonstrated to be sensitive to subtle differences in structure. In this study, we combine a charge-reduction method, cation-to-anion proton-transfer reactions (CAPTR), with energy-dependent IM-MS and varied solution conditions to probe their combined effects on the gas-phase structures of IgG1κ and IgG4κ from human myeloma. CAPTR paired with MS-only analysis improves the confidence of charge-state assignments and the resolution of the interfering protein species. Collision cross-section distributions were determined for each of the charge-reduced products. Similarity scoring was used to quantitatively compare distributions determined from matched experiments analyzing samples of the two antibodies. Relative to workflows using energy-dependent IM-MS without charge-state manipulation, combining CAPTR and energy-dependent IM-MS enhanced the differentiation of these antibodies. Combined, these results indicate that CAPTR can benefit many aspects of antibody characterization and differentiation.

Quantitatively Differentiating Antibodies Using Charge-State Manipulation, Collisional Activation, and Ion Mobility – Mass Spectrometry. Theresa A. Gozzo, Matthew F. Bush. Anal. Chem.2024, 96, 505–513. (Link)

The structural stability of biomolecules in the gas phase remains an important topic in mass spectrometry applications for structural biology. Here, we evaluate the kinetic stability of native-like protein ions using time-dependent, tandem ion mobility (IM). In these tandem IM experiments, ions of interest are mobility-selected after a first dimension of IM and trapped for up to ∼14 s. Time-dependent, collision cross section distributions are then determined from separations in a second dimension of IM. In these experiments, monomeric protein ions exhibited structural changes specific to both protein and charge state, whereas large protein complexes did not undergo resolvable structural changes on the timescales of these experiments. We also performed energy-dependent experiments, i.e., collision-induced unfolding, as a comparison for time-dependent experiments to understand the extent of unfolding. Collision cross section values observed in energy-dependent experiments using high collision energies were significantly larger than those observed in time-dependent experiments, indicating that the structures observed in time-dependent experiments remain kinetically trapped and retain some memory of their solution-phase structure. Although structural evolution should be considered for highly charged, monomeric protein ions, these experiments demonstrate that higher-mass protein ions can have remarkable kinetic stability in the gas phase.

Are the Gas-Phase Structures of Molecular Elephants Enduring or Ephemeral? Results from Time-Dependent, Tandem Ion Mobility. Benjamin P. Zercher, Seoyeon Hong, Addison E. Roush, Yuan Feng, Matthew F. Bush. Anal. Chem.2023, 95, 9589–9597. (Link|PubMed)

Lipidomic consequences of phospholipid synthesis defects in Escherichia coli revealed by HILIC-ion mobility-mass spectrometry. Kelly M. Hines, Libin Xu. Chem. Phys. Lipids 2019, 219, 15-22. (Link)

Continue reading “Lipidomic consequences of phospholipid synthesis defects in Escherichia coli revealed by HILIC-ion mobility-mass spectrometry”

Principles of Ion Selection, Alignment, and Focusing in Tandem Ion Mobility Implemented Using Structures for Lossless Ion Manipulations (SLIM). Rachel M. Eaton, Samuel J. Allen, Matthew F. Bush. J. Am. Soc. Mass Spectrom. 2019, 30, 1115–1125. (Link)

Continue reading “Principles of Ion Selection, Alignment, and Focusing in Tandem Ion Mobility”

Effects of Charge State on the Structures of Serum Albumin Ions in the Gas Phase: Insights from Cation-to-Anion Proton-Transfer Reactions, Ion Mobility, and Mass Spectrometry. Meagan M. Gadzuk-Shea, Matthew F. Bush. J. Phys. Chem. B 2018, 122, 9947–9955. (Link)

Ion Mobility of Proteins in Nitrogen Gas: Effects of Charge State, Charge Distribution, and Structure. Daniele Canzani, Kenneth J. Laszlo, Matthew F. Bush. J. Phys. Chem. A 2018, 122, 5625−5634. (Link)
Continue reading “Ion Mobility of Proteins in Nitrogen Gas: Effects of Charge State, Charge Distribution, and Structure”