Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology

Abstract

Native mass spectrometry (MS) allows the interrogation of structural aspects of macromolecules in the gas phase, under the premise of having initially maintained their solution-phase non-covalent interactions intact. In the more than 25 years since the first reports, the utility of native MS has become well established in the structural biology community. The experimental and technological advances during this time have been rapid, resulting in dramatic increases in sensitivity, mass range, resolution, and complexity of possible experiments. As experimental methods are improved, there have been accompanying developments in computational approaches for analysing and exploiting the profusion of MS data in a structural and biophysical context. Here, based on discussions within the EU COST Action BM1403 on Native MS and Related Methods for Structural Biology with broad participation from Europe and North America, we consider the computational strategies currently being employed by the community, aspects of best practice, and the challenges that remain to be addressed.

Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry

“…Integration of information from different native and non-native techniques can provide valuable structural insights. 59,60 2.1.2 Collisional activation induces protein unfolding and subunit release. The term 'complex-up' was coined in 2019; 17 however, early examples of subunit release via activation of protein complexes in the gas phase were reported in 1994 by Smith and co-workers.…”

“…Spectral interpretation of native MS has largely relied on manual analysis, although deconvolution soware such as UniDec and iFAMS has been developed in recent years. 60,114 Likewise, analysis of top-down MS data has largely involved manual analysis or manual validation due to the complexity of the data. Data interpretation for complex-down spectra is similar to TDMS of denatured proteins; therefore, many existing soware packages for TDMS can be retrotted for complex-down data, including Pro-Sight PTM 2.0, 115 ProSight Lite, 116 MASH Suite, [117][118][119] Pro-teinGoggle, 120 TopPIC, 121 Informed-Proteomics, 122 Masstodon, 123 and others.…”

Compaction of RNA Hairpins and Their Kissing Complexes in Native Electrospray Mass Spectrometry

“…Developing force fields adapted to gas-phase calculations would also be worthwhile. 8 However, a gas-phase nucleic acid force field would need to be polarizable, 51 and the modeling procedure should account for mobile protons, as suggested for proteins. Figure S1: Representative electrospray mass spectra of the hairpins and kissing complexes in soft pre-IMS conditions.…”

The emergence of mass spectrometry for characterizing nanomaterials. Atomically precise nanoclusters and beyond

“…Ion mobility coupled to mass spectrometry (IM-MS) is becoming an indispensable tool for gas phase structural biology. [192][193][194] In an IM-MS experiment, ions are driven through a buffer gas by a weak electric field, prior to their injection in a mass spectrometer. Ions with different size and shape, or different charges, adopt different velocities in the drift gas and then reach the mass spectrometer at different times.…”