Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles

TLDR

Interpretation of mass spectra is difficult because overlapping mass and charge components confound the m/z ratio, and existing peak‑assignment or fitting methods struggle with complexity and computational cost. The authors introduce a Bayesian framework to disentangle mass and charge dimensions in spectra. They implemented this framework in the UniDec software, using charge‑state priors to rapidly and flexibly deconvolve mass and ion‑mobility mass spectra with minimal user input. Testing on increasingly complex systems demonstrated that UniDec can resolve lipid binding to membrane proteins, track subunit exchange dynamics, and quantify polydispersity in protein assemblies and lipoprotein nanodiscs, thereby enhancing analysis of ion‑mobility and mass spectra.

Abstract

Interpretation of mass spectra is challenging because they report a ratio of two physical quantities, mass and charge, which may each have multiple components that overlap in m/z. Previous approaches to disentangling the two have focused on peak assignment or fitting. However, the former struggle with complex spectra, and the latter are generally computationally intensive and may require substantial manual intervention. We propose a new data analysis approach that employs a Bayesian framework to separate the mass and charge dimensions. On the basis of this approach, we developed UniDec (Universal Deconvolution), software that provides a rapid, robust, and flexible deconvolution of mass spectra and ion mobility-mass spectra with minimal user intervention. Incorporation of the charge-state distribution in the Bayesian prior probabilities provides separation of the m/z spectrum into its physical mass and charge components. We have evaluated our approach using systems of increasing complexity, enabling us to deduce lipid binding to membrane proteins, to probe the dynamics of subunit exchange reactions, and to characterize polydispersity in both protein assemblies and lipoprotein Nanodiscs. The general utility of our approach will greatly facilitate analysis of ion mobility and mass spectra.