Methods for Inferring Interaction Potentials from Cross-Linking Mass Spectrometry Data

Abstract

Cross-linking mass spectrometry (XL-MS) has emerged as a powerful quantitative technique for probing intra-protein structural information as well as protein-protein interactions at an unprecedented scale. XL-MS data yield information on the pairwise spatial proximity of proteins through inter-molecular linkers. However, systematic methods for adapting such data for coarse-grained interacting particle models remain limited. Predominant focus is put on directly fitting radial distribution functions (RDFs), while numerous observables, e.g. coordination numbers, which are functionals of the RDF, cannot be uniquely inverted. In this work, we develop a framework for parameterizing interaction potentials from such observables in potentially phase-separated mixtures, as encountered in XL-MS results. We establish a connection between this problem and the inverse Henderson problem and adapt algorithms such as Iterative Boltzmann Inversion and Iterative Monte Carlo to its numerical solution. We derive exact and low-density limit gradient approximations and propose two new algorithms based on an adaptation of the predictor-corrector~framework. In total, we evaluate several optimization algorithms on biologically realistic ten-component test systems. We demonstrate that for homogeneous fluids, all methods achieve exceptional efficiency and accuracy. Critically, we further demonstrate successful parametrization in a challenging three-phase system. Here, three algorithms, namely Adam and gradient descent employing the low-density derivative as well as Newton's method with the exact gradient, reliably recover the correct parameters. These results establish a clear pathway from XL-MS experiments to coarse-grained protein models for systems where phase separation governs biological function, potentially enabling new investigations of biomolecular condensates and protein aggregation.