Thermal Tracks: A Gaussian process-based framework for universal melting curve analysis enabling unconstrained hit identification in thermal proteome profiling experiments

Abstract

Thermal Tracks is a Python-based statistical framework for analyzing protein thermal stability data that overcomes key limitations of existing thermal proteome profiling (TPP) work-flows. Unlike standard approaches that assume sigmoidal melting curves and are constrained by empirical null distributions (limiting significant hits to approximately 5 % of data), Thermal Tracks uses Gaussian Process (GP) models with squared-exponential kernels to flexibly model any melting curve shape while generating unbiased null distributions through kernel priors. This framework is particularly valuable for analyzing proteome-wide perturbations that significantly alter protein thermal stability, such as pathway inhibitions, genetic modifications, or environmental stresses, where conventional TPP methods may miss biologically relevant changes due to their statistical constraints. Furthermore, Thermal Tracks excels at analyzing proteins with un-conventional melting profiles, including phase-separating proteins and membrane proteins, which often exhibit complex, non-sigmoidal thermal stability behaviors. Thermal Tracks is freely available from GitHub and is implemented in Python, providing an accessible and flexible tool for proteome-wide thermal profiling studies.