A novel projection approximation algorithm for the fast and accurate computation of molecular collision cross sections (II). Model parameterization and definition of empirical shape factors for proteins

► We derive atomic parameters for use with the projected superposition approximation (PSA). ► We apply the PSA method to 396 protein structures from the Protein Data Bank with up to 300 kDa in weight. ► We define an empirical shape factor to estimate the PSA cross section for proteins. ► The empirical shape factor is accurate to approximately 10%.