Collisions with background gas can perturb the transition frequency of trapped ions in an optical atomic clock. We develop a non-perturbative framework based on a quantum channel description of the scattering process, and use it to derive a master equation which leads to a simple analytic expression for the collisional frequency shift. As a demonstration of our method, we calculate the frequency shift of the Sr$^+$ optical atomic clock transition due to elastic collisions with helium.