The future Europa Clipper NASA mission to Europa will carry the MAss Spectrometer for Planetary EXploration (MASPEX), which will analyze the compounds making up Europa's exosphere, and plumes, if present. Europa's exosphere is likely to feature abundant atomic oxygen, a product of sputtering of Europa's surface by energetic particles from Jupiter's radiation belts, or photolysis of oxygen-bearing molecules in the exosphere. Due to its very high reactivity, this atomic oxygen could induce chemical processes within MASPEX. These processes could involve materials composing the instrument, or other compounds from Europa's exosphere. In both cases, the possible effect on the instrument's measurements is a concern. In this work we first review previous relevant experiments on the effect of atomic oxygen on several candidate metals and conclude that stainless steel with a gold coating is the most satisfactory choice for MASPEX's antechamber walls, and alumina for the impact plate. We then perform simulations of adsorption/desorption processes within the instrument's antechamber to bound the effect of atomic oxygen on other compounds from Europa's exosphere. We find that the accumulation of atomic oxygen during a flyby would lead to a reduction of the apparent abundance of water by as much as 0.125% (Δ[H₂O]/[H₂O] = -1.25 × 10^-3). Evaluating the exact extent of this effect during data post-processing would require constraining the atomic oxygen abundance, which would have to be achieved with other instruments, such as the ultraviolet spectrometer.