Abstract: The adsorption of bovine serum albumin (BSA), immunoglobulin G (IgG) and fibrinogen (Fgn) on fluorinated selfassembled monolayers have been studied using time of flight secondary ion mass spectrometry (ToF-SIMS) and Spectroscopic Ellipsometry (SE). The objective of the work has to establish the utility of ToF-SIMS for the determination of the amount of protein adsorbed on the surface. Quantification of surface adsorbed proteins was carried out using SE and a good correlation between ToF-SIMS results and SE was achieved. The surface distribution of proteins were also analysed using Atomic Force Microscopy (AFM). We show that the surface distribution of proteins strongly affect the ToFSIMS results.