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Structure and orientation of mols. are key properties of functionalized surfaces. Using time-of-flight secondary ion mass spectrometry (TOF-SIMS), here we investigate how to modulate these parameters upon the immobilization process varying the conditions of self-assembly. The mol. of interest, a template-assembled synthetic protein (TASP), consists of a central peptide ring with orthogonally arranged residues. Thioalkane chains allow the directed self-assembly of the mol. on a gold surface; four serine residues on the opposite side of the ring can be used as anchoring sites for various functional sensing mols. The TASP conformation and its orientation in self-assembled monolayers (SAMs) play a central role for the accessibility of these serine residues. To study the influence of the self-assembly conditions, two series of samples were prepd. Pure TASP monolayers of different surface densities are compared to mixed TASP/alkanethiol monolayers prepd. by sequential adsorption varying sequence and particular incubation times as well as by coadsorption modifying incubation times and TASP/alkanethiol mass ratios. Switching the TASP orientation from a state where the mols. are lying flat on the surface to an upright orientation turned out to be possible by inserting the TASP into a preformed alkanethiol monolayer of an appropriate surface d. This study demonstrates that TOF-SIMS is an excellent tool not only to investigate the surface compn., but also the mol. structure of functionalized surfaces. [on SciFinder (R)]