The ever growing demand for the development of new technologies and materials has led to extensive studies inspired by biological functional complexes. Peptides with their outstanding ability to efficiently self-assemble can express a broad spectrum of intriguing functionalities. A key question in mimicking their assembly and function is the precise understanding of the specific interactions between the contained amino acids on the level of a sub-molecular length scale. An excellent tool to probe samples at these length scales is available with scanning tunneling microscopy (STM) and its operation under the controlled conditions of ultra-high vacuum (UHV) and low temperature. Within this thesis it is demonstrated how high-resolution studies by STMin combination with a controlled sample preparation by electrospray ion beam deposition (ES-IBD) under UHV conditions allows for the structural determination of peptides on surfaces. Furthermore the results presented here contribute to the development of a method capable of directly identifying individual amino acids within a peptide sequence. The structural and electronic properties of molecules on surfaces crucially depend on their interaction with the underlying substrate. Implementing a thin dielectric layer on the metallic surface, electronically decouples molecules from the substrate and enables an unperturbed observation of the molecular electronic structure. In Chapter 2 the properties of hexagonal boron nitride (h-BN) on Rh(111) as decoupling layer are assessed on behalf of the structural and electronic properties of the molecular model system pentacene adsorbed on it. In a second part of this chapter the discovery and the characterization of a new phase of h-BN/Rh(111) is described. In Chapter 3, we gained insight into the properties of amino acids on metal surfaces by utilizing the capability of the STM to probe the structure and the electronic characteristics in high resolution imaging and scanning tunneling spectroscopy (STS). As a second important aspect of this chapter, the modification of STM tips with amino acids is investigated as a method to enhance the structural and electronic resolution. An experimental protocol allowing to adhere amino acids on the STM tip be could developed. Using functional STM tips in STS experiments on amino acids enabled the observation of specific molecular resonances. An obstacle in investigating large bio-polymers, such as natural peptides, is their high structural complexity and conformational freedom. Therefore the utilization of custom designed synthetic sequences tailored towards a specific property is a good approach. In Chapter 4 studies performed on two synthetic peptide sequences deposited by ES-IBD on an Au(111) surface are discussed. The first sequence assembled in ordered two-dimensional networks. A folded gas-phase conformation could be utilized to rationalize the observed structures in the networks. Subsequently it was shown that the self-assembly behavior of the peptide could be steered towards chain-like assemblies by modifying the sequence at the peptide C-terminal. Using specific amino acid functionalized STM tips a sensitivity towards an amino acid of the same type in the peptide sequence could be observed. Thereby a partial sequencing of the synthetic peptide was enabled.