Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Despite the fact that synchrotron based x-ray crystallography and cryo-electron microscopy have made major contributions in determining thousands of protein structures even from micro-sized crystals, they suffer from some limitations that have not been overcome. These include radiation damage, the natural inability to crystallize of a number of proteins and experimental conditions for structure determination that are incompatible with the physiological environment. Today the ultrashort and ultra-bright pulses of X-ray free-electron lasers (XFELs) have made attainable the dream to determine protein structure before radiation damage starts to destroy the samples. However, the signal-to-noise ratio remains a great challenge to obtain usable diffraction patterns from a single protein molecule. With the perspective to overcome those challenges, we describe here a new methodology that has the potential to overcome the signal-to-noise-ratio and protein crystallization limits. Using a multidisciplinary approach, we propose to create ordered, two dimensional protein arrays with defined orientation attached on a self-assembled-monolayer. We develop a literature-based, flexible toolbox capable of assembling different kinds of proteins on a functionalized surface and consider using a graphene cover layer that will allow performing experiments with proteins in physiological conditions.