Polyalanine molecules (PA) with an α-helix conformation have recently attracted a great deal of interest, as the propagation of electrons through the chiral backbone structure comes along with spin polarization of the transmitted electrons. By means of scanning tunneling microscopy and spectroscopy under ambient conditions, PA molecules adsorbed on surfaces of epitaxial magnetic Al2O3/Pt/Au/Co/Au nanostructures with perpendicular anisotropy were studied. Thereby, a correlation between the PA molecules ordering at the surface with the electron tunneling across this hybrid system as a function of the substrate magnetization orientation as well as the coverage density and helicity of the PA molecules was observed. The highest spin polarization values, P, were found for well-ordered self-assembled monolayers and with a defined chemical coupling of the molecules to the magnetic substrate surface, showing that the current-induced spin selectivity is a cooperative effect. Thereby, P deduced from the electron transmission along unoccupied molecular orbitals of the chiral molecules is larger as compared to values derived from the occupied molecular orbitals. Apparently, the larger orbital overlap results in a higher electron mobility, yielding a higher P value. By switching the magnetization direction of the Co layer, it was demonstrated that the non-spin-polarized STM can be used to study chiral molecules with a submolecular resolution, to detect properties of buried magnetic layers and to detect the spin polarization of the molecules from the change in the magnetoresistance of such hybrid structures.