An electrospray (ES)-based deposition system enabling the coating an impervious substrate, such as a glass slide, with biological materials in a vacuum. Distilled water or a buffer is used as the solvent; no other solvents are used thereby eliminating hazardous waste from the process. Movement across differential pumping stages causes evaporation of the solvent occurs resulting in shrinkage of the remaining constituents with an increase of the charge density. The resulting ion beam enters a vacuum chamber and the beam impinges on the substrate, whereby a thin layer is deposited thereon. The spray can be focused to a specific area allowing patterning of the substrate if desired. The amount of coating can be controlled and a specified number of coats of the same or different molecules can be added to the surface.