Disclosed are apparatus and methods for depositing solvent-free molecules on surfaces of samples, with particular application to imaging mass spectrometry. A vacuum chamber is configured to have controllable matrix translation apparatus for controlling the position of one or more solvent-free matrices within the chamber. Sublimation apparatus is used to sublimate molecules from the solid phase matrices. One or more samples are placed separately from the solvent-free matrices within the chamber. Condensation apparatus individually cools the samples to deposit sublimated molecules on the samples. Controllable sample translation apparatus is used to control the position of the samples within the chamber. Rotatable sample holding apparatus may be used to hold and move the samples to allow deposition of molecules on multiple samples at substantially the same time. Rotatable matrix holding apparatus may also be used to hold and move a plurality of matrices to create a homogenous mixture of molecules that are deposited onto one or more samples. As surface characterization system may be used to monitor deposition of the molecules to determine their thickness and roughness. A computer may be configured to control the matrix translation apparatus, the sublimation apparatus, the condensation apparatus, and the sample translation apparatus to provide for automated deposition of solvent-free molecules on the samples.