Taking advantage of the drop-on-demand capabilities of inkjet printing, the first example of a single tissue being used as a substrate for preparing combinatorial arrays of different matrix-assisted laser desorption/ionization (MALDI) matrices in multiple concentrations on a single chip is reported. By varying the number of droplets per spot that were printed, a gradient array of different amounts of matrix material could be printed on a single chip, while the selection of matrices could be adjusted by switching different matrix materials. The result was a two-dimensional array of multiple matrices on a single tissue slice, which could be analyzed microscopically and by MALDI to elucidate which combination of matrix and printing conditions offered the best resolution in terms of spot-to-spot distance and signal-to-noise ratios for proteins in the recorded MS spectra. This combinatorial approach enables the efficient optimization of possible matrices in an organized, side-by-side array format, which can particularly be useful for the detection of specific protein markers.