Colloidal crystals have been used as a new separation medium utilizing C18 modified surfaces employing both adsorption and electrophoretic principles. Separations of cationic, hydrophobic dyes of varying chain lengths and peptides have been observed using this process. Progress in these materials leads to the potential for protein separation using the crystals in both one and two dimensions. Colloids deposited onto silicon substrates were used as MALDI plates for analysis of proteins ranging from 5 to 66 kDa. Ionization and detection was successfully achieved using sinapinic acid as a matrix applied to the surface. One and two dimensional separations were simulated, analyzed, and mapped using MALDI-TOF. Separations were simulated by spotting proteins of a wide range of molecular weights in one and two dimensional patterns. Sensitivity of the analysis varied dependent on the modification, but was observed in the femtamole range for lysozyme.