An atmospheric molding protocol has been used to prepare an ionic methacrylate-based copolymer sample support chips for MALDI (pMALDI)-MS by targeting selected groups of various monomers copolymerized during molding, namely, carboxy, sulfo, dimethylalkyamino, and trimethylalkylammonium groups. The new disposable array chips provide analyte-oriented enhancement of protein adsorption to the modified substrates without requiring complicated surface coating or derivatization. The MALDI-MS performance of the new ionic copolymer chips was evaluated for lysozyme, β-lactoglobulin A, trypsinogen and carbonic anhydrase I using washing with solutions prepared in pH or ionic strength steps. On cationic chips, the proteins are washed out at pH lower than their pl values, and on anionic chips at pH higher than their p/ values. The ability of the microfabricated pMALDI chip set to selectively adsorb different proteins from real samples and to significantly increase their MS-signal was documented for the transmembrane photosystem I protein complex from the green alga Chlamydomonas reinhardtii. The proteins were almost exclusively adsorbed according to calculated p/ values and grand average of hydropathy (GRAVY) indexes. The new disposable chips reduce manipulation times and increase measurement sensitivity for real-world proteomic samples. The simple atmospheric molding procedure enables additional proteomic operations to be incorporated on disposable MALDI-MS integrated platforms. © 2006 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.