A Nafion membrane was tested as a new tool for a fast and easy sample pretreatment for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) measurements. This membrane material was used for ion exchange and carbohydrate purification with minimal quantities of sample solution. An ion exchange method for carbohydrates was developed and demonstrated on a Dextran sample. The cations of the original sample were replaced within minutes by potassium or cesium ions. Another feature of this membrane was the fact that proteins and peptides adsorb on the acid surface. This behavior was investigated as a purification step for carbohydrates with high peptide and protein impurity concentrations. It was found that oligosaccharide libraries from rat- and mouse IgG mass spectra can be obtained clearly in the presence of high peptide impurities.