Polyacrylamide gel electrophoresis is a powerful tool for protein mixture separation frequently used in proteomic studies. This article describes the problems which can arise during the identification process of separated proteins by matrix assisted laser desorption/ionization mass spectrometry. Presence of residual acrylamide monomers in the peptide samples leads to a significant peptide signal suppression. In the case of protein prohibitin, isolated from the MCF 7 breast cancer cell line, the peptide signal suppression was observed in 50% of all detected peptides. <alternatives> [...] </alternatives>
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