False labelling due to quenching failure of N-hydroxy-succinimide-ester-coupled dyes

In comparative fluorescence gel electrophoresis experiments, cross-talk was detected. It was traced back to a failure in the quenching process in typical labelling protocols. Despite a huge excess of potential reaction sites for the N-hydroxy-succinimide-ester-coupled dye, sufficient active dye molecules were available after the quenching step to label protein molecules un-specifically. It could be shown that only a 100-fold increase in the amount of quencher will silence residual dye to such an extent that no artificial signals are detected.