Polyacrylamide-gel-electrophoresis (PAGE) is one of the most widely applied techniques for protein separation. Thereby, the proteins migrate within a polyacrylamide matrix driven by the force of an electric field. Various denaturing and non-denaturing methods have been developed for different separation strategies such as isoelectric focussing (separation according to net charge), SDS-PAGE (separation according to size) or BN-PAGE (separation of protein complexes). Both one- and two dimensional systems can be applied granting the possibility to separate thousands of different proteins and protein isoforms. The good compatibility to mass spectrometric methods is a further advantage of these methods.

For Electrospray-Ionization-Tandem-Mass Spectrometry (ESI-MS/MS) protein- or peptide-solutions are sprayed in an electric field. The obtained protein-/peptide-ions are desolvated and analyzed in the QToF by an electric field. All incoming ions can sequentially be isolated, fragmented and the obtained fragment ions are ejected towards the detector.