A multi-channel gel electrophoresis apparatus for efficiently collecting molecules isolated by gel electrophoresis so they can be further analyzed, identified, or used as reagents or medications. The apparatus using a novel “tagless” strategy that combines multi-dimensional separation of endogenous complexes with mass spectrometric monitoring of their composition. In this procedure, putative protein complexes are identified based on the co-migration of collections of polypeptides through multiple orthogonal separation steps. A majority of E. coli proteins are shown to remain in stable complexes during fractionation of a crude extract through three chromatographic steps.