Microelectrospray ionization-mass spectrometry was used to directly observe electron transferring flavoprotein⅐flavoprotein dehydrogenase interactions. When electron transferring flavoprotein and porcine dimethylglycine dehydrogenase or sarcosine dehydrogenase were incubated together in the absence of substrate, a relative molecular mass corresponding to the flavoprotein⅐electron transferring flavoprotein complex was observed, providing the first direct observation of these mammalian complexes. When an acyl-CoA dehydrogenase family member, human short chain acyl-CoA dehydrogenase, was incubated with dimethylglycine dehydrogenase and electron transferring flavoprotein, the microelectrospray ionization-mass spectrometry signal for the dimethylglycine dehydrogenase⅐electron transferring flavoprotein complex decreased, indicating that the acyl-CoA dehydrogenases have the ability to compete with the dimethylglycine dehydrogenase/sarcosine dehydrogenase family for access to electron transferring flavoprotein. Surface plasmon resonance solution competition experiments revealed affinity constants of 2.0 and 5.0 M for the dimethylglycine dehydrogenaseelectron transferring flavoprotein and short chain acyl-CoA dehydrogenase-electron transferring flavoprotein interactions, respectively, suggesting the same or closely overlapping binding motif(s) on electron transferring flavoprotein for dehydrogenase interaction.Mass spectrometry and surface plasmon resonance are proving valuable techniques for functional proteomics, because each provides powerful detection and identification capabilities for assessing in vivo protein-protein interactions (1). In this work, the interactions between electron transferring flavoprotein (ETF) 1 and two flavoprotein dehydrogenase families are assessed by microelectrospray ionization-mass spectrometry and surface plasmon resonance, demonstrating the complementarity of the two techniques.ETF is a mitochondrial matrix electron acceptor that interacts with and accepts electrons from at least 10 flavoprotein dehydrogenases (2). ETF donates these electrons to the electron transport chain via ETF⅐ubiquinone oxidoreductase (3, 4). The acyl-CoA dehydrogenases, the first family of dehydrogenases identified to interact with ETF, are homotetramers with conserved tertiary and quaternary structures, one noncovalently bound FAD coenzyme molecule/protein subunit, and similar catalytic mechanisms (5-9). Very long chain, long chain, medium chain, and short chain (SCAD) acyl-CoA dehydrogenases catalyze the first step of fatty acid -oxidation in the mitochondrial matrix. The other members of this family, including isovaleryl-CoA dehydrogenase (IVD), are involved in branched chain amino acid metabolism. The second family of dehydrogenases that interact with ETF consists of dimethylglycine dehydrogenase (DMGDH) and sarcosine dehydrogenase (SDH) (10 -12). These monomeric flavoproteins are active in choline catabolism. They also localize to the mitochondrial matrix but contain one molecule of covalently bound FAD/enz...