Mapping protein-protein interactions by quantitative proteomics.
Proteins exert their function inside a cell generally in multiprotein complexes. These complexes are highly dynamic structures changing their composition over time and cell state. The same protein may thereby fulfill different functions depending on its binding partners. Quantitative mass spectrometry (MS)-based proteomics in combination with affinity purification protocols has become the method of choice to map and track the dynamic changes in protein-protein interactions, including the ones occurring during cellular signaling events. Different quantitative MS strategies have been used to characterize protein interaction networks. In this chapter we describe in detail the use of stable isotope labeling by amino acids in cell culture (SILAC) for the quantitative analysis of stimulus-dependent dynamic protein interactions.
Dengjel
Joern
J
Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
Kratchmarova
Irina
I
Blagoev
Blagoy
B
D000596:Amino Acids / Q000737:chemistry; D002457:Cell Extracts / Q000737:chemistry; D002853:Chromatography, Liquid; D004591:Electrophoresis, Polyacrylamide Gel; D006367:HeLa Cells; D006801:Humans; D047468:Immunoprecipitation; D007553:Isotope Labeling; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D015398:Signal Transduction; D053719:Tandem Mass Spectrometry
D000596:Amino Acids; D002457:Cell Extracts; D011506:Proteins