One goal of our research is to identify proteins that interact with each other during specific signaling events. Our lab has a special interest in the study of signal transduction in neurons, especially the ephrin signaling pathway. The basic strategy for these experiments is to isolate protein complexes by immunoprecipitation or affinity chromatography, separate the proteins by SDS-PAGE and then identify proteins of interest from the gel. We do this by excising the protein band from the gel, cleaving the protein with a specific protease such as trypsin, then determining the amino acid sequences of the peptides by Q-TOF tandem mass spectrometry. The masses and tandem mass spectra (containing peptide sequence information) of the peptides are then used to search genome databases to identify the proteins. To get more information about the relative amounts of each protein that participate in signaling complexes in the stimulated and nonstimulated states, we use stable isotope coding methods (for example, stable isotope labeling in cell culture, or SILAC).

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