I am using immunoprecipitation to determine whether two overexpressed proteins interact. One is fused to S-tag, the other is fused to mCherry. Irrespective of the fact that there is no evidence of an interaction in the experiment, I am still able to IP the individual proteins themselves. However, both target proteins, when IP'd with their respective antibodies, appear shifted up about 10kD compared to input and sup samples. I can't figure out why this is. I am eluting the IP by boiling in SDS, and I have tried increasing the SDS concentration to 2%, thinking that it might be antibody fragments that are stuck on the protein, but this does not change anything. Any ideas?
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