Dynabeads should be handled in the same way like a normal agarose resin.
The best advice for further MS analysis is to remove as much as possible detergents. That can be done washing extensively with buffers lacking detergents.
This is really important if you are going for a direct in-solution digestion.
Otherwise (in case of in -gel digestion, FASP or peptide-cleaning) the detergents will be lately removed and you can elute your samples even in Laemmli buffer.
This protocol for immunoprecipitation using Dynabeads works well, one can adapt it to work with the antibody of interest.
https://www.lifetechnologies.com/se/en/home/references/protocols/proteins-expression-isolation-and-analysis/gfp-protocol/immunoprecipitation-protocol-using-anti-gfp-antibodies.html
I have no answer. In fact, I need advice! I have not used this technique, but have acquired Dynabeads to try.
MY problem is the need to identify a protein for which I have an antibody, with the possibility that my unknown protein is NOT the antigen, but a different protein in what is a fraction separated only by size on Sepharose CL-6B. Electron microscopy is the only method for its detection. If I immunoprecipitate the known antigen, can I find the unknown in what did not precipitate???
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