Does anybody know a good way to see proteins in a vaccine? I see only a couple of bands running protein gels from a vaccine, while I see lots of proteins on simply bacterial cells. What effect do oils and aluminium hydroxide have on proteins or our ability to separate them on gel electrophoresis? Do we need a special protein extraction procedure and how would you recommend to extract proteins if so?
What kind of vaccine are you running on the gel? If it is a subunit vaccine that only contains certain proteins you may only want to see a couple bands. It is also possible that if the bacteria protein amounts are much less in the vaccine than the culture that you are running along side. In this case the bands may be some kind of stablizing protein that is added to the vaccine (BSA, etc.). More information about the specific vaccine formulation may allow for a better answer.
As for adjuvants interfering with running a gel. If the samples are denatured and heated it doubt this is a problem, but if you are running under native conditions it may affect your results.
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