We have a working immunoprecipitation protocol for my protein of interest, which has recoveries over 90% when using small volumes of serum (200-500 uL). We now want to scale up and immunoprecipitate more protein so it can be used in mass spectrometry. Problem is that we can't seem to get our recoveries over 25% anymore.

Fun detail is that this percentage is more or less valid despite the concentration of the protein in serum. With 10x more proteins you also get 10x more protein on your beads. So saturation of the beads is not a problem. We tried increasing the incubation time from 1 hour to overnight. This helps a bit, but still does not come close to the recoveries we're used to.

Does anyone has any tips or clues on how to continue?

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