Strength of the interaction is a huge limitation in using MS. It could also be a problem if the proteins form homomultimers. You might also have to take care that your proteins are stable in a buffer compatible with MS, in the absence of Tris, like phosphate buffer. Be sure to first use different ratios of your proteins to first optimise the ratio when the interaction is best, and then go for MS if the interaction is really strong, with atleast 25-50% protein involved in the interaction. It is a technique with potential but can be tricky!
Strength of the interaction is a huge limitation in using MS. It could also be a problem if the proteins form homomultimers. You might also have to take care that your proteins are stable in a buffer compatible with MS, in the absence of Tris, like phosphate buffer. Be sure to first use different ratios of your proteins to first optimise the ratio when the interaction is best, and then go for MS if the interaction is really strong, with atleast 25-50% protein involved in the interaction. It is a technique with potential but can be tricky!
One more consideration: TOF mass analyzers are more compatible for this kind of studies compared trap type of mass analyzers (ion trap, orbitrap, FT-ICR), due to the less interactions between the analyte ions and separation in space.
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