What is the importance of urea in mass spectrometry? We use 8M urea to FASP our proteins prior to mass spectrometry. What is the significance of using 8M urea? and how does it affect the proteins?
I think that the OP was asking about relevance of using urea with respect to the FASP method. In the FASP method, the primary denaturant is SDS . Protein are denatured with a ~4% SDS solution (buffered to pH 7.5 - 8.0). Then 8 M urea solution is used to replace the SDS. Urea serves two purposes here, first it keeps the protein denatured and in solutions as SDS is replaced/washed off. Second, because urea is a chaotropic agent, it reduces the size of SDS micelles which otherwise would block the pores of the membrane filter.
Read the original article here: http://www.nature.com/nmeth/journal/v6/n5/abs/nmeth.1322.html
8M urea is a denaturant, as @Chris mentioned. Denaturing proteins is important for molecular (aka classical) mass spectrometry. If you analyzed a non-denatured protein, you'd get information not only on the primary structure, but also on noncovalent interaction (2+°):
The classical MS approach, so-called “molecular MS,” analyzes, in the gas phase of the mass spectrometer, individual species initially present in solution after destruction of the noncovalent framework. On the other hand, “supramolecular MS” or “nondenaturing MS” aims at transferring intact noncovalent complexes that preexist in solution into the gas phase of the instrument.
(Sanglier et al. 2008, Methods Mol. Biol.)
Denaturing proteins is important for molecular/classical mass spec because it ensures your analysis only reflects the covalent bonds (primary structure) present in your target protein.