I've been reading a lot of literature on tagging proteins for analysis in MS and am getting a bit confused by one aspect. I'm wondering what the consensus view is as to which beads are the best for immunoprecipitation of Flag tagged proteins prior to MS. It seems many articles I've read are using the agarose m2 beads (Sigma). However, does the use of magnetic beads conjugated to the m2 antibody give better results and less non specific binding? In this case what I'm looking for is a big factor in which to use. I want to use the mass spec to identify binding partners of my protein of interest.