This new study ASAP at JPR is an incredibly thorough (QUANTITATIVE!) analysis of different pull down and digestion techniques for Protein-Protein Interaction (PPI) experiments.
Honestly, I'm filing it away as a reference for the next time I try to do one of these. This thing is a textbook of how to optimize a PPI experiment.
Of course, this isn't the first one of these we've seen, but rather than doing PSM counts or even # of peptide/proteins ID'ed, this study does LFQ with MaxQuant (quadrupole Orbitrap) and then use stable isotope SRM quantification.
An interesting observation is that higher abundance proteins are easily quantifiable just about regardless of the pull-down and digestion methods. To get to the lower abundance things, they really need to fine tune the methodology.