Hi, we have recently purchased Protein Simple Peggy Sue that is capable to do both charge based and size based assays. The main advantage of charge based assay is that you get the information about post translational modification and you can easily quantify it. It works perfectly for some proteins like ERK. If you have more complex PTMs you are mostly unable to assign the shifts to particular phosphorylation, but you can monitor the changes (AKT kinase). Some proteins look incompatible with recommended condition of IEF and they probably need a lot of optimization. The main disadvantage for me is the price of assay.

The size based assay can be compared to standard PAGE and WB, the main advantage over standard method is that you can compare up to 96 samples in one run and you need only small volume. The main disadvantage is again the price.

Thanks for that quick and very thorough reply!