This is a nice analysis that comes from a pretty simple set of experiments that were just done nicely. The article from Mostovenko et. al., (open access!) compares multiple methods of fractionating both an E.coli digest and a single digest of human plasma.
The methods compared are: SDS-PAGE vs. SCX vs. IEF. The output is unique peptides and overlap between methods. Interestingly, in the bacterial digest, SDS-PAGE and SCX run kind of neck and neck, while IEF lags behind. However, in the plasma digest, SCX fractionation is the clear winner.
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