Two proteins that differ greatly in size (molecular weight) but not overall charge would best be separated by Gel-filtration chromatography.
Gel filtration chromatography, a form of size exclusion chromatography, can be used to separate molecules and complexes in a sample into fractions with a specific size range, to remove all molecules greater than a specific size from the sample, or to perform both of these tasks simultaneously. When in aqueous solution, compounds like small molecules, proteins, protein complexes, polysaccharides, and nucleic acids can be separated using gel filtration chromatography. The procedure is known as gel permeation chromatography when an organic solvent serves as the mobile phase.
Additional applications for gel filtration chromatography include:
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