SDS-PAGE is an established and well understood electrophoresis technique that allows for the qualitative analysis of protein molecular weight and (semi-)quantitative analysis of (covalent) protein aggregates and fragments.
In general, electrophoresis is a separation technique based on the migration of charged molecules in response to an electric field, toward the electrode of opposite charge. It is performed mainly in polyacrylamide gels. The most common polyacrylamide gel electrophoresis (PAGE) technique employs the detergent sodium dodecyl sulfate (SDS). SDS denatures proteins and binds those non-covalently providing an overall negative charge. Since the bound SDS/protein (w/w) ratio is practically protein independent, under a given electric field SDS-bound proteins migrate through a gel with a velocity depending primarily on their size, enabling molecular weight estimation. Moreover, by comparing electrophoretic profiles of proteins analyzed under reducing and non-reducing conditions, information about the nature of covalent bonds (disulfide mediated or not) can be obtained. Noncovalent aggregates are usually not detected, because SDS dissociates noncovalent bonds.
Native PAGE, however, can provide information about noncovalent aggregation since electrophoresis is performed in the absence of denaturing agents. In native gels, proteins generally retain their native conformation and their mobility is governed by the ratio of electric charge to hydrodynamic size.