In SDS-PAGE, the SDS molecules coat the polypeptide. This is important for two reasons:
1) the negative charge of the SDS masks the natural charge of the polypeptide and gives all polypeptides the same charge per mass ratio. Since the charge-to-mass ratio for all polypeptides is the same, they will be equally attracted toward the positive electrode.
2) the SDS denatures the polypeptides so that all the polypeptides are linear. This prevents the shape and packing of the polypeptides from becomming a factor in their migration through the gel.
As a result, migration of the peptides through the polyacrylamide gel is dependent on only the lenght of the polypeptide strand. Longer fragments will encounter more resistance while passing through the gel, while smaller fragments can more easily travelse the gel. The length of the polypeptide strand is roughly proportional to its molecular weight, so SDS-PAGE is useful for molecular weight determination.
When analyzing the results of an SDS-PAGE analysis, the distance traveled through the gel is linearly proportional to the log of the molecular weight of the polypeptide.