In SEC, mass is not measured so much as the hydrodynamic volume of the polymer molecules, that is, how much space a particular polymer molecule takes up when it is in solution. However, the approximate molecular weight can be calculated from SEC data because the exact relationship between molecular weight and hydrodynamic volume for polystyrene can be found. For this, polystyrene is used as a standard. But the relationship between hydrodynamic volume and molecular weight is not the same for all polymers, so only an approximate measurement can be obtained.
Another drawback is the possibility of interaction between the stationary phase and the analyte. Any interaction leads to a later elution time and thus mimics a smaller analyte size.
When performing this method, the bands of the eluting molecules may be broadened. This can occur by turbulence caused by the flow of the mobile phase molecules passing through the molecules of the stationary phase. In addition, molecular thermal diffusion and friction between the molecules of the glass walls and the molecules of the eluent contribute to the broadening of the bands. Besides broadening, the bands also overlap with each other. As a result, the eluent usually gets considerably diluted. A few precautions can be taken to prevent the likelihood of the bands broadening. For instance, one can apply the sample in a narrow, highly concentrated band on the top of the column. The more concentrated the eluent is, the more efficient the procedure would be. However, it is not always possible to concentrate the eluent, which can be considered as one more disadvantage.