*PVDF (polyvinylidene difluoride, since you ask) is a polar membrane, nitrocellulose – non-polar. If your protein is charged in your transfer buffer, you should stick to (pun intended) PVDF. If your protein is hydrophobic, use nitrocellulose. Because of its hydrophobicity, PVDF requires pre-wetting with methanol. Also, add SDS to your transfer buffer to improve blotting efficiency.
*Both membranes come in three pore sizes – 0.1, 0.25 and 0.45 μm. The smaller your proteins, the smaller pore size membrane you should use. Nitrocellulose is better for capturing smaller (