gel electrophoresis - How do SDS-PAGE gels differ in a Bis-Tris system vs. a Tris-Glycine system?

SDS PAGE system rely on the fact that protein is denatured and surrounded by the SDS negatively charged detergent micelle. This eliminates most of the charge and idiosyncratic solubility differences from one protein to another and gives a reasonable separation based only on size of the protein which is related to the size of the SDS micelle around each molecule.

Bis-Tris and Tris-glycine buffers have quite different charge shielding characteristics. Bis (also known as 2-[Bis(2-hydroxyethyl)amino]-2-(hydroxymethyl)-1,3-propanediol) has a tertiary amine with a pKa of 6.46 and a pKb of 7.54. glycine is a zwitterion at any pH between 2.3 and 9.6. This creates a difference in the way that the buffer shields the SDS PAGE micelles from the rest of the electrical field, slowing down (probably glycine slows things down a bit) the time to resolution, but also giving the micelles more time to migrate.

So for SDS PAGE systems, the resolution of the gel has at least as much to do with the size of the gel pores (based on the acrylamide and bis-acrylamide percentages), the amount of protein you are putting into a given volume of loading well, and the size differences of the bands you are tying to separate. (you need to get pretty lucky to separate a 100.54 kda band from a 100.85 kDa band, but 1.5 to 1.8 kDa is easier 10 to 14 kDa is even easier). Also consider adjusting the current or voltage of the power supply. The buffer system is only one consideration in planning your experiment and often not the primary factor of quality.