text: One of the most common uses for molecular-weight size markers is in gel electrophoresis. The purpose of gel electrophoresis is to separate proteins by physical or chemical properties, which include charge, molecular size, and pH.< When separating based on size, the ideal method is SDS-PAGE or polyacrylamide gel electrophoresis and molecular-weight size markers are the appropriate standards to use.
  Gels can vary in size. The number of samples to be run will determine the appropriate gel size. All gels are divided into lanes that run parallel through the gel. Each lane will contain a specific sample. Typically, molecular-weight size standards are placed in an outer lane. If a gel has a particularly high number of lanes, then multiple ladders may be placed across the gel for higher clarity.
  Proteins and standards are pipetted on the gel in appropriate lanes. Sodium dodecyl sulfate (SDS) interacts with proteins, denaturing them, and giving them a negative charge. Since all proteins have the same charge-to-mass ratio, protein mobility through the gel will solely be based on molecular weight.  Once the electric field is turned on, protein migration will initiate. Upon completion, a detection mechanism such as western blotting can be used, which will reveal the presence of bands.  Each band represents a specific protein. The distance of travel is solely based on molecular weight; therefore, the molecular weight of each protein can be determined by comparing the distance of an unknown protein to the standard of known molecular weight.