The main application of size-exclusion chromatography is the fractionation of proteins and other water-soluble polymers, while gel permeation chromatography is used to analyze the molecular weight distribution of organic-soluble polymers. Either technique should not be confused with gel electrophoresis, where an electric field is used to "pull" molecules through the gel depending on their electrical charges. The amount of time a solute remains within a pore is dependent on the size of the pore. Larger solutes will have access to a smaller volume and vice versa. Therefore, a smaller solute will remain within the pore for a longer period of time compared to a larger solute.
Another use of size exclusion chromatography is to examine the stability and characteristics of natural organic matter in water. In this method, Margit B. Müller, Daniel Schmitt, and Fritz H. Frimmel tested water sources from different places in the world to determine how stable the natural organic matter is over a period of time. Even though size exclusion chromatography is widely utilized to study natural organic material, there are limitations. One of these limitations include that there is no standard molecular weight marker; thus, there is nothing to compare the results back to. If precise molecular weight is required, other methods should be used.