A critical and fundamental factor in both analytical and preparative chromatography is the use of true buffers. In other words, mobile phases with buffering capacity. For example, in peptide purification, there are concentrated bands of various components of the sample, including the target peptide, moving through the column and you need to have control over their tendency to dissociate...
A lot of mistakes are made here in using substances without much buffering capacity. For example, the traditional method in reversed phase chromatography is the use of 0.1% trifluoroacetic acid (TFA) but there are very good reasons to use true buffers instead. By selecting the right pH value, electrostatic attraction and repulsion between molecules can be controlled. Consider your particular purification needs and put in the time to test buffers to a relevant extent, it could make all the difference.
