Separation in reversed phase liquid chromatography depends on non-polar analytes being retained by a hydrophobic stationary phase such as a C18 column. If the sample contains ionic (polar) components, they may not be sufficiently retained by the stationary phase for adequate separation. The primary methods of improving retention are via ion pairing or pH modification.

Improving separation via ion pair chromatography

Ion pairing is a technique that can aid in separation by pairing an alkyl salt with the ionic components in the sample. The carbon chain will interact with the stationary phase, and the salt with the ion, thus allowing improved separation of ionic species. Typically, the longer the alkyl chain, the greater the retention by the column. Basic species react best with sodium alkyl sulfonates, and acidic with quaternary ammonium salts or alkyl amines.

All mobile phases using salts must contain at least 10% water in order to avoid precipitation. Using a dedicated column for ion pair chromatography, particularly with longer alkyl chain lengths, is recommended for silica based stationary phases, as non-reversible adsorption may occur.