Some of our Cogent HPLC column application notes that feature Aqueous Normal Phase (ANP) use 50% isopropanol (IPA) as part of the aqueous component of the mobile phase. The main reason for this use is to help keep the column free of undesired adsorbed contaminants from a sample or sample matrix.
Contaminants can change the retention behavior of your analyte in any HPLC method and can also slowly elute off the column as carryover peaks in subsequent runs or as baseline noise and drift. We have found IPA (or methanol can be used) to be good at washing these contaminants off the column during the final part of an ANP gradient run. When performing HPLC or LCMS, adding IPA to the A (aqueous) solvent component will be effect the chromatography compared to using only aqueous-containing solvents, so it is something you should add in the method before it has been fully developed.