Evaluation of stationary phases for 2-dimensional HPLC of proteins

RP-separation with TFA-based water/acetonitrile eluents is widely used for peptides and small proteins but is well known difficult for large or membrane proteins. Especially in proteomics or other complex biological matrices reliable elution patterns are difficult to achieve. New commercial stationary phases are validated regarding long term stability, protein recovery, carry over, symmetry and selectivity using 10 different proteins with different molar weights, isoelectric points and glycosylation. It could be demonstrated that some stationary phases had poor protein elution performances. They did not elute a protein at all or with minor recovery, peak symmetries. Sometimes bad and formidable carry over effects for peak areas in the following run were observed. Selectivity in separation of different isomers or glycosylated proteins is also different. The results suggest that neither surface area nor pore diameter play an important role in the application of reversed phases for HPLC of proteins. The investigations leads one to suppose that the bonding chemistry seems to be an important aspect. Most critical fact is that some RP-phases did not elute a protein at all others only 20% of the injected protein mass, which makes the objective of an RP-chromatogram highly questionable.