I am developing a peptide mapping method for an approx. 100 kD glycoprotein. I use a Vydac C18 column (5 um, 2.1x250 mm) and a typical TFA and acetonitrile gradient. However, the chromatogram is very complicated and I am not able to create an acceptable map. This is due to the complexity of the digest and the resolution limitations of the system. Optimization of the digest and separation conditions did not help.
Now I intend to try some HPLC columns from other suppliers. Any advise on which type and brand to use?

My colleagues and I put a seminar together on the subject. You can find it at Waters.com under Columns and Supplies - Waters Applications Bibliography. Search for peptides than select "A method development strategy for biopharmaceuticals" number 980276. It shows the principles how one can improve the separation,from coarse adjustment to fine-tuning and what the compromises are. If you have additional questions you can contact me at Uwe.Neue@Prodigy.net