I am using heparin affinity chromatography with a TSKgel Heparin 5PW column and an HP1100. The runnning buffers are A: 20mM Tris pH7.5, B: 20mM Tris 1M NaCl pH7.5. Equilibration/binding is at 15% B, elution at 100% B.
The assay is to give a rough purity of our desired protein (it is aprox. 20% of a protein mixture). Unfortunately, if our protein is present, another protein co-purifies (Lactoferrin). In the absence of our protein there is no lactoferrin in the elution. The problem is that lactoferrin is known to bind lots of proteins possibly through a positively charged area.
What I would like to know is how to stop the lactoferrin sticking to our protein without affecting the affinity of the protein for heparin.
Any suggestions would be welcome.

I know that lactoferrin has been purified using bovine milk gangliosides ligands with affinity chrmatography. So I was thinking maybe you could add some cheap mixed gangliosides to your sample and the lactoferrin might prefferentialy bind to the gangliosides and not your protein. Just a thought, good luck.