One option is to use a magnetic separator, such as the SuperMag Multitube Separator from Ocean Nanotech.  The iron nanoparticle-protein complex should stick to the side of the tube (next to the magnet) and then you can remove the supernatant containing the unbound protein.  Remove the tube from the magnetic separator and resuspend the pure nanoparticle-protein complex in a suitable buffer.  It works well for nanoparticles > 20 nm.  They have a protocol on their website that describes the method:  http://www.oceannanotech.com/upload/110926104829622028fte075.pdf. 

i think you can use a magnet and separate your bare iron nanoparticles from coated nanoparticles. there are some other methods have been used for nanoparticle protein separation: centrifuge: but it may be disturb your corona, specially in soft area. filter: according to your nanoparticle size you may can use filter with appropriate pore size. size exclusion chromatography: i think it is best way for nanoparticle protein separation from any other bare nanoparticles and non bonded proteins. 

the below link help you have a better point of view:

http://pubs.acs.org/doi/abs/10.1021/cr100440g

You may follow immunoprecipitation based pulldown assay to separate the protein-nanocomplex, so many immunoprecipitation methods available via online check then proceed

Thank you all for your suggestions. But the problem is, the protein is a heme containing protein and magnetic separation would not be a better choice as both the free protein and as well the nanoparticle-bound protein contain iron. If immunoprecipitation done it ll result in colloidal suspension if resuspend the precipitate in buffer as the nanoparticle is insoluble/sparingly soluble. but we need it in solution form as we proceed to MS analysis

Try to use MACs column

I highly recommend you to use Magnetic-activated cell sorting (MACS) column

http://en.wikipedia.org/wiki/Magnetic-activated_cell_sorting

Article Monoclonal antibody conjugated magnetic nanoparticles could ...

Another options :

1. Agarose Gel electrophoresis and extraction into solution

2. Dialysis

3. Analytical centrifugation

best,