Invitrogen/Life Tech. sells the CBQCA (3-(4carboxybenzoyl)quinoline- 2-carboxaldehyde) kit, which measures protein concentration down to 10 nmol/mL. It reacts with primary amines and forms fluorescent derivatives excited at 465 nm with emission at 550 nm: http://products.invitrogen.com/ivgn/product/C6667. Of course, you will need a fluorescence microplate reader or fluorometer for the measurements.

When I get your question right you would like to determine the concentration of a specific protein in a rather complex sample, right? The CBQCA assay would be useful to determine the protein concentration of all proteins in the given sample. For the sensitive analysis of one protein ELISA would be fine (if specific antibodies for your protein are available) or mass spectrometry would be great. For the latter, you can detect down to attomole range using state of the art triple quadrupole instruments. Using mass spec, you in general go for a protein-specific peptide and perform tryptic digest.

I can recommend a new fluorescent method very sensitive that can help you, here is the information

http://www.ozbiosciences.com/assay-kits/103-fluorescent-protein-assay-kit.html

Good Luck