The biodistribution of colloidal carriers after their administration in vivo depends on the adsorption of some plasma proteins and apolipoproteins on their surface. Poly(methoxypolyethyleneglycol cyanoacrylate-co-hexadecylcyanoacrylate) (PEG-PHDCA) nanoparticles have demonstrated their capacity to cross the blood-brain barrier (BBB) by a mechanism of endocytosis. In order to clarify this mechanism at the molecular level, proteins and especially apolipoproteins adsorbed at the surface of PEG-PHDCA nanoparticles were analyzed by complementary methods such as CE and Protein Lab-on-chip((R)) in comparison with 2-D PAGE as a method of reference. Thus, the ability of those methodologies to identify and quantify human and rat plasma protein adsorption onto PEG-PHDCA nanoparticles and conventional PHDCA nanoparticles was evaluated. The lower adsorption of proteins onto PEG-PHDCA nanoparticles comparatively to PHDCA nanoparticles was evidenced by 2-D PAGE and Protein Lab-on-chip((R)) methods. CE allowed the quantification of adsorbed proteins without the requirement of a desorption procedure but failed, in this context, to analyze complex mixtures of proteins. The Protein Lab-on-chip((R))) method appeared to be very useful to follow the kinetic of protein adsorption from serum onto nanoparticles; it was complementary to 2-D PAGE which allowed the identification (with a relative quantification) of the adsorbed proteins. The overall results suggest the implication of the apolipoprotein E in the mechanism of passage of PEG-PHDCA nanoparticles through the BBB.