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There is an enormous interest in exploiting nanoparticles in various biomedical applications since their size scale is similar to that of biological molecules (e.g., proteins, DNA) and structures (e.g., viruses and bacteria). As the field continues to develop, quantitative and qualitative studies on particle-cell interaction, with respect to their size and surface, are required in order to advance nanotechnology for biomedical applications. This will be important for assessing nanoparticle toxicity (i.e. translocation into cells and interference with viability and cellular function), for advancing nanoparticles for imaging, drug delivery, and therapeutic applications (i.e. targeting specific cells, organs, or tumors), and for designing multifunctional nanoparticles. Due to the lack of systematic study to date, data are difficult to compare since the parameters and particles in each of the published studies differ substantially. However, the scientific community, in general, agrees that the size and colloidal behavior play a crucial role in cellular interaction/uptake, biodistribution, clearance and cytotoxicity. Surface functionalization of nanoparticles still remains a difficult task and represents not only a chemical challenge but constitutes a basic requirement for future scientific investigations. Alteration of surface charges and/or stabilization by the addition of bi- / multi-functional molecules, such as differently charged proteins or plasmids, frequently leads to particle flocculation and rapid sedimentation. The biological functionality, in such cases, is achieved by covalent binding of bio-active molecules on a preexisting single surface coating. A fixed bed magnetic reactor has been developed with a quadrupole repulsive arrangement of permanent magnets which allows for surface derivatization by magnetically immobilizing superparamagnetic iron oxide nanoparticles (SPIONs). The yield and quality of the resulting functionalized SPIONs was significantly improved with reduction in reaction times using solid phase synthesis strategy. In this way, pH changes across the isoelectric point, washing steps or even solvent exchanges could be easily tolerated thereby avoiding the problems of colloidal instability during the derivatization steps. It was shown that the surface functionalization of SPIONs using a magnetic fixed bed reactor was superior to the liquid phase reaction in terms of reaction yield, particle size distribution, colloidal stability and scalability. In particular, cell organelle targeting peptide derivatized on SPIONs surface was obtained from the reactor. The combination of functionalized SPIONs and their ability to be recovered using a magnetic column coupled with biomolecular mass spectrometry has allowed to explore a complex intracellular pathway using a peptide that is known to target HeLa cell organelle. Here the concept of biomolecular interaction network elucidation with an organelle-targeting peptide was demonstrated. Besides that, the colloidal stability and cellular uptake of polymer coated SPIONs were also studied. Preliminary results showed that minor modifications of the nanoparticle surface lead to an altered behavior in stability, uptake, and toxicity. Also, different charges on the particle surfaces were found responsible for differential uptake of particles in cell media. Colloidal stability and its influence on biological properties will provide a profound base for future discussions on toxicity and potential application of nanoparticles in the field of biomedicine.