The integration of synthetic, experimental and theoretical tools into a self-consistent data analysis methodology allowed us to develop unique new levels of detail in nanoparticle characterization. We describe our methods using an example of Au13 monolayer-protected clusters (MPCs), synthesized by ligand exchange methods. The combination of atom counting methods of scanning transmission electron microscopy and Au L3-edge EXAFS allowed us to characterize these clusters as icosahedral, with surface strain reduced from 5% (as in ideal, regular icosahedra) to 3%, due to the interaction with ligands. Charge transfer from Au to the thiol and phosphine ligands was evidenced by S and P K-edge XANES. A comparison of total energies of bare clusters of different geometries was performed by equivalent crystal theory calculations.