Using ab initio calculations, we have studied the modification of the electronic structure of the MoS2(0001) surface by several point defects: a surface S vacancy and different transition metal atoms substituting a S atom (Pd, Au, Fe, and V). With a S vacancy, a gap state appears with weight mostly on the Mo and S atoms surrounding the vacancy. The substitutional atoms of complete d band (Pd and Au) do not present magnetic polarization and slightly modify the DOS near the Fermi energy. On the other hand, the incomplete d band atoms (Fe and V) present spin polarization and modify significantly the states near the band edges. From calculated STM images and STS curves, we show that this chemical signature can be measured and used to characterize the surface defects of the substrate which are suitable nucleation centers for nanocluster growth.