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Chemical bonding states of boron (B) in shallow P+/N junctions were studied by soft X-ray photoelectron spectroscopy (SXPES). The concentration profiles of B having different binding energies were successfully determined the SXPES combined with the step-by-step etching of Si substrates. The concentration profiles of B having the lowest binding energy can be assigned as activated B, which agreed quite well with those of holes determined by the Hall measurements, while those having the middle and highest binding energies must be attributed to deactivated B. Effects of the spike-RTA and flush lamp annealing (FLA) were compared regarding the concentration profiles of B and UV Raman spectroscopy. Arsenic (As) doped layers were also studied by the X-ray photoelectron spectroscopy and the two different bonding states were revealed for As atoms embedded in Si substrates.