The active site of [NiFe] hydrogenase is a binuclear metal complex composed of Fe and Ni atoms and is called the Ni-Fe site, where the Fe atom is known to be coordinated to three diatomic ligands. Two mass spectrometric techniques, pyrolysis-MS (pyrolysis-mass spectrometry) and TOF-SIMS (time-of-flight secondary ion mass spectrometry), were applied to several proteins, including native and denatured forms of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F, [Fe4S4]2-ferredoxin from Clostridium pasteurianum, [Fe,S2]-ferredoxin from Spirulna platensis, and porcine pepsin. Pyrolysis-MS revealed that only native hydrogenase liberated SO/SO2 (ions of m/z 48 and 64 at an equilibrium ratio of SO and SO2) at relatively low temperatures before the covalent bonds in the polypeptide moiety started to decompose. TOF-SIMS indicated that native Miyazaki hydrogenase released SO/SO2 (m/z 47.97 and 63.96) as secondary ions when irradiated with a high-energy Ga+ beam. Denatured hydrogenase, clostridial ferredoxin, and pepsin did not release SO as a secondary ion. The FT-IR spectrum of the enzyme suggested the presence of CO and CN. These lines of evidence suggest that the three diatomic ligands coordinated to the Fe atom at the Ni-Fe site in Miyazaki hydrogenase are SO, CO, and CN. The role of the SO ligand in helping to cleave H2 molecules at the active site and stabilizing the Fe atom in the diamagnetic Fe(II) state in the redox cycle of this enzyme is discussed.