OBJECTIVE To analyze the peptide mass mapping and localization of disulfide bonds of recombinant human granulocyte-macrophage colony stimulating factor(rhGM-CSF) by using mass spectrometry combined with ultra-performance liquid chromatography. METHODS The bulk of rhGM-CSF was denatured, reduced, alkylated and finally digested by the enzyme of trypsin and V8 respectively to analyse the peptide mass mapping. The bulk was denatured, alkylated and digested by V8 and V8 with trypsin respectively to identify the sites of disulfide bonds. RESULTS Fourteen matched peptides were found in the peptide mass mapping of rhGM-CSF digested by trypsin and eighteen matched peptides were found digested by V8. The fraction of coverage was both 100.0%. The site of disulfide bond Cys55-Cys97 was identified by digestion of V8, and the types of disulfide bonds Cys55-Cys97 and Cys89-Cys122 were identified by digestion of V8 with trypsin. CONCLUSION The peptide mass mapping analysis and localization of disulfide bonds using LC-MS/MS can be used for the quality control of recombination protein.