Abstract: AIMTo identify recombinant protein rhFKBP12 by new technique ESI-quadrupole-oa-TOF tandem mass spectrometry. METHODSThe molecular weight of rhFKBP12 was measured by ESI-MS. Digest rhFKBP12 by trypsin at 37℃ over night. The tryptic digested peptides were measured and then two doublely charged peptides were selected to measure their amino acid sequence by ESI-MS/MS. Search database with the measured amino acid sequence to identify rhFKBP12. RESULTSThe calculated molecular weight of rhFKBP12 was 11 819.54 and the measured value was 11 820.38. The measurement percent error was only 0.007%. The sequence measured by ESI-MS/MS was QVETMS and EEGVAQMSV and then the database search results with them were both hFKBP12. CONCLUSIONThe study proves that the primary structure of rhFKBP12 is correct and there is no amino acid deletion, mutation and modification in its expression, refolding and purification. It also shows that ESI-MS/MS is a good method to identify protein with advantage of sensitivity, high speed and accuracy.