Abstract: AIM　To characterize the primary structure of recombinant L-asparaginase II product. METHODS　The molecular weight of the protein was measured by pneumatically-assisted electrospray ionization mass spectrometry with flow injection mode. Subsequently, tryptic peptide mapping was performed by high performance liquid chromatography on a C₈ column with tandem UV and MS detection. An easy-to-use and simple denaturation process with trichloroacetic acid was conducted prior to tryptic digest so as to release the digest resistance from the protein structure. The amino acid sequences of the tryptic peptides were elucidated based on their in-source collision-induced dissociation spectra. RESULTS　The measured molecular mass was different from the theoretical value. Three amino acid variations were unambiguously detected along the peptide backbone derived from the gene-encoding sequence. CONCLUSION　This paper revealed that LC/ESI/MS had provided a promising and robust technique in primary structure analysis and quality control of DNA-derived recombinant protein pharmaceuticals.