Abstract: Objective To develop a gas chromatography–mass spectrometry (GC–MS) detection method for quantification of the nonpolar amino acids in amniotic fluid of congenital malformation including alanine (Ala), leucine (Leu), isoleucine (Ile), proline (Pro) and phenylalanine (Phe). To compare the different amino acids in amniotic fluid between pregnant women with congenital malformation and normal control and anayze the corresponding pathogenesis. Methods After precipitated protein of the 100 μL supernatant of amniotic fluid by methyl alcohol, the supernatant was dried by nitrogen. The extractions were treated with MSTFA for derivatization. Then gas chromatography-mass spectrometry was used to detect and analyze the amino acids. Results This method was proved to be good sensitivity, precision, accuracy and recoveries. Under the optimum testing conditions, the limit of detection (LOD) was 0.12~0.38 mg/L. The calibration curves showed good linearity over the investigated concentration range between 0.5 and 10 mg/L. The recoveries were 91.12 % to 104.41 %. The relative standard deviation of intra and inter-day were 0.84 % to 9.33 %. The developed method was applied to the quantification of 5 nonpolar amino acids in amniotic fluid of 17 pregnant women with congenital malformation and 13 normal control pregnant woman. The contents of leucine and isoleucine decreased in disease group compared to controls. The difference of the other three amino acids between the two groups had no statistical significance. Conclusions The validation results showed that the method was suitable for detection of the amino acids in amniotic fluid and having broad prospect of clinical application. Leucine may participate in the pathogenesis of congenital malformation.

Key words: Key Words: congenital malformation, amniotic fluid, gas chromatography-mass spectrometric, nonpolar amino acids