Abstract: ObjectiveTo compare different precipitation methods for breast cancer mitochondrial protein analysis with Au chips and to lay a foundation for subcellular protein analysis with Au chips.MethodsMitochondrial protein was abstracted from breast cancer cell line MCF-7 and precipitated by acetone,trichloroacetic acid-acetone(TCA-Acetone),and ammonium sulfate,respectively.The samples were added to Au chips and analyzed with surface enhanced laser desorption/ ionization time-of-flight mass spectra(SELDI-TOF-MS).The results were collected by Biomaker Wizard Softw are.ResultsThe number of protein peaks was 39,71,and 14 at 2 kD-100 kD disposed by TCA-acetone,acetone,ammonium sulfate, respectively.Five protein peaks at 8.6 kD,10.0 kD,11.3 kD,14.0 kD,and 15.6 kD with high abundance were selected and compared by q test.ConclusionAcetone precipitation is the best way for proteins of molecular weight(Mr)less than 11 kD.While TCA-acetone precipitation is better for proteins of Mr over 11kD.So Au chips can get better result by integrated use of the two precipitation methods.