PROBLEM TO BE SOLVED: To provide a cell fractionation method to obtain a cell fraction sample which can be directly used for shotgun proteome analysis.SOLUTION: When cells are fractionated into cytoplasmic matrix, intracellular organelle, and cell nucleus by using a surfactant solution comprising a mixture of ethylene glycol or its derivative or analogue and one or two or more surfactant which can be modified to have lipid-soluble characteristics, a protein in each fraction can be directly used for shotgun proteome analysis.