It is of great significance in analysis of protein copy numbers in a single cell or in a limited number of cells.We established a new method to analyze proteome in hundred-cell-scales.Whole cells were digested directly into mass spectrometry(MS)-identifiable peptides in a single step.Nano-high performance liquid chromatography(HPLC)coupling with MS systems was applied to the identification.We identified 100-800 proteins from 100 cell sample scales.Fairly reproducibility was achieved,showing stability and reliability of the method.Gene Ontology analysis revealed that protein identification was quite representative including those of membrane proteins,even though no surfactants were used.