A shotgun proteome analysis method and its performance for protein identification from 500 to 5000 cells are described. Sample preparation, which was done in one tube, involved the use of a surfactant (NP-40) for cell lysis, followed by acetone precipitation of the proteins. The resulting protein pellet was washed with cold acetone to remove remaining surfactant, and the pellet was then solubilized in NH(4)HCO(3). After trypsin digestion of the proteins, the digest was analyzed by the use of nanoflow liquid chromatography (LC) quadrupole time-of-flight mass spectrometry (QTOF MS). Sample injection and gradient speed in running LC QTOF MS were optimized. It was shown that this method could identify an average (n = 3) of 167 +/- 21, 237 +/- 30, 491 +/- 63, and 619 +/- 59 proteins from 500, 1000, 2500, and 5000 MCF-7 breast cancer cells, respectively. To demonstrate the potential use of this method for generating proteome profile from circulating tumor cells (CTCs) isolated from human blood, a healthy human blood sample was spiked with MCF-7 cells, and this mixture was processed and then subjected to antibody tagging of the MCF-7 cells. The tagged cells were sorted and collected using flow cytometry. The proteome profiles of small numbers of cells isolated in this way were found to be similar to those of the original MCF-7 cells, suggesting the possibility of the use of this method for cell typing of CTCs.