Secretome (secreted proteins) has been arousing considerable attention because of its potential to develop novel biomarkers for the early detection and diagnosis of diseases. Like other proteome systems, a secretome generally consists of thousands of proteins with a wide dynamic range of abundance. The effective way to decrease the complexity of the analyte is to combine different prefractionation methods with orthogonal separation capabilities. The newly appeared OFFGEL fractionation system provides the ability to separate the peptides into discrete liquid fractions according to their differences in isoelectric point (pI), and has demonstrated high efficiency and repeatability for the analysis of the complex proteins. Here the OFFGEL fractionation system was evaluated for the separation of peptides digests from secreted proteins of hepatocellular carcinoma cells (HCC), using a 12-wells device encompassing the pH range of 3 - 10. In combination with the online reversed phase liquid chromatography and mass spectrometry, peptides from the digestion of MHCC97L secreted proteins were separated and identified. Preliminary results showed that nearly 80% of the peptides identified were specific to one fraction, and 40% of the proteins were obtained from the fractions 1 -3 from the acid end. The average of peptide pI values distributed in each fraction is consistent with the theoretical pIs, and the pI distribution of the peptides focused on the low pH range showed a smaller deviation. Finally, 2 995 proteins were identified from secretome of MHCC97L cell lines. Thus the data show that the OFFGEL system provides a highly valuable tool to fractionate peptides from complex protein samples.