Abstract: Proteome means the whole proteins expressed by genome in a cell or tissue.Two- dimensional electrophoresis (2-DE), computer image analysis and mass spectrometry were known as the three key techniques in proteome research. Peptide mass fingerprinting (PMF) is becoming a widely used and rapidly developed technique for protein identification after 2- DE. In this study, a systematic method to identify the proteins after 2-DE by PMF was developed. Proteins were digested in-gel by trypsin and the masses of peptides were measured by matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI- TOFMS). the data obtained from PMF were used for protein database searching and protein identification. the proteins from human lung cancer cell isolated by 2-DE were identified by The method developed in this research.