There is a growing interest in applying proteomics to gain insight into the mechanism of tumorigenesis, develop new markers for molecular diagnosis and accelerate drug development. In an attempt to find new stage-specific tumor markers, patients suffering from squamous cell lung carcinomas (SQCLC) at different pathologic stages have been selected to achieve differential protein expression patterns. Two-dimensional polyacrylamide gel electrophoresis (2-DE) profiles of human SQCLC and normal tissue were compared. Differential protein spots were identified with peptide mass fingerprinting (PMF) based on matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and database searching. A total of 63 unique proteins were identified in this experiment. Among them, peroxiredoxin 1 (PRDX1) expression level was significantly increased from stage I to III, and had a slight decrease at stage IV; whereas, a lasting decrease in the expression level of tropomyosins 3 (TPM3), was observed with the malignant progression from I stage to IV stage. These results provide further insight into malignant transformation in SQCLC and proteins may serve as new biomarkers for early diagnosis.