Comparative proteome analysis of human lung squamous carcinoma using two different methods: two-dimensional gel electrophoresis and iTRAQ analysis.

Discovery of early-diagnosis biomarkers is the key to improve the early-diagnosis and prognosis of human lung squamous carcinoma (hLSC). In order to identify more exhaustive and systematic protein biomarkers for early-diagnosis of hLSC, we chose LCM purifed cells from hLSC tissues and paired normal bronchial epithelia(NBE) tissues and used two methods, the classical 2-DE/MS approach and the new iTRAQ analysis. We found a total of 63 differential proteins, 22 proteins in 2-DE and 59 proteins in iTRAQ analysis, between hLSC and NBE tissues. Among them, 18 proteins were quantified using both methods. The expression level of 15 proteins (68.2%) in 2-DE was consistent with that in iTRAQ analysis. Series of proteins involved in cytoskeleton, chaperone, GTP binding, metabolic process, cell apoptosis, cell proliferation and differentiation, signal transduction, transcription and translation were identified, suggesting their possible role in the emergence of oncogenic pathways leading to carcinogenesis of hLSC. These proteins may make as potential biomarkers for diagnosis of hLSC. The two methods gave us closely related but different information about proteins, suggesting they are complementary or at least supplementary methods at present. Our results show both the usefulness of iTRAQ reagent technology for identification of further potential marker proteins as well as for prevalidation of biomarker.