Understanding the molecular process of lung cancer development is important for development of novel diagnostic, preventive, and therapeutic strategies. Proteomics is a promissing approache to extend such understanding. One of the major limitations of this approache is the inability to reveal and identify lower abundant proteins. Fractionation and enrichment of cancer proteome is a logic step in expanding the application of proteomics in tumor classification and biomarker discovery. Immobilized metal ion adsorption chromatography (IMAC), also know as metal chelate affinity chromatography (MCAC), selectively enrich proteins with exposed surface histidine, cysteine, and tryptophan. To test the utility of IMAC in protein marker identification, we performed IMAC enrichment using proteins extracted from 4 lung cancer cell lines and 4 immortalized human bronchia epithelia (HBE) cell lines, followed by 2-dimensional electrophoresis (2DE) of the enriched proteins. Using this strategy, we observed substantially more proteins differentially presented between the two groups of cell lines. More than 100 such proteins were revealed when a broad range (pH 3-10) isoelectric focusing condition was used. The identities of 33 of the protein spots were further characterized by tandem mass spectrometry. Many of the proteins were low abundant proteins. Among them, stratifin, thioredoxin peroxidase, and guanine monophosphate synthetase, have transcript abundance ranging from 0.3% to 5% of the abundance of the actin transcript in lung tissues. Our results demonstrate a utility of IMAC-2DE approach in proteomics analysis of tumorigenic processes. (Supported by Department of Defense grant W81XWH-04-1-0142)

[Proc Amer Assoc Cancer Res, Volume 47, 2006]