Proteomics Profiling of Human Melanoma, Breast Cancer, Glioblastoma, Lung carcinoma, Osteosarcoma and Cervical Cancer Cell Lines

Most often, global proteomic analysis is performed using one type of cell line. However, protein expression may differ from cell line to cell line within a single organism. In this study, we investigated over 22 different types of human cell lines by 1D-LC-MS/MS analysis using nanoLC coupled to a q-TOF mass spectrometer. 100μg each of protein samples from 22 different types (7 melanoma, 8 breast cancer, 4 glioblastoma, 1 non-small cell lung carcinoma, 1 osteosarcoma, 1 cervical cancer) of human cancer cell lysates were reduced, alkylated and trypsin digested. After drying, digests were reconstituted in 0.1% formic acid for LC-MS analysis. 1-2μg of tryptic peptides from different types of cancer cell lysates were analyzed in triplicates on HPLC-Chip/ 6520 or 6550 QTOF Mass Spectrometer using 90 min gradient. The data was analyzed and semi-quantified using Spectrum Mill bioinformatics tool. In this study, we demonstrated a label free 1D-LC-MS/MS approach for proteomics phenotyping of several different types of human cancer cell lines. About 5000 unique human proteins and 50000 unique peptides were identified in the preliminary analysis of about 22 different human cancer cell lines. Proteomic comparison of melanoma and breast cancer cells showed about 30% of the total proteins unique to each cell type and about 68% of proteins were differentially expressed. Overall about 75% of the total proteins were differentially expressed between different types of cancer cell lines. In this large scale proteomics profiling study we found that protein expression between different types of cells varies significantly.