title: Quantitative proteome analysis of breast cancer cell lines using 18O-labeling and an accurate mass and time tag strategy.
abstract: Proteome comparison of cell lines derived from cancer and normal breast epithelium provide opportunities to identify differentially expressed proteins and pathways associated with specific phenotypes. We employed 16O/18O peptide labeling, FT-ICR MS, and an accurate mass and time (AMT) tag strategy to simultaneously compare the relative abundance of hundreds of proteins in non-cancer and cancer cell lines derived from breast tissue. A cell line reference panel allowed relative protein abundance comparisons among multiple cell lines and across multiple experiments. A peptide database generated from multidimensional LC separations and MS/MS analysis was used for subsequent AMT tag-based peptide identifications. This peptide database represented a total of 2299 proteins, including 514 that were quantified in five cell lines using the AMT tag and 16O/18O strategies. Eighty-six proteins showed at least a threefold protein abundance change between cancer and non-cancer cell lines. Hierarchical clustering of protein abundance ratios revealed that several groups of proteins were differentially expressed between the cancer cell lines.
authors.affiliation: UCSF Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
authors.forename: Anil J
authors.initials: AJ
authors.lastname: Patwardhan
authors.forename: Eric F
authors.initials: EF
authors.lastname: Strittmatter
authors.forename: David G
authors.initials: DG
authors.lastname: Camp
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.forename: Maria G
authors.initials: MG
authors.lastname: Pallavicini
mesh_terms: D001943:Breast Neoplasms / Q000737:chemistry* / Q000378:metabolism; D045744:Cell Line, Tumor; D002478:Cells, Cultured; D005260:Female; D006801:Humans; D013058:Mass Spectrometry; D010103:Oxygen Isotopes; D020543:Proteome; D017550:Spectroscopy, Fourier Transform Infrared
chemical_list: D010103:Oxygen Isotopes; D020543:Proteome