Premium
Quantitative proteome analysis of breast cancer cell lines using 18 O‐labeling and an accurate mass and time tag strategy
Author(s) -
Patwardhan Anil J.,
Strittmatter Eric F.,
Camp David G.,
Smith Richard D.,
Pallavicini Maria G.
Publication year - 2006
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200500582
Subject(s) - proteome , proteomics , biology , peptide , cell culture , breast cancer , quantitative proteomics , cancer , cancer cell lines , computational biology , cancer cell , microbiology and biotechnology , bioinformatics , biochemistry , genetics , gene
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 16 O/ 18 O 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 16 O/ 18 O 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.