Comparison of Normal and Breast Cancer Cell Lines Using Proteome, Genome, and Interactome Data

• Published in: Journal of proteome research Vol. 4; no. 6; pp. 1952 - 1960
• Main Authors: Patwardhan, Anil J, Strittmatter, Eric F, Camp, David G, Smith, Richard D, Pallavicini, Maria G
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 01.11.2005
• Subjects: Amino Acid Sequence; Breast Neoplasms - pathology; Cell Line; Cell Line, Tumor; Cell Membrane - metabolism; Chromatography, Liquid; Cluster Analysis; Databases, Protein; Gene Expression Regulation, Neoplastic; Genomics - methods; Humans; Mass Spectrometry; Metabolism; Molecular Sequence Data; Peptide Mapping; Peptides - chemistry; Protein Array Analysis; Protein Binding; Protein Processing, Post-Translational; Proteins - chemistry; Proteomics - methods
• ISSN: 1535-3893; 1535-3907
• DOI: 10.1021/pr0501315

Normal and cancer cell line proteomes were profiled using high throughput mass spectrometry techniques. Application of protein-level and peptide-level sample fractionation combined with LC−MS/MS analysis enabled identification of 2235 unmodified proteins representing a broad range of functional and compartmental classes. An iterative multistep search strategy was used to identify post-translational modifications, revealing several proteins that are preferentially modified in cancer cells. Information regarding both unmodified and modified protein forms was combined with publicly available gene expression and protein−protein interaction data. The resulting integrated dataset revealed several functionally related proteins that are differentially regulated between normal and cancer cell lines. Keywords: post-translational modifications • breast cancer • proteome • mass spectrometry • membrane proteins • high throughput • subcellular • multidimensional liquid chromatography • functional genomics • pathways