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

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