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

J Proteome Res. Nov-Dec 2005;4(6):1952-60. 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • 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*


  • Peptides
  • Proteins