A high-throughput strategy for protein profiling in cell microarrays using automated image analysis

Proteomics. 2007 Jun;7(13):2142-50. doi: 10.1002/pmic.200700199.


Advances in antibody production render a growing supply of affinity reagents for immunohistochemistry (IHC), and tissue microarray (TMA) technologies facilitate simultaneous analysis of protein expression in a multitude of tissues. However, collecting validated IHC data remains a bottleneck problem, as the standard method is manual microscopical analysis. Here we present a high-throughput strategy combining IHC on a recently developed cell microarray with a novel, automated image-analysis application (TMAx). The software was evaluated on 200 digital images of IHC-stained cell spots, by comparing TMAx annotation with manual annotation performed by seven human experts. A high concordance between automated and manual annotation of staining intensity and fraction of IHC-positive cells was found. In a limited study, we also investigated the possibility to assess the correlation between mRNA and protein levels, by using TMAx output results for relative protein quantification and quantitative real-time PCR for the quantification of corresponding transcript levels. In conclusion, automated analysis of immunohistochemically stained in vitro-cultured cells in a microarray format can be used for high-throughput protein profiling, and extraction of RNA from the same cell lines provides a basis for comparing transcription and protein expression on a global scale.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antibodies / immunology
  • Cell Line
  • Cell Line, Tumor
  • Cells, Cultured
  • Gene Expression
  • Humans
  • Image Processing, Computer-Assisted / methods*
  • Immunohistochemistry / methods*
  • Microarray Analysis / methods*
  • Proteins / analysis*
  • Proteins / genetics
  • Proteins / immunology
  • Proteomics / methods
  • Reproducibility of Results
  • Software


  • Antibodies
  • Proteins