Laser Capture Microdissection Applications in Breast Cancer Proteomics

  • René B. H. Braakman
  • Theo M. Luider
  • John W. M. Martens
  • John A. Foekens
  • Arzu UmarEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 755)


Breast cancer tissues are characterized by cellular heterogeneity, representing a mixture of, e.g., healthy epithelial ducts, invasive or in situ tumor cells, surrounding stroma, infiltrating immune cells, blood vessels, and capillaries. As a consequence, protein extracts from whole tissue lysates also represent a variety of cell types present in the tissues under examination. This, however, seriously hampers the analysis of tumor cell-specific signals, which is of interest when performing biomarker discovery-type of studies. Therefore, laser capture microdissection is a perfect tool to isolate a relatively pure population of cells of interest, such as tumor cells. In this chapter, we describe the use of the PALM MicroBeam system for laser microdissection and pressure catapulting. Protocols are provided for sectioning, staining, microdissection, sample preparation, and mass spectrometric analysis of snap frozen breast cancer tissue.

Key words

Breast cancer Laser capture microdissection nLC MALDI Mass spectrometry Proteomics Biomarker discovery 



The authors wish to thank Annemieke Timmermans for helpful discussions and technical assistance on tissue sectioning and staining. RBHB and AU are (partly) financially supported through the Center for Translational Molecular Medicine, CTMM BreastCARE project 030–104, and through the Netherlands Genomics Initiative.


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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • René B. H. Braakman
    • 2
  • Theo M. Luider
    • 3
  • John W. M. Martens
    • 2
  • John A. Foekens
    • 2
  • Arzu Umar
    • 1
    • 2
    Email author
  1. 1.Netherlands Proteomics CenterErasmus MC RotterdamRotterdamThe Netherlands
  2. 2.Department of Medical Oncology, Center for Translational Molecular Medicine, and Cancer Genomics CentreErasmus MC RotterdamRotterdamThe Netherlands
  3. 3.Department of Neurology and Laboratory of Clinical and Cancer ProteomicsErasmus MC RotterdamRotterdamThe Netherlands

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