High-throughput profiling of formalin-fixed paraffin-embedded tissue using parallel electrophoresis and matrix-assisted laser desorption ionization mass spectrometry.

Aerni HR, Cornett DS, Caprioli RM
Anal Chem. 2009 81 (17): 7490-5

PMID: 19650658 · PMCID: PMC2747050 · DOI:10.1021/ac900974j

Analysis of formalin-fixed paraffin-embedded tissues (FFPE) is increasingly recognized as a strategy for the discovery and validation of clinically useful biomarker candidates. Large tissue collections including tissue microarrays (TMAs) are available, but current analytical strategies for their characterization have limited throughput. In this report, we describe a workflow for rapid analysis of hundreds of FFPE tissue specimens. The strategy combines parallel sample processing and on-chip electrophoresis with automated matrix-assisted laser desorption ionzation mass spectrometry (MALDI MS) analysis. The method is optimized for small quantities of clinically valuable tissues allowing detection of hundreds of peptides from a single core in a TMA section. We describe results from the optimization of the method and apply it for the analysis of tissue microarrays containing formalin fixed tissue specimens from human kidney.

MeSH Terms (12)

Animals Antigens Electrophoresis Formaldehyde Humans Kidney Mice Paraffin Embedding Peptides Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization Tissue Array Analysis Tissue Fixation

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