High-throughput profiling of formalin-fixed paraffin-embedded tissue using parallel electrophoresis and matrix-assisted laser desorption ionization mass spectrometry.
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.
Aerni
Hans-Rudolf
HR
Mass Spectrometry Research Center, Department of Chemistry, Vanderbilt University, 465 21st Avenue South, Medical Research Building 3, Room 9160, Nashville, Tennessee 37232-8575, USA.
Cornett
Dale S
DS
Caprioli
Richard M
RM
D000818:Animals; D000941:Antigens / Q000032:analysis; D004586:Electrophoresis / Q000191:economics / Q000379:methods*; D005557:Formaldehyde; D006801:Humans; D007668:Kidney / Q000737:chemistry; D051379:Mice; D016612:Paraffin Embedding; D010455:Peptides / Q000032:analysis*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000191:economics / Q000379:methods*; D046888:Tissue Array Analysis / Q000379:methods*; D016707:Tissue Fixation
D000941:Antigens; D010455:Peptides; D005557:Formaldehyde