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Sample Preparation of Formalin-Fixed Paraffin-Embedded (FFPE) Tissue for Proteomic Analyses

  • Diem Tran
  • Mark Daniels
  • Ben Colson
  • Dikran Aivazian
  • Antonio Boccia
  • Ingrid Joseph
  • Steffan Ho
  • Steve French
  • Alex Buko
  • Jing WeiEmail author
Chapter

Abstract

A sample preparation procedure has been developed to prepare Formalin-Fixed Paraffin-Embedded (FFPE) tissues for proteomic profiling. Protocols have been established for processing FFPE sections on slides, including deparaffinization, rehydration, protein extraction, and enzymatic digestion, all using in-house developed and optimized buffers and techniques. These methods are practical and allow for parallel sample processing. The efficiency of protein extraction from FFPE tissue is comparable to the results from fresh or frozen tissue. The prepared samples can be directly coupled to a wide range of proteomic technologies, including isobaric labeling and on-line multidimensional chromatography. Comprehensive proteomic profiling of prepared FFPE tissue was performed using a fully automated tandem multidimensional liquid chromatography (LC) system coupled with on-line electrospray ionization (ESI) tandem mass spectrometry (MS): LC/LC-MS/MS. Routinely around 4,000 unique proteins of high confidence could be identified from 100 μg of extracted protein. The method presented here will be valuable for others who plan to analyze FFPE tissues.

Keywords

FFPE iTRAQ Mass Spectrometry Multidimensional Chromatography Proteomics 

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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Diem Tran
    • 1
  • Mark Daniels
    • 1
  • Ben Colson
    • 1
  • Dikran Aivazian
    • 1
  • Antonio Boccia
    • 1
  • Ingrid Joseph
    • 1
  • Steffan Ho
    • 1
  • Steve French
    • 2
  • Alex Buko
    • 2
  • Jing Wei
    • 1
    Email author
  1. 1.Biogen IdecSan DiegoUSA
  2. 2.Biogen IdecCambridgeUSA

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