A novel method for analyzing formalin-fixed paraffin embedded (FFPE) tissue sections by mass spectrometry imaging

Yutaka Aoki, Atsuhiko Toyama, Takashi Shimada, Tetsuyoshi Sugita, Chikage Aoki, Yukari Umino, Atsushi Suzuki, Daisuke Aoki, Yataro Daigo, Yusuke Nakamura, Taka Aki Sato

Research output: Contribution to journalArticlepeer-review

29 Citations (Scopus)


Significant advances have been made in the past decade in the field of mass spectrometry imaging (MS imaging). It is a relatively unestablished technique aimed at direct, high-sensitive and spatially exclusive detection of biological molecules from the surface of tissue sections, so that semi-quantitative distribution map of the analyte can be reconstituted from the mass spectra obtained. There is tremendous potential in its application especially in clinical field, such as biomarker discovery or pharmacokinetic study. However, vast majority of the work has been performed on frozen tissue sections, while it remains generally unpractical to produce frozen sections with clinically resected tumor samples. Here we report our novel sample preparation technique that enabled MS imaging from formalin-fixed paraffin embedded (FFPE) tissue section, including retrospective archive as old as 11 years. FFPE sections were first dewaxed with pre-warmed xylene, and exposed tissue surface was enzymatically digested in nanoliter scale droplets to retain analyte localization. As a result, we succeeded in obtaining MS images of peptide peaks derived from several proteins, identified by MS/MS analysis, using ovarian cancer FFPE sections. The qualities of mass spectra obtained by this method were not significantly different from those obtained from frozen sections. By this, we opened the door to retrospective study of past clinical cases in aim to discover molecular biomarker.

Original languageEnglish
Pages (from-to)205-214
Number of pages10
JournalProceedings of the Japan Academy Series B: Physical and Biological Sciences
Issue number7
Publication statusPublished - 2007


  • Formalin-fixed paraffin embedded
  • Mass spectrometry imaging
  • Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
  • Ovarian cancer

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Physics and Astronomy(all)


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