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Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue
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Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue

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Proteomics analysis of an individual formalin-fixed paraffin-embedded tissue section using isobaric-tag amplification

Ara Cho1, Jinsung Ahn1, Andrew Kim1

  • 1Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea.

Rapid Communications in Mass Spectrometry : RCM
|October 11, 2023
PubMed

Insights

Isobaric labeling with TMT-labeled peptides/proteins enhances low-abundance protein detection in FFPE tissues. This method enables robust proteomic analysis for retrospective clinical studies.

Area of Science:

  • Proteomics
  • Biochemistry
  • Molecular Biology

Background:

  • Formalin-fixed paraffin-embedded (FFPE) tissues are crucial for retrospective clinical studies.
  • Detecting low-abundance proteins and achieving proteome-scale data from FFPE samples presents mass spectrometry challenges.

Purpose of the Study:

  • To implement an isobaric labeling approach for improved detection of low-abundance proteins in FFPE tissues.
  • To enhance the qualitative and quantitative analysis of FFPE samples.

Main Methods:

  • Utilized isobaric labeling with synthetic peptides or proteins for qualitative and quantitative protein measurement.
  • Incorporated tandem mass tag (TMT)-labeled recombinant proteins/synthetic peptides into TMT-labeled metastatic breast cancer FFPE tissues.

Main Results:

  • Successfully detected coexisting CD276 (B7-H3) and CD147 proteins.
  • Identified over 6000 proteins in FFPE samples through targeted analysis.
  • Demonstrated enhanced detection of target proteins using isobaric labeling and TMT-labeled peptides/proteins.

Conclusions:

  • Isobaric labeling with synthetic peptides/proteins is a valuable strategy for FFPE tissue analysis.
  • This technique facilitates comprehensive analysis of low-abundance proteins and proteome-scale investigations.
  • The methodology holds potential for advancing retrospective clinical studies and understanding disease mechanisms.
Abstract

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