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

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.