Mapping the Spatial Distribution of Tryptic Peptides in Formalin-Fixed Paraffin-Embedded Tissues Using Desorption...

Area of Science:

• Proteomics
• Mass Spectrometry Imaging
• Biomarker Discovery

Background:

• Spatial proteomics provides insights into cellular environments and disease pathology.
• Matrix-assisted laser desorption/ionization (MALDI)-MSI is a common tool, but desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) offers complementary protein detection.
• DESI-MSI has been limited to fresh-frozen tissues, excluding widely available formalin-fixed paraffin-embedded (FFPE) clinical specimens.

Purpose of the Study:

• To optimize and apply DESI-MSI for spatial proteomic analysis of FFPE tissues.
• To enhance tryptic peptide detection in FFPE samples through optimized pretreatment and DESI parameters.
• To explore the potential of DESI-MSI for biomarker discovery in archived clinical specimens.

Main Methods:

• Systematic optimization of sample pretreatment and DESI-MSI parameters using FFPE mouse brain tissue.
• Application of the optimized workflow to FFPE canine melanocytoma tissue.
• Protein identification using nano liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS).

Main Results:

• Successful optimization of DESI-MSI for FFPE tissue analysis, improving peptide detection.
• Demonstration of DESI-MSI's capability to perform spatial proteomic analysis on FFPE samples.
• Identification of potential protein biomarkers in FFPE canine melanocytoma tissue.

Conclusions:

• DESI-MSI is a viable platform for spatial proteomic analysis of FFPE tissues.
• This method expands the utility of spatial proteomics to FFPE tissues, including archived clinical specimens.
• DESI-MSI holds promise for advancing biomarker discovery and understanding disease mechanisms in clinical samples.