A Protocol for the Acquisition of Comprehensive Proteomics Data from Single Cases Using Formalin-Fixed Paraffin...

Area of Science:

• Biochemistry
• Molecular Biology
• Oncology

Background:

• Molecular analysis of small or rare patient tissue samples is limited by technology and resource constraints, particularly the availability of reliable antibodies.
• Targeted approaches offer limited insight into the complex molecular landscape of tissues.

Purpose of the Study:

• To describe a workflow combining two mass spectrometry approaches for comprehensive, unbiased molecular analysis of small tissue samples.
• To demonstrate the utility of this workflow using precancerous lesions from the endometrium and fallopian tube.

Main Methods:

• Utilized Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) for spatial molecular profiling and correlation with histology.
• Employed Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) for identification and quantification of proteins from consecutive tissue sections.
• Applied these complementary techniques to analyze protein abundance in precancerous and healthy endometrial and fallopian tube tissues from a single patient.

Main Results:

• Successfully generated spatial intensity maps of molecular features using MALDI-MSI.
• Identified and quantified hundreds of proteins in precancerous and adjacent healthy tissue regions using LC-MS/MS.
• Observed an indicative migratory phenotype in the analyzed precancerous lesions.

Conclusions:

• The described complementary mass spectrometry approach maximizes molecular data acquisition from small or single tissue samples.
• Initial findings suggest a migratory phenotype in endometrial and fallopian tube precancerous lesions, warranting further investigation into their malignant potential.