AFA assisted workflows for high-throughput mass spectrometry based proteomic analysis of FFPE samples
Anu Jain, Ph.D.
Monday, June 16, 2025
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Chapters
Introduction
Why use formalin fixed paraffin embedded (FFPE) samples
Workflow for analyzing FFPE samples
Adaptive focused acoustics
Laser Capture Microdissection (LCM)
Evaluation of AFA assisted method
Accelerated with AFA yields the highest protein / peptide numbers
Overlap between the proteins and peptides identified
Evaluation with lower input
Analysis of 10, 50 and 100 cells from FFPE tissue samples
Reproducible results across 10, 50 and 100 cells
Analysis of 10, 50 and 100 cells from FFPE tissue samples
Effective for single cell analysis
Analysis of FFPE tissue punches
AFA set up for analyzing FFPE tissue core
Collection of tissue samples
Comparison with probe sonicator
Similar number of proteins and peptides identified
A good overlap of identifications
Peptides of similar length identified
Number of missed cleavages
Summary and conclusions
Acknowledgements
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