Optimized proteomic analysis of preserved biological tissue samples

Formalin-fixed paraffin-embedded tissue, or FFPE, is a valuable resource for proteomic studies needed to drive clinically relevant insights. However, obtaining patient-derived samples in sufficient numbers to represent different disease subtypes while also accounting for variables such as age and sex, poses a significant challenge.

To meet this challenge, Moe Haines, John Thorup, Michael Gillette, Shankha Satpathy and others in the Carr lab at the Broad Institute of MIT and Harvard presented an optimized workflow for enhanced proteomic analysis of FFPE samples. They published their findings in Molecular & Cellular Proteomics. In this workflow, they use a combination of pathology, guided dissection, Adaptive Focused Acoustics sonication, digestion and liquid chromatography-tandem mass spectrometry to identify up to 10,000 unique proteins and 11,000 fully localized phosphorylation sites in FFPE tissue. This work demonstrates the ability to derive biologically relevant results from clinically derived tumor samples and offers a significantly reduced overall processing time, thus widening the scope of analysis. This provides a useful avenue for more thorough proteomic analysis of preserved biological samples.