Toward Improving the Proteomic Analysis of Formalin-fixed, Paraffin-embedded Tissue

Carol B Fowler; Timothy J O'Leary; Jeffrey T Mason


Expert Rev Proteomics. 2013;10(4):389-400. 

In This Article

Expert Commentary

Extraction methods and workflows have advanced to the point where the field is slowly moving past the 'proof-of-concept' stage to performing systematic analysis of archival FFPE tissue. Extraction methodologies are becoming more systematic and it is possible to recover peptides from FFPE tissues that yield a reasonable representation of the proteins recovered from identical fresh or frozen specimens. These extraction methodologies have made LC/MS-based analysis of FFPE tissue possible and there has been a marked increase in published proteomics studies for FFPE tissue. However, it is important to note that differences in pre-analytical factors can greatly affect the levels of proteins, DNA and RNA in archival tissue specimens. Although nothing can be done to overcome these limitations for archival tissues, moving forward the implementation of standardized protocols for tissue handling and preservation would improve the proteomic analysis of FFPE tissues. Advances in MALDI-IMS make morphology-based proteomic tissue analysis accessible for the first time. Consequently, MS and array-based proteomics of FFPE tissues are emerging as complementary technologies to IHC and anatomical pathology for the study of disease.