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

Five-Year View

With the advances in extraction and analysis technology, there will be progressively more proteomic studies of FFPE tissues for which the clinical course of disease and response to therapy has been established. Quantitation of differentially expressed proteins will also be more common in FFPE tissue, with the increased utilization of RPPAs and quantitative MS. While LC/MS-based proteomics will continue to be an important tool for biomarker discovery, advances in MALDI-IMS will allow for more rapid analysis of tissue sections. Since MALDI-IMS can be performed on intact tissue samples, no time-consuming tissue extraction is needed, and morphological information will not be lost as the tissue remains intact. Results from anatomic and diagnostic pathology can be related to the MS, and since MALDI-IMS is a 'poly-omic' method, proteomic, glycomic and metabolomic analyses can be performed on the same tissue section. Unfortunately, lipidomic studies using FFPE tissue are not practical due to the removal of most lipids during tissue histology.