Biomarker Discovery in FFPE tissues by SRM

The identification of clinically relevant biomarkers represents an important challenge in oncology. This can be addressed with biomarker discovery studies in formalin-fixed paraffin-embedded (FFPE) tissues. However, reliably measuring large sets of proteins in FFPE tissues remains challenging. Here we demonstrate the use of liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) as a promising technique for such applications.
An LC-MS/MS method was developed to simultaneously quantify hundreds of peptides extracted from FFPE samples. 200 proteins were measured in 48 triple-negative (TNBC), 19 HER2-overexpressing, and 20 luminal A breast tumors.
Quantitative information was obtained for 185 proteins, including known markers such as HER2, hormone receptors, ki-67, or inflammation-related proteins. MS results for these proteins matched IHC or CISH data. In addition, several proteins representing potential biomarkers were identified as differentially expressed in TNBC samples.
Comparison of our results with data from the literature showed that MS assays can reliably and simultaneously measure many proteins in FFPE tissues using the analysis of surrogate peptides. Therefore LC-MS/MS is a powerful tool for the relative quantification of proteins in FFPE tissues and for biomarker discovery.