Accelerating Sample Preparation for Proteomics of Formalin Fixed Paraffin Embedded Tumor Tissues to Enable Biomarker Analysis

Archived tumor specimens are routinely preserved by formalin fixation and paraffin embedding. Despite the conventional wisdom that proteomics might be ineffective due to the crosslinking and pre-analytical variables, these samples have been demonstrated to be useful for both discovery and targeted proteomics. Building on this capability, proteomics approaches can be used to maximize our understanding of cancer biology and clinical relevance by studying preserved tumor tissues annotated with the patients’ medical histories. Proteomics of formalin fixed paraffin embedded (FFPE) tissues also integrates with histological and molecular pathology strategies, so that additional biopsies or resected tumor aliquots do not need to be used. The acquisition of data from the same tumor sample also overcomes concerns about biological variation between samples due to intratumoral heterogeneity. However, the sample preparation for FFPE can be onerous, particularly for very precious (i.e., limited) samples. Therefore, we compared a modified version of the well-established filter-aided sample preparation strategy to a recently introduced kit-based EasyPep method using laser capture microdissected lung adenocarcinoma tissues from a genetically engineered mouse model. This model system allows control over the tumor preparation and pre-analytical variables, while also enabling the development of methods for spatial proteomics to examine intratumoral heterogeneity.