Proteomic analysis of frozen tissue samples using laser capture microdissection

The discovery of effective cancer biomarkers is essential for the development of both advanced molecular diagnostics and new therapies/ medications. Finding and exploiting useful clinical biomarkers for cancer patients is fundamentally linked to improving outcomes. Towards these aims, the heterogeneous nature of tumors represents a signi fi cant problem. Thus, methods establishing an effective functional linkage between laser capture microdissection (LCM) and mass spectrometry (MS) provides for an enhanced molecular pro fi ling of homogenous, speci fi cally targeted cell populations from solid tumors. Utilizing frozen tissue avoids molecular degradation and bias that can be induced by other preservation techniques. Since clinical samples are often of a small quantity, tissue losses must be minimized. Therefore, all steps are carried out in the same single tube. Proteins are identi fi ed through peptide sequencing and subsequent matching against a speci fi c proteomic database. Using such an approach enhances clinical biomarker discovery in the following ways. First, LCM allows for the complexity of a solid tumor to be reduced. Second, MS provides for the pro fi ling of proteins, which are the ultimate bio-effectors. Third, by selecting for tumor proper or microenvironment-speci fi c cells from clinical samples, the heterogeneity of individual solid tumors is directly addressed. Finally, since proteins are the targets of most pharmaceuticals, the enriched protein data streams can then be further analyzed for potential biomarkers, drug targets, pathway elucidation, as well as an enhanced understanding of the various pathologic processes under study. Within this context, the following method illustrates in detail a synergy between LCM and MS for an enhanced molecular pro fi ling of solid tumors and clinical biomarker discovery.