Profiling the tumor microenvironment proteome in prostate cancer using laser capture microdissection coupled to LCâ¿¿MSâ¿¿A technical report.

Laser capture microdissection (LCM) allows microscopic procurement of specific cell types from tissue sections. Here, we present an optimized workflow for coupling LCM to LC⿿MS/MS including: sectioning of tissue, a standard LCM workflow, protein digestion and advanced LC⿿MS/MS. Soluble proteins extracted from benign epithelial cells, their associated stroma, tumor epithelial cells and their associated stromal cells from a single patient tissue sample were digested and profiled using advanced LC⿿MS/MS. The correlation between technical replicates was R(2) = 0.99 with a mean % CV of 9.55% ± 8.73. The correlation between sample replicates was R(2) = 0.97 with a mean % CV of 13.83% ± 10.17. This represents a robust, systematic approach for profiling of the tumor microenvironment using LCM coupled to label-free LC⿿MS/MS.