Profiling the tumor microenvironment proteome in prostate cancer using laser capture microdissection coupled to LC–MS—A technical report

Publication date: March 2016 Source:EuPA Open Proteomics, Volume 10 Author(s): L. Staunton, C. Tonry, R. Lis, S. Finn, J. O’Leary, M. Loda, M. Bowden, S.R. Pennington 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 R2 =0.99 with a mean % CV of 9.55%±8.73. The correlation between sample replicates was R2 =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. Graphical abstract
Source: EuPA Open Proteomics - Category: Bioinformatics Source Type: research