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

L Staunton; C Tonry; R Lis; S Finn; J O Leary; M Loda; M Bowden; S R Pennington

doi:10.1016/j.euprot.2015.11.001

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

EuPA Open Proteom. 2015 Dec 29:10:19-23. doi: 10.1016/j.euprot.2015.11.001. eCollection 2016 Mar.

Authors

L Staunton¹, C Tonry¹, R Lis², S Finn³, J O Leary³, M Loda², M Bowden², S R Pennington¹

Affiliations

¹ Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
² Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, 450 Brookline Ave., Boston, MA, USA.
³ St James⿿s Hospital, James⿿s St., Dublin 8, Ireland.

Abstract

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.

Keywords: LCM, Laser capture microdissection; LC⿿MS/MS, Liquid chromatography tandem mass spectrometry; Label-free LC⿿MS/; Laser capture microdissection; MS.