Shotgun and targeted plasma proteomics to predict prognosis of non-small cell lung cancer

Abstract

Lung cancer is the leading cause of cancer deaths worldwide. Clinically, the treatment of non-small cell lung cancer (NSCLC) can be improved by the early detection and risk screening among population. To meet this need, here we describe in detail a shotgun following the targeted proteomics workflow that we previously applied for human plasma analysis, which involves (1) the application of extensive peptide-level fractionation coupled with label-free quantitative proteomics for the discovery of plasma biomarker candidates for lung cancer and (2) the usage of the multiple reaction monitoring (MRM) assays for the follow-up validations in the verification phase. The workflow features simplicity, low cost, high transferability, high robustness, and flexibility with specific instrumental settings.