Protocol for analysis of plasma proteomes from patients with hepatocellular carcinoma receiving combination therapy

Plasma shows distinct metabolomic and proteomic signatures in response to combination therapy with lenvatinib and anti-programmed death-1 (PD-1) antibody in treating hepatocellular carcinoma (HCC). Here, we present a protocol for analyzing plasma proteomes from patients with HCC receiving combination therapy. We describe steps for interpreting mass spectrometry data by database searching using MaxQuant and filtering and processing database search outcomes. We then detail procedures for downstream analyses including normalization, differential expression analysis, functional enrichment analysis, correlation analysis, consensus clustering, and survival analysis. For complete details on the use and execution of this protocol, please refer to Li et al.¹.