We have investigated the characteristics of the plasma proteome related to the response to combination therapy with lenvatinib and anti-PD1 antibody in treating hepatocellular carcinoma (HCC) as reported by Li et al (Cell Rep 43, 113877. 10.1016/j.celrep.2024.113877.). Here, we provide the protocols to perform protein database search using MaxQuant program. We describe the systematic steps needed to filter and process the initial results obtained from the MaxQuant database search, including the selection of the most effective normalization method from eight potential options. We employ the limma algorithm to identify differential proteins across various comparisons, such as responders versus non-responders, pre-treatment versus post-treatment groups, and cancerous versus healthy samples. Furthermore, this protocol covers comprehensive procedures for conducting functional enrichment, gene set enrichment analysis (GSEA), correlation analysis, consensus clustering, and survival analysis.