Abstract: This study evaluated the protein identification capabilities of the Top14 high-abundance protein removal kit (Top14) and the DMB MagicOmics low-abundance enrichment kit (DMB) on serum samples from healthy individuals (HC) and hepatocellular carcinoma (HCC) patients. For HC samples, DMB treatment led to identifying 2.6 times proteins more than Top14 and 3.9 times more than untreated samples. For HCC samples, DMB achieved 3.7 times increase in protein identification over Top14 and 6.2 times increase over untreated samples. Although the Top14 kit was effective in removing high-abundance proteins, it was less proficient in detecting low-abundance proteins when compared to the DMB method. In terms of protein identification frequency, the DMB-treated samples had a significantly higher number of quantifiable proteins than both the Top14 and Blank groups. Over 50% of the proteins identified in the Top14 and Blank groups were also identified in the DMB group, ensuring a comprehensive proteome coverage as evidenced by KEGG analysis. The DMB method significantly outperformed the others in HCC serum samples, identifying 47 differentially expressed (DE) proteins, in contrast to 15 and 17 identified of the Top14 group and untreated samples, respectively, highlighting its superior ability to uncover critical biomarkers for disease analysis. KEGG pathway analysis showed that DE proteins identified by DMB were involved in 21 distinct pathways, significantly more than 5 and 1 pathways identified by Top14 group and untreated samples, demonstrating DMB’s advanced proteomic profiling capability. This study also underscored HSP90AB1, SPP1, ACTR3, SNCA, PECAM1, and SRC proteins increased in HCC serum samples based on DMB method, marking them as promising HCC biomarkers for disease screening.