Comparative\nProteomics and <i>N</i>‑Glycoproteomics\nReveal the Effects of Different Plasma Protein Enrichment Technologies

Human plasma proteomic and glycoproteomic analyses have\nemerged\nas an alternate avenue to identify disease biomarkers and therapeutic\napproaches. However, the vast number of high-abundance proteins in\nplasma can cause mass spectrometry (MS) suppression, which makes it\nchallenging to detect low-abundance proteins (LAP). Currently, immunoaffinity-based\ndepletion methods and strategies involving nanomaterial protein coronas\nhave been developed to remove high-abundance proteins (HAP) and enhance\nthe depth of plasma protein identification. Despite these advancements,\nthere is a lack of systematic comparison and evaluation of the qualitative\nand quantitative effects of different strategies on the human plasma\nproteome and glycoproteome. In this study, we evaluated the performance\nof four depletion methods including combinatorial peptide ligand libraries\n(CPLL), Top 2, Top 14, and the nanomaterial protein corona formed\nby magnetic nanoparticles (MN) in both plasma proteomics and <i>N</i>-glycoproteomics. Compared to the CPLL, Top 2, and Top\n14 strategies, the MN approach significantly increased the number\nof identified peptides and proteins. However, it demonstrated a relatively\nlower efficacy in identifying intact <i>N</i>-glycopeptides\nand <i>N</i>-glycoproteins. In contrast, the immunoaffinity-based\ndepletion methods are better suited to glycoproteomics due to higher\nidentification numbers. We believe that this work provides valuable\ninsights and options for various research objectives, as well as clinical\napplications.