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Peptide pull-down (PPD) is an in vitro affinity purification technique used to detect and identify proteins that interact with specific peptide sequences. In this method, biotinylated synthetic peptides serve as “baits” immobilized on streptavidin-coated magnetic or agarose beads. After incubation with cell lysates or nuclear extracts, non-specifically bound proteins are removed through washing steps, and specific interacting proteins are eluted and enriched for subsequent analysis by SDS-PAGE, Western Blot, or mass spectrometry (LC-MS/MS). PPD is particularly suited for studying protein-protein interactions mediated by short linear motifs (SLiMs) and for investigating the regulatory effects of post-translational modifications (e.g., histone modifications) on protein interactions. When combined with quantitative proteomic approaches such as SILAC (Stable Isotope Labeling by Amino Acids in Cell Culture), PPD can effectively discriminate specific interactors from background noise, enabling high-sensitivity interactome screening.

Lipid Pull-down is an in vitro affinity purification technique used to systematically identify proteins that interact with specific lipid molecules. In this method, target lipids (e.g., phosphoinositides, sphingolipids, cholesterol) are immobilized on solid-phase supports (such as agarose or magnetic beads) via covalent coupling or biotin-avidin systems. After incubation with cell lysates or tissue extracts, non-specifically bound proteins are removed through washing steps, and specific lipid-interacting proteins are eluted and enriched for subsequent analysis by Western Blot or mass spectrometry. Lipid Pull-down serves as a core tool for investigating lipid signaling, membrane protein recruitment, and lipid raft dynamics. It is widely applied to dissect protein-binding networks of phosphoinositide phosphorylated derivatives, sphingolipid-protein interactions, and cholesterol-associated protein complexes. Combined with quantitative proteomics, this approach enables high-throughput, high-sensitivity screening of lipid-binding proteins.

Glycan Pull-down encompasses a family of affinity purification techniques based on carbohydrate-protein interactions, utilizing immobilized carbohydrates (such as lectins, boronate affinity ligands, or glycan probes) as baits to specifically capture glycoproteins, glycopeptides, or carbohydrate-binding proteins from complex biological samples. This technology represents one of the core tools in glycoproteomics and is widely applied in glycoprotein enrichment, glycan-protein interaction identification, disease biomarker discovery, and drug target screening. Combined with mass spectrometry (LC-MS/MS) analysis, Glycan Pull-down enables highly sensitive detection of low-abundance glycoproteins and site-specific glycosylation characterization, providing critical technical support for understanding the roles of protein glycosylation in cellular signal transduction, immune responses, and disease pathogenesis.