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Small molecule pull-down is an affinity purification-based chemical proteomics technique. A biotin or other affinity tag is chemically conjugated to a biologically active small molecule compound to construct a small molecule affinity probe. After incubation with cell lysates or live cells, the probe-target protein complex is specifically captured using streptavidin magnetic beads or agarose beads. Following washing to remove non-specifically bound proteins, the enriched proteins are subjected to Western Blot for targeted validation or high-resolution mass spectrometry for proteomic identification, enabling systematic screening and identification of direct target proteins and their interaction networks. This technique is a core tool for drug target discovery, mechanism of action elucidation, and off-target effect assessment.

Metabolite pull-down is an affinity-based chemical proteomics technique in which a target metabolite (or its biotin/photoaffinity probe) is immobilized on a solid-phase matrix and incubated with cell lysates or protein mixtures to selectively capture its direct protein binding partners. After stringent washing to remove non-specific interactions, the enriched proteins are identified by mass spectrometry (MS), thereby elucidating the molecular mechanism of action of the metabolite. This approach is widely used in drug target discovery, natural product mechanism deconvolution, and signaling pathway investigation.

Surface plasmon resonance (SPR) is an optical biosensing technique that monitors biomolecular interactions in real time by detecting changes in the refractive index at a metal film surface. When polarized light illuminates the metal layer, it generates evanescent waves that resonate with surface plasmon waves produced by free electrons at a specific angle or wavelength, causing a sharp dip in reflected light intensity; binding events between ligands (such as immobilized glycans) and analytes (such as antibodies) alter the local refractive index, shifting the resonance angle and thereby enabling label-free quantification of binding specificity, affinity, kinetics, and concentration. Leveraging this principle, SPR has proven exceptionally effective for glycan-targeting antibody screening and analysis: diverse glycan architectures, derived from chemical synthesis or biological sources, either purified or blended, can be immobilized on biosensor chips in defined geometric patterns to create plasmonic glycan arrays. These platforms support exhaustive antibody profiling, pathological biomarker discovery, and standardized large-scale analysis of dynamic binding parameters and immunoglobulin concentrations.

Isothermal Titration Calorimetry (ITC) is a label-free biophysical technique that directly measures the heat released or absorbed during molecular binding events by titrating a ligand into its macromolecular target until saturation, thereby preserving native molecular behaviour without the need for labelling or immobilisation. In a single experiment, ITC provides a complete thermodynamic profile encompassing binding affinity (Kd), molar free energy change (ΔG), enthalpy change (ΔH), entropy change (ΔS), and binding stoichiometry (n), enabling differentiation between enthalpy- and entropy-driven interactions. Owing to its quantitative precision, ITC is widely regarded as the gold standard for analysing protein–ligand, protein–protein, and nucleic acid interactions, and it plays a pivotal role in drug discovery by determining binding strength and energetic favourability to support rational drug design and candidate selection. Furthermore, ITC continues to provide essential label-free evaluation in antibody development, formulation studies, and structural biology, making it an indispensable tool as biopharmaceutical molecules grow increasingly complex.