Mass spectrometry (MS) has emerged as an indispensable tool for identifying and quantifying proteins in complex biological systems [1,2]. Chemical approaches enable the selective labeling and enrichment of target proteins, improving the detection of low-abundance species and enhancing the specificity of proteomic analyses [3, 4, 5]. Chemical proteomics employs diverse reaction mechanisms for selective protein labeling: (1) Covalent activity-based reactions target specific amino acid residues, such as cysteine and serine, providing insights into enzyme activity and substrate specificity [6,7]; (2) Bioorthogonal reactions, including copper-catalyzed azide–alkyne cycloaddition (CuAAC) and strain-promoted azide–alkyne cycloaddition (SPAAC), allow protein labeling without interfering with native biological processes [8]; (3) Photoactivation reactions utilize light-activated probes, such as aryl azides and diazirines, to capture dynamic protein interactions [9,10]; and (4) Proximity-dependent biotinylation, such as BioID and TurboID, employs biotin ligases to label and identify the molecular neighborhood of a protein of interest [11,12]. These strategies have significantly advanced the study of protein function and dynamics in biological systems. This review discusses recent applications integrating MS with these methodologies, including activity-based protein profiling (ABPP), proximity labeling (PL), and proteolysis-targeting chimeras (PROTACs) (Figure 1).