Proteomic searches using affinity-based chromatography (e.g., biotin-[strept]avidin) have been severely hampered by low protein recovery yields, protein destruction and denaturation, and the release of background proteins from the support. These limitations confound protein identification. A new acylhydrazone-based cleavable linker was developed to permit the efficient isolation of proteins with a traceable tag allowing detection and identification under mild conditions. The utility of the acylhydrazone linker was validated in a proteomic search wherein aldehyde dehydrogenase-1 was selectively captured and isolated from the mouse soluble liver proteome without interfering background proteins. The use of acylhydrazone linkers is expected to be generalized, allowing for the selective release of tagged molecules from noncovalent and covalently tagged supports.