Site-specific protein labeling methods allow cell biologists to access the vast array of existing chemical probes for the study of specific proteins of interest in the live cell context. Here we describe the use of the transglutaminase enzyme from guinea pig liver (gpTGase), whose natural function is to cross-link glutamine and lysine sidechains, to covalently conjugate various small molecule probes to recombinant proteins fused to a 6-or 7-amino acid transglutaminase recognition sequence, called a Q-tag. We demonstrate labeling of Q-tag fusion proteins both in vitro and on the surface of living mammalian cells with biotin, fluorophores, and a benzophenone photoaffinity probe. To illustrate the utility of this labeling, we tagged the NF-κB p50 transcription factor with benzophenone, crosslinked with UV light, and observed increased levels of p50 homodimerization in the presence of DNA and the binding protein myotrophin Compared to green fluorescent protein (GFP), non-genetically-encoded probes such as organic dyes and inorganic nanoparticles offer the possibility of smaller probe sizes and access to a much wider array of functionality, from photocrosslinking and photoregulation to imaging of cellular processes by non-optical methods such as electron microscopy, magnetic resonance imaging, and positron emission tomography. The major limitation to the use of these probes in cells, however, is the shortage of robust methods for targeting them to specific proteins of interest. Recently, many new methodologies for protein labeling in cells have been reported. 1-3 Most of these use special peptide or protein handles, which are genetically fused to the target protein and recruit the probe of interest via a covalent or non-covalent interaction. There is great variation among these methods in terms of labeling specificity, speed, stability, tag size, toxicity, and versatility for probe structure and cell type, and no single method yet excels in all these respects. Thus new methods are still needed to facilitate the routine use of nongenetically-encoded probes in the cellular context. Transglutaminases (TGases) are enzymes that catalyze amide bond formation between glutamine and lysine sidechains, with the loss of ammonia ( Figure 1). They are ubiquitous in multicellular organisms and function in protein cross-linking events in migration, apoptosis, and wound healing, as well as in physiological disorders such as Huntington's disease and Celiac Sprue. 4-6 One of the most well-studied TGases is the guinea pig liver transglutaminase (gpTGase), which is a 77 kD monomeric protein expressed in the cytosol. 5 gpTGase has unique properties which make it ideal for protein labeling applications: it exhibits high specificity for its glutamine-containing protein substrate, but wide tolerance for the structure of the aminecontaining substrate. 7 Instead of lysine, amines as diverse as fluorescein cadaverine 8 and biotin cadaverine 9 can be utilized by gpTGase. Also peptide substrates have been found which are efficiently modi...