Transcription factors (TFs) are families of proteins that bind to specific DNA sequences, or TF response elements (TFREs), and function as regulators of many cellular processes. Because of the low abundance of TFs, direct quantitative measurement of TFs on a proteome scale remains a challenge. In this study, we report the development of an affinity reagent that permits identification of endogenous TFs at the proteome scale. The affinity reagent is composed of a synthetic DNA containing a concatenated tandem array of the consensus TFREs (catTFRE) for the majority of TF families. By using catTFRE to enrich TFs from cells, we were able to identify as many as 400 TFs from a single cell line and a total of 878 TFs from 11 cell types, covering more than 50% of the gene products that code for the DNA-binding TFs in the genome. We further demonstrated that catTFRE pull-downs could quantitatively measure proteome-wide changes in DNA binding activity of TFs in response to exogenous stimulation by using a labelfree MS-based quantification approach. Applying catTFRE on the evaluation of drug effects, we described a panoramic view of TF activations and provided candidates for the elucidation of molecular mechanisms of drug actions. We anticipate that the catTFRE affinity strategy will find widespread applications in biomedical research.TF activity profiling | transcriptional coregulator | drug effects screening A lmost all biological processes, ranging from cell cycle regulation to organ development, are controlled by the transcriptional regulatory system (1). In the classic cell membraneto-nucleus signal transduction paradigm, transcription factors (TFs) are the final effectors. They are activated and bind to consensus DNA sequences to execute specific transcriptional programs in response to the signal. Thus, the ability to monitor TF activity is important for the delineation of signal transduction pathways when the cells are perturbed (e.g., treated with a drug), or when organs are under the influence of developmental cues.Approximately 1,500 TF coding genes are reported to be in the human genome (2). TFs can be grouped into different families depending on the structure of their DNA binding domains. There are approximately 50 TF families (2), and each family prefers to bind a specific DNA consensus sequence. For example, nuclear receptors (NRs) are ligand-modulated TFs that recognize one or two hormone response element sequences such as 5′-AGAACA-3′ or 5′-AGGTCA-3′ (3). Previous studies have demonstrated the importance of linking an extracellular signaling event to the activation of TFs. For example, assigning Forkhead box (Fox) P3 to a signaling module that is crucial for regulatory T-cell development has accelerated our understanding of signal transductions and gene functions (4).The abundance of TFs in the cells is currently inferred from mRNA profiling. Yang et al. identified 45 of 49 known NRs from several tissues in mice and linked NR expression to the circadian clock (5). Bookout et al. surveyed the expression of al...