Transcription Factor Response Elements on Tip: A Sensitive Approach for Large-Scale Endogenous Transcription Factor Quantitative Identification

The ability to map endogenous transcription factors (TFs) DNA binding activity at the proteome scale will greatly enhance our understanding of various biological processes. Here we report a highly sensitive, rapid, and high-throughput approach, transcription factor response elements on tip-mass spectrometry (TOT-MS), that allows for quantitative measurement of endogenous TFs. A total of 150 TFs from 1 μg of nuclear extracts can be quantified with single shot mass spectrometry detection in 1 h of machine time. Up to 755 TFs, which is comparable to the depth of RNA-seq, were identified by TOT coupled with on-tip small size reverse-phase liquid chromatography. We further demonstrated the capability of TOT-MS by interrogating the dynamic change of TFs in the epidermal growth factor (EGF) signaling pathway. This approach should find broad applications in elucidating the TF landscape from limited amounts of biological materials.