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.