Identifying Unknown Enzyme-Substrate Pairs from the Cellular Milieu with Native Mass Spectrometry

The enzyme-substrate complex is inherently transient, rendering its detection difficult. In our framework, IsoLAIT (Isotope-Labeled, Activity-based Identification and Tracking), designed for bisubstrate systems, the common substrate, such as S-adenosyl-L-methionine (AdoMet) for methyltransferases, is replaced by an analogue (e.g., S-adenosyl-L-vinthionine) that, as a probe, creates a tightly bound [enzyme•substrate-probe] complex upon catalysis by thiopurine-S-methyltransferase (TPMT, EC 2.1.1.67). Then, this persistent complex is identified by native mass spectrometry from the cellular milieu without separation. Furthermore, the probe’s isotope pattern flags even unknown substrates and enzymes. IsoLAIT can be broadly applicable for other enzyme systems, particularly those catalyzing group transfer and with multiple substrates, such as glycosyltransferases and kinases.