Chemical activators and inhibitors are useful probes to identify substrates and downstream effects of
enzymes; however, due to the complex signaling environment within cells, it is challenging to distinguish
between direct and indirect effects. This is particularly the case for phosphorylation, where a single
(de)phosphorylation event can trigger rapid changes in many other phosphorylation sites. An additional
complication arises when a single catalytic entity, which acts in form of many different holoenzymes with
different substrates, is activated or inhibited, as it is unclear which holoenzymes are affected, and in turn
which of their substrates are (de)phosphorylated. Direct target engaging MS-based technologies to study
targets of drugs do not address these challenges. Here, we tackle this by studying the modulation of protein
phosphatase-1 (PP1) activity by PP1-disrupting peptides (PDPs), as well as their selectivity toward PP1, by
using a combination of mass spectrometry-based experiments. By combining cellular treatment with the PDP
with in vitro dephosphorylation by the enzyme, we identify high confidence substrate candidates and begin
to separate direct and indirect effects. Together with experiments analyzing which holoenzymes are
particularly susceptible to this treatment, we obtain insights into the effect of the modulator on the complex
network of protein (de)phosphorylation. This strategy holds promise for enhancing our understanding of PP1
in particular and, due to the broad applicability of the workflow and the MS-based read-out, of chemical
modulators with complex mode of action in general.