Chemical methods that provide a readout of biochemical changes within a cell at the protein level enable precise characterization of biological phenotypes that may not always be encoded in the genome or inferred from the transcriptome. Post-translational regulation of protein activity differs from genetic and transcriptional as it usually occurs on a timescale of seconds to minutes rather than hours and days. This regulation is associated with dynamic changes in protein landscapes as a direct result of protein conformational changes induced by post-translational modifications of critical amino acid residues, protein translocations, and changes in protein interactomes. Herein, we reflect on current broad-scale mass spectrometry-enabled chemical biology methods used to interrogate different protein states and dynamic protein landscapes and provide an outlook on the field of state-dependent chemical biology.