The response of a cell to its extracellular environment is a multi-step process beginning with signal transduction that is governed by "subtle changes" often resulting in protein expression. Proteomics is the tracking of this protein expression. Post-translational modification (PTM) is a "subtle change" that has a major influence on signal transduction. Phosphorylation and glycosylation propagate signals by sequential, reversible modifications. High-sensitivity, high-resolution and multiple MS capabilities of Fourier transform ion cyclotron resonance mass spectrometry permit localization of the PTM(s) with electron-capture dissociation, and then structural determination of the PTM with infrared multiphoton dissociation.