Psychiatric disorders such as major depression are linked to early mortality, and patients affected by these conditions are at an increased risk of developing other diseases that are characteristic of the old and very old. Antidepressants are prescribed in the treatment of depression, although the mechanism of how they exert their therapeutic effects is only partly understood. To shed further light on their mode of action, this chapter presents a protocol using two-dimensional differential in-gel electrophoresis (2D-DIGE) combined with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry for identifying a proteomic signature in guinea pig brains after treatment with the antidepressant, fluoxetine. As this signature pointed toward changes in synaptic structure, we also present a protocol for Western blot analysis targeting selected proteins identified by the combined 2D-DIGE-MALDI-TOF mass spectrometry procedure. Such validation experiments are critical for the translation of putative biomarkers into preclinical and clinical studies.