Using histological analysis of the induction of secondary somatic embryogenesis (SSE) in cassava (Manihot esculenta Crantz) as a guide, we performed 2-DE for protein separation and matrix-assisted laser desorption ionization-time of flight-tandem mass spectrometry (MALDI-TOF-TOF-MS) for protein identification in cotyledons of cassava somatic embryos undergoing SSE. Reference map obtained by 2-DE within a pH range of 3–10 and a size range of 6–97kDa revealed approximately 410 eletrophoretically resolved spots populated primarily by acidic (pI