Abstract:Proteins extracted from the cortex of fungiinfected nutritive corms and non infected secondary corms of Gastrodia elata were separated by two dimensional polyacrylamide gel electrophoresis (2-DE) with immobilized pH gradients (IPG).Reference maps were obtained with a good reproducibility. Approximately 900 proteins per 2-DE gel were isolated with molecular weights ranging 12-97kD and pI 3-10.The spots showed a symmetric shape indicating a good resolution in both electrophoresis dimensions.Five proteins of high levels observed in a secondary corm gel were excised and identified using peptide mass fingerprinting and matrixassisted laser desorption ionization timeof flight mass spectrometry.A summary of the identified proteins and their putative functions are presented.One of them,spot no.4 is identified as a RNA binding protein involved in transcription.Technical details concerning database queries and protein identification success rates in the absence of a sequenced genome are reported and discussed.Parameters for sample preparation are critically investigated.