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An optimized two-dimensional polyacrylamide gel electrophoresis (2-DE) system for analyzing plant proteins was developed by evaluating different reagents and concentrations used in the sample extraction solutions and lysis buffers. Two main sample preparation methods, referred to as trichloroacetic acid (TCA)-acetone method and phenol extraction-ammonium acetate/methanol (phenol-NH4Ac/methanol) precipitation method, were compared. Four ecotypes of reed plants (Phragmites communis Trin.) from the desert region of north-western China were used as experimental materials: (1) swamp reed (SR) which grows in water about 1 m deep; (2) dune reed (DR) which grows on 5 similar to 10 m high sand dunes; (3) heavy salt meadow reed (HSMR) which grows on low-lying salt flats; and (4) light salt meadow reed (LSMR) which grows in the transition area between DR and HSMR growing areas. The optimized phenol-NH4Ac/methanol precipitation method consisted of extracting leaf proteins of different ecotypes of reed with water-saturated phenol and then precipitating with a 5-fold volume of 0.1 mol/L NH4Ac in methanol, followed by dissolving in the lysis buffer. The optimized protein lysis buffer consisted of 7 mol/L urea, 2 mol/L thiourea, 4% CHAPS, 2% Ampholine(pH 3.5 similar to 10 : pH 5 similar to 8 = 1 : 4) and 65 mmol/L DTT. The prepared protein sample (80 mu g) was then separated by 2-DE gel and detected by silver staining method. This improved 2-DE system resulted in a 2-D protein profile of higher resolution and higher protein yields as analyzed by PDQuest software. Good results were also obtained when this 2-DE system was used in 2-D analysis of proteins from other plant materials, such as rice leaves, indicating that it is a suitable 2-DE system for analyzing leaf proteins of different plant species.