Protein extraction methods compatible with proteomic analysis for the cotton seedling

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An efficient protein extraction method to ensure successful separation by two-dimensional electrophoresis (2-DE) is a critical step for any proteomics study. The objective of this study was to compare four previously published protein extraction protocols to identify a suitable protein extraction method to extract total proteins from cotton (Gossypium hirsutum L.) seedlings, a recalcitrant plant tissue. The results suggested that trichloroacetic acid/acetone precipitation combined with phenol extraction method (Method D) produced the purest sample and the most proteins spots (321), particularly basic proteins in the 2-DE image. The extraction method combining acetone precipitation and phenol (Method B) gave 216 spots in the 2-DE image. The trichloroacetic acid/acetone precipitation method (Method A) is not suitable for the cotton seedlings because only small molecular weight proteins were visualized in the 2-DE image. The phenol extraction method (Method C) showed 240 spots in the 2-DE gel but gave higher gel background. We subsequently selected and optimized Method D to extract protein from cotton seedlings. After optimization, more than 900 spots were detected on the 2-DE gel with pH 3–10 nonlinear gradient strip and 10% sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS–PAGE) gel using Coomassie brilliant blue G-250 staining. Our results suggest that the optimized Method D is expected to have excellent applications in proteomic studies of cotton seedlings.

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