The objective of this study was to investigate the effect of extraction methods on two-dimensional electrophoresis (2- DE) maps of whey proteome in cow milk and to explore an optimal extraction method. Samples were extracted from cow milk by different isoelectric precipitations and ultracentrifugation methods. 2-DE maps were analyzed by PDQuest 8.0 software. The results of 2-DE maps showed that milk whey protein could be effectively extracted by the above methods with less background, no significant strips and good repeatability. However, there were still some residual caseins appearing in each map. 2-DE maps of whey protein refined by isoelectric precipitations were relatively informative when compared with the gel maps obtained by ultracentrifugation. Moreover, the richness of different whey proteins in various maps extracted by adjusting pH to 4.6 as isoelectric point was slightly higher than adjusting pH to 4.8. The results indicated that adjusting pH to 4.6 as isoelectric point to extract whey protein had some advantages than adjusting pH to 4.8 and ultracentrifugation. However, all the methods used in this study could effectively remove high abundant casein to improve the detection sensitivity of low abundance proteins.
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