Development of an effective sample preparation approach for proteomic analysis of silkworm eggs using two-dimensional gel electrophoresis and mass spectrometry

Sample preparation is still the first and important step toward successful two-dimensional gel electrophoresis (2DE) and identification in proteomics study. The 2DE profiling of eggs of silkworm specie by using conventional one-step extraction, however, is unsatisfactory because high-abundance proteins such as egg-specific protein (ESP) and No 30 family (30 KP) in the extract lead to difficulties in detecting most of biologically relevant proteins. Based on the tendency of these abundant proteins to be soluble in Tris–HCl buffer, we report herein a robust approach in which the extract enriched in ESP and 30 KP was fractionationed and mixed with the re-extract of residual pellet in an optimal proportion. In comparison with the one-step method, the 2DE pattern was improved by this new method with over one-third enhancement in spots. A total of 48 unique proteins obtained have been furthermore identified by mass spectrometry (MS) and MS/MS. The identified proteins are found to include heat shock proteins families, ribosomal proteins, disulfide isomerase proteins, Glutathione S-transferase, and elongation factor, etc., which are mainly involved in some important processes. To our knowledge, this is the first time that the several proteins have been detected in silkworm eggs by proteomics means. This simple and reproducible approach would raise the opportunity of discovering and identifying more biomarkers and determining their possible roles in further studies.