Proteome analysis of human stomach tissue: Separation of soluble proteins by two-dimensional polyacrylamide gel electrophoresis and identification by mass spectrometry

Two‐dimensional gel electrophoresis (2‐DE) maps for human stomach tissue proteins have been prepared by displaying the protein components of the tissue by 2‐DE and identifying them using mass spectrometry. This will enable us to present an overview of the proteins expressed in human stomach tissues and lays the basis for subsequent comparative proteome analysis studies with gastric diseases such as gastric cancer. In this study, 2‐DE maps of soluble fraction proteins were prepared on two gel images with partially overlapping pH ranges of 4–7 and 6–9. On the gels covering pH 4–7 and pH 6–9, about 900 and 600 protein spots were detected by silver staining, respectively. For protein identification, proteins spots on micropreparative gels stained with colloidal Coomassie Brilliant Blue G‐250 were excised, digested in‐gel with trypsin, and analyzed by peptide mass fingerprinting with delayed extraction‐matrix assisted laser desorption/ionization‐mass spectrometry (DE‐MALDI‐MS). In all, 243 protein spots (168 spots in acidic map and 75 spots in basic map) corresponding to 136 different proteins were identified. Besides these principal maps, overview maps (displayed on pH 3–10 gels) for total homogenate and soluble fraction, are also presented with some identifications mapped on them. Based on the 2‐DE maps presented in this study, a 2‐DE database for human stomach tissue proteome has been constructed and is available at http://proteome.gsnu.ac.kr/DB/2DPAGE/Stomach/. The 2‐DE maps and the database resulting from this study will serve important resources for subsequent proteomic studies for analyzing the normal protein variability in healthy tissues and specific protein variations in diseased tissues.