Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC-MS/MS. 1. Preparation of more than 4000 native protein maps.
Soluble proteins of human bronchial smooth muscle cells (HBSMC) were separated by nondenaturing micro 2DE and a 30 mm × 40 mm area of the CBB-stained slab gel (1.0 mm thick) was cut into 1.1 mm × 1.1 mm squares, then the proteins in the 972 gel pieces (squares) were applied to quantitative LC-MS/MS. Grid-cutting of the gel was employed to; (i) ensure the total analysis of the proteins in the area, (ii) standardize the conditions of analysis by LC-MS/MS, (iii) reconstruct the protein distribution patterns from the quantity data [1]. Totally 4323 proteins were identified in successfully analyzed 967 squares and the quantity distribution of each was reconstructed as a color density pattern (a native protein map). The quantity of the proteins distributed from 3.6% to 1 × 10(-5) % of the total protein quantity in the grid area. Each protein map was characterized by several features, including the position of quantity peak square, number of detected squares, and degree of concentration (focused or dispersed). About 4% of the proteins were detected in 100 or more squares, suggesting that they might be ubiquitous and interacting with other proteins. In contrast, many proteins showed more concentrated quantity distribution and the quantity peak positions of 565 proteins with a defined degree of concentration were summarized into a quantity peak map. These results for the first time visualized the distribution patterns of cellular proteins on a nondenaturing 2D gel.
School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, P. R. China.|Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, P. R. China.|Key Laboratory of Industrial Biotechnology of Guangdong Higher Education Institutes, South China University of Technology, Guangzhou, P. R. China.
Ya
Y
Jin
School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, P. R. China.
Jun
J
Zhang
School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, P. R. China.
Qi
Q
Yuan
Faculty of Science, Ehime University, Matsuyama, Japan.
Takashi
T
Manabe
School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, P. R. China.|Key Laboratory of Industrial Biotechnology of Guangdong Higher Education Institutes, South China University of Technology, Guangzhou, P. R. China.
Wen
W
Tan
D001980:Bronchi / Q000166:cytology*; D002478:Cells, Cultured; D002853:Chromatography, Liquid / Q000379:methods; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods*; D006801:Humans; D032389:Myocytes, Smooth Muscle / Q000737:chemistry*; D063347:Native Polyacrylamide Gel Electrophoresis; D020543:Proteome / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry
D020543:Proteome
Cellular proteins; LC-MS/MS; Native protein map; Nondenaturing micro 2DE; Quantitative protein-protein interaction