Two‐dimensional electrophoretic profiling of normal human kidney glomerulus proteome and construction of an extensible markup language (XML)‐based database

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Abstract
To contribute to physiology and pathophysiology of the glomerulus of human kidney, we have launched a proteomic study of human glomerulus, and compiled a profile of proteins expressed in the glomerulus of normal human kidney by two‐dimensional gel electrophoresis (2‐DE) and identification with matrix‐assisted laser desorption / ionization‐time of flight mass spectrometry (MALDI‐TOF MS) and / or liquid chromatography‐tandem mass spectrometry (LC‐MS / MS). Kidney cortices with normal appearance were obtained from patients under surgical nephrectomy due to renal tumor, and glomeruli were highly purified by a standard sieving method followed by picking‐up under a phase‐contrast microscope. The glomerular proteins were separated by 2‐DE with 24 cm immobilized pH gradient strips in the 3–10 range in the first dimension and 26 × 20 cm sodium dodecyl sulfate polyacrylamide electrophoresis gels of 12.5% in the second dimension. Gels were silver‐stained, and valid spots were processed for identification through an integrated robotic system that consisted of a spot picker, an in‐gel digester, and a MALDI‐TOF MS and / or a LC‐MS / MS. From 2‐DE gel images of glomeruli of four subjects with no apparent pathologic manifestations, a synthetic gel image of normal glomerular proteins was created. The synthetic gel image contained 1713 valid spots, of which 1559 spots were commonly observed in the respective 2‐DE gels. Among the 1559 spots, 347 protein spots, representing 212 proteins, have so far been identified, and used for the construction of an extensible markup language (XML)‐based database. The database is deposited on a web site (http://www.sw.nec.co.jp/bio/rd/hgldb/index.html) in a form accessible to researchers to contribute to proteomic studies of human glomerulus in health and disease.