Use of ENCODE Resources to Characterize Novel Proteoforms and Missing Proteins in the Human Proteome

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• 作者：Carol L. Nilsson ; Ekaterina Mostovenko ; Cheryl F. Lichti ; Kelly Ruggles ; David Feny枚 ; Kate R. Rosenbloom ; William S. Hancock ; Young-Ki Paik ; Gilbert S. Omenn ; Joshua LaBaer ; Roger A. Kroes ; Matthias Uhl茅n ; Sophia Hober ; 脕kos V茅gv谩ri ; Per E. Andr茅n ; Erik P. Sulman ; Frederick F. Lang ; Manuel Fuentes ; Elisabet Carlsohn ; Mark R. Emmett ; Joseph R. Moskal ; Frode S. Berven ; Thomas E. Fehniger ; Gy枚rgy Marko-Varga
• 刊名：Journal of Proteome Research
• 出版年：2015
• 出版时间：February 6, 2015
• 年：2015
• 卷：14
• 期：2
• 页码：603-608
• 全文大小：369K
• ISSN：1535-3907

文摘

We describe the utility of integrated strategies that employ both translation of ENCODE data and major proteomic technology pillars to improve the identification of the 鈥渕issing proteins鈥? novel proteoforms, and PTMs. On one hand, databases in combination with bioinformatic tools are efficiently utilized to establish microarray-based transcript analysis and supply rapid protein identifications in clinical samples. On the other hand, sequence libraries are the foundation of targeted protein identification and quantification using mass spectrometric and immunoaffinity techniques. The results from combining proteoENCODEdb searches with experimental mass spectral data indicate that some alternative splicing forms detected at the transcript level are in fact translated to proteins. Our results provide a step toward the directives of the C-HPP initiative and related biomedical research.