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An FD-LC-MS/MS Proteomic Strategy for Revealing Cellular Protein Networks: A Conditional Superoxide Dismutase 1 Knockout Cells Tomoko Ichibangase, Yasuhiro Sugawara, Akio Yamabe, Akiyo Koshiyama, Akari Yoshimura, Takemi Enomoto, Kazuhiro Imai* Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, Japan Abstract Systems biology aims to understand biological phenomena in terms of complex biological and molecular interactions, and thus proteomics plays an important role in elucidating protein networks. However, many proteomic methods have suffered from their high variability, resulting in only showing altered protein names. Here, we propose a strategy for elucidating cellular protein networks based on an FD-LC-MS/MS proteomic method. The strategy permits reproducible relative quantitation of differences in protein levels between different cell populations and allows for integration of the data with those obtained through other methods. We demonstrate the validity of the approach through a comparison of differential protein expression in normal and conditional superoxide dismutase 1 gene knockout cells and believe that beginning with an FD-LC-MS/MS proteomic approach will enable researchers to elucidate protein networks more easily and comprehensively. Citation: Ichibangase T, Sugawara Y, Yamabe A, Koshiyama A, Yoshimura A, et al. (2012) An FD-LC-MS/MS Proteomic Strategy for Revealing Cellular Protein Networks: A Conditional Superoxide Dismutase 1 Knockout Cells. PLoS ONE 7(9): e45483. doi:10.1371/journal.pone.0045483 Editor: Andy T. Y. Lau, Shantou University Medical College, China Received February 8, 2012; Accepted August 21, 2012; Published September 18, 2012 Copyright: 2012 Ichibangase et al. This is an open-access article distributed under the terms of the Creative Comm