title: Dramatic improvement of proteomic analysis of zebrafish liver tumor by effective protein extraction with sodium deoxycholate and heat denaturation.
abstract: Majority of the proteomic studies on tissue samples involve the use of gel-based approach for profiling and digestion. The laborious gel-based approach is slowly being replaced by the advancing in-solution digestion approach. However, there are still several difficulties such as difficult-to-solubilize proteins, poor proteomic analysis in complex tissue samples, and the presence of sample impurities. Henceforth, there is a great demand to formulate a highly efficient protein extraction buffer with high protein extraction efficiency from tissue samples, high compatibility with in-solution digestion, reduced number of sample handling steps to reduce sample loss, low time consumption, low cost, and ease of usage. Here, we evaluated various existing protein extraction buffers with zebrafish liver tumor samples and found that sodium deoxycholate- (DOC-) based extraction buffer with heat denaturation was the most effective approach for highly efficient extraction of proteins from complex tissues such as the zebrafish liver tumor. A total of 4,790 proteins have been identified using shotgun proteomics approach with 2D LC, which to our knowledge is the most comprehensive study for zebrafish liver tumor proteome.
authors: Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.
authors: Jigang
authors: J
authors: Wang
authors: Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.
authors: Yew Mun
authors: YM
authors: Lee
authors: Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.
authors: Caixia
authors: C
authors: Li
authors: Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.
authors: Ping
authors: P
authors: Li
authors: Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.
authors: Zhen
authors: Z
authors: Li
authors: Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.
authors: Teck Kwang
authors: TK
authors: Lim
authors: Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.
authors: Zhiyuan
authors: Z
authors: Gong
authors: Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.
authors: Qingsong
authors: Q
authors: Lin