Nunn Brook L, Shaffer Scott A, Scherl Alexander, Gallis Byron, Wu Manhong, Miller Samuel I, Goodlett David R
Goodlett Laboratory.
Brief Funct Genomic Proteomic. 2006 Jun;5(2):154-68. doi: 10.1093/bfgp/ell024.
Shotgun proteomics is rapidly becoming one of the most efficient and popular tools to examine protein expression in cells. Numerous laboratories now have a wide array of low- and high-performance mass spectrometry instrumentation necessary to complete proteome-wide projects. Often these laboratories have time and financial constraints that prohibit all projects from being conducted on high-performance state-of-the-art mass spectrometers. Here, we compare shotgun proteomic results using a direct 'lyse, digest and analyse' approach on a high-performance mass spectrometer (i.e. the LTQ-FT) with the results from a much lower-performance instrument (i.e. the LCQ-DUO) where, for the latter, various traditional protein pre-fractionation steps and gas-phase fractionation were used to increase the proteome coverage. Our results demonstrate that shotgun proteomic analyses conducted on the lower-performance LCQ-DUO mass spectrometer could adequately characterize a PhoP constitutive strain of Salmonella typhimurium if proteome pre-fractionation steps and gas-phase fractionation were included.
鸟枪法蛋白质组学正迅速成为检测细胞中蛋白质表达的最有效且最受欢迎的工具之一。现在，众多实验室拥有一系列完成全蛋白质组项目所需的高性能和低性能质谱仪器。这些实验室常常受到时间和资金的限制，无法在高性能的最先进质谱仪上开展所有项目。在此，我们将在高性能质谱仪（即LTQ-FT）上采用直接“裂解、消化和分析”方法获得的鸟枪法蛋白质组学结果，与在性能低得多的仪器（即LCQ-DUO）上获得的结果进行比较，对于后者，使用了各种传统的蛋白质预分级步骤和气相分级来增加蛋白质组覆盖率。我们的结果表明，如果纳入蛋白质组预分级步骤和气相分级，在性能较低的LCQ-DUO质谱仪上进行的鸟枪法蛋白质组学分析能够充分表征鼠伤寒沙门氏菌的PhoP组成型菌株。
