Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
J Proteomics. 2012 Oct 22;75(18):5749-61. doi: 10.1016/j.jprot.2012.08.007. Epub 2012 Aug 18.
Large scale quantitative phosphoproteomics depends upon multidimensional strategies for peptide fractionation, phosphopeptide enrichment, and mass spectrometric analysis. Previously, most robust comprehensive large-scale phosphoproteomics strategies have relied on milligram amounts of protein. We have set up a multi-dimensional phosphoproteomics strategy combining a number of well-established enrichment and fraction methods: An initial TiO(2) phosphopeptide pre-enrichment step is followed by post-fractionation using sequential elution from IMAC (SIMAC) to separate multi- and mono-phosphorylated peptides, and hydrophilic interaction liquid chromatography (HILIC) of the mono-phosphorylated peptides (collectively abbreviated "TiSH"). The advantages of the strategy include a high specificity and sample preparation workload reduction due to the TiO(2) pre-enrichment step, as well as low adsorptive losses. We demonstrate the capability of this strategy by quantitative investigation of early interferon-γ signaling in low quantities of insulinoma cells. We identified ~6600 unique phosphopeptides from 300 μg of peptides/condition (22 unique phosphopeptides/μg) in a duplex dimethyl labeling experiment, with an enrichment specificity>94%. When doing network analysis of putative phosphorylation changes it could be noted that the identified protein interaction network centered upon proteins known to be affected by the interferon-γ pathway, thereby supporting the utility of this global phosphoproteomics strategy. This strategy thus shows great potential for interrogating signaling networks from low amounts of sample with high sensitivity and specificity.
大规模定量磷酸化蛋白质组学依赖于多维策略,用于肽分离、磷酸肽富集和质谱分析。以前,大多数强大的综合大规模磷酸化蛋白质组学策略都依赖于毫克数量的蛋白质。我们建立了一种多维磷酸化蛋白质组学策略,结合了多种成熟的富集和分离方法:首先进行 TiO(2)磷酸肽预富集步骤,然后通过 IMAC(SIMAC)的顺序洗脱进行后分离,以分离多磷酸化肽和单磷酸化肽,以及单磷酸化肽的亲水相互作用液相色谱(HILIC)(统称为“TiSH”)。该策略的优点包括 TiO(2)预富集步骤带来的高特异性和减少样品制备工作量,以及低吸附损失。我们通过对低剂量胰岛素瘤细胞中早期干扰素-γ信号的定量研究证明了该策略的能力。我们在双二甲标记实验中从 300μg/条件的肽中鉴定了约 6600 个独特的磷酸肽(22 个独特的磷酸肽/μg),富集特异性>94%。当对假定磷酸化变化的网络分析时,可以注意到,所鉴定的蛋白质相互作用网络集中在已知受干扰素-γ途径影响的蛋白质上,从而支持这种全局磷酸化蛋白质组学策略的实用性。因此,该策略具有从少量样品中以高灵敏度和特异性检测信号网络的巨大潜力。