Computational annotation of plant metabolomics profiles via a novel network-assisted approach
Computational annotation of plant metabolomics profiles via a novel network-assisted approach
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DOI：
10.1007/s11306-013-0504-2
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发表时间：
2013-08-01
期刊：
影响因子：
3.6
通讯作者：
Neumann, Steffen
中科院分区：
文献类型：
--
作者：
Gaquerel, Emmanuel;Kuhl, Carsten;Neumann, Steffen
质谱法已成为植物代谢组学研究的首选分析方法。然而，代谢物注释仍然是一个重大挑战，这意味着将化合物库中的结构搜索与从代谢物调控研究中推断的生物学知识相结合。在这里，我们提出了一种新的综合方法来处理和利用高分辨率LC-MS配置文件的源内碎片模式中包含的丰富的结构信息。在该方法中，首先从通过xcms处理提取的个体质量特征计算相关矩阵。然后检测对应于代谢物源内片段化的质量特征共调节模式，并使用R包CAMERA将其组装成化合物光谱，并使用MetFrag处理以进行基于片段的计算机结构解析。我们验证了这种方法的性能的快速注释的12个最大的化合物光谱，包括4个O-酰基糖和6个17-羟基香叶基芳樟醇二萜苷在昆虫攻击烟草叶的代谢谱。此外，我们还展示了基于相关矩阵中已知和未知化合物之间的共调控模式和两种先前未表征的O-酰基糖的结构注释来细化MetFrag代谢物注释的能力。总之，这种新的方法有助于使用一种或几种代谢物的质量特征强度之间的相关性从源内碎片化模式进行化合物注释。此外，这一分析提供了进一步的支持，昆虫植食激活主要的代谢重组N。渐细的叶子。
Mass spectrometry (MS) has become the analytical method of choice in plant metabolomics. Nevertheless, metabolite annotation remains a major challenge and implies the integration of structural searches in compound libraries with biological knowledge inferred from metabolite regulation studies. Here we propose a novel integrative approach to process and exploit the rich structural information contained in in-source fragmentation patterns of high-resolution LC-MS profiles. In this approach, a correlation matrix is first calculated from individual mass features extracted by xcms processing. Mass feature co-regulation patterns corresponding to metabolite in-source fragmentation are then detected and assembled into compound spectra using the R package CAMERA and processed for in silico fragment-based structure elucidation using MetFrag. We validate the performance of this approach for the rapid annotation of the twelve largest compound spectra, including four O-acyl sugars and six 17-hydroxygeranyllinalool diterpene glycosides in metabolic profiles of insect-attacked Nicotiana attenuata leaves. Additionally, we demonstrate the power of refining MetFrag metabolite annotations based on co-regulation patterns between known and unknown compounds in the correlation matrix and proposed structural annotations on two previously un-characterized O-acyl sugars. In summary, this novel approach facilitates compound annotation from in-source fragmentation patterns using correlation between intensities of mass features of one or several metabolites. Additionally, this analysis provides further support that insect herbivory activates major metabolic reconfigurations in N. attenuata leaves.