Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies

The identification of metabolites by mass spectrometry constitutes a major bottleneck which considerably limits the throughput of metabolomics studies in biomedical or plant research. Here, we present a novel approach to analyze metabolomics data from untargeted, data-independent LC-MS/MS measurements. By integrated analysis of MS1 abundances and MS/MS spectra, the identification of regulated metabolite families is achieved. This approach offers a global view on metabolic regulation in comparative metabolomics. We implemented our approach in the web application “MetFamily”, which is freely available at http://msbi.ipb-halle.de/MetFamily/. MetFamily provides a dynamic link between the patterns based on MS1-signal intensity and the corresponding structural similarity at the MS/MS level. Structurally related metabolites are annotated as metabolite families based on a hierarchical cluster analysis of measured MS/MS spectra. Joint examination with principal component analysis of MS1 patterns, where this annotation is preserved in the loadings, facilitates the interpretation of comparative metabolomics data at the level of metabolite families. As a proof of concept, we identified two trichome-specific metabolite families from wild-type tomato Solanum habrochaites LA1777 in a fully unsupervised manner and validated our findings based on earlier publications and with NMR.借助质谱（mass spectrometry）技术对代谢物进行鉴定，是制约生物医学与植物研究领域代谢组学（metabolomics）研究通量的核心瓶颈之一。本研究提出一种全新方法，用于分析非靶向、数据非依赖型液相色谱-串联质谱（LC-MS/MS）检测所得的代谢组学数据。通过整合分析MS1信号丰度与MS/MS质谱图，可实现受调控代谢物家族的鉴定。该方法可提供比较代谢组学研究中代谢调控的全局视角。我们将该方法集成至名为“MetFamily”的Web应用程序中，该工具可通过http://msbi.ipb-halle.de/MetFamily/免费获取。MetFamily可在基于MS1信号强度的代谢物特征与MS/MS层面对应的结构相似性之间建立动态关联。基于实测MS/MS质谱图的层级聚类分析，可将结构相关的代谢物注释为代谢物家族。结合MS1特征的主成分分析（Principal Component Analysis）联合解析，且该注释信息保留于载荷矩阵中，可助力在代谢物家族层面解读比较代谢组学数据。作为概念验证，我们以完全无监督的方式从野生型番茄Solanum habrochaites LA1777中鉴定出两个毛状体（trichome）特异性代谢物家族，并结合既往发表文献与核磁共振波谱（NMR）对研究结果进行了验证。