Systems-level analysis of isotopic labeling in untargeted metabolomic data by X13CMS.
Systems-level analysis of isotopic labeling in untargeted metabolomic data by X13CMS.
复制标题
通过 X13CMS 对非目标代谢组数据中的同位素标记进行系统级分析。
DOI：
10.1038/s41596-019-0167-1
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发表时间：
2019
期刊：
影响因子：
14.8
通讯作者：
Patti,GaryJ
中科院分区：
文献类型：
--
作者：
Llufrio,ElizabethM;Cho,Kevin;Patti,GaryJ
在非靶向代谢组学数据中识别以前未报告的代谢物（所谓的“未知物”）已成为一个日益活跃的研究领域。然而，相当少的注意力一直致力于确定未知的代谢途径。然而，对于每一种未知的代谢物结构，都可能存在一种尚未被发现的化学转化。阐明这些生物化学联系对于推进我们对细胞代谢的了解至关重要，并且可以通过追踪同位素标记的前体来实现。除了它们在映射代谢命运中的作用之外，同位素标记还提供了对途径动力学的关键见解（即，代谢通量），其不能从常规的无标记代谢组学分析获得。例如，当在条件之间定量地比较标记时，同位素示踪剂可以使得能够推断相对途径活性。为了发现代谢途径活动中意外的化学转化或意外的差异，我们开发了X13 CMS，这是一种用于在系统级分析液相色谱/质谱（LC/MS）数据的平台。在向细胞、动物或患者提供同位素富集的代谢物（例如，13 C、15 N或2 H），X13 CMS鉴定已掺入同位素示踪剂的化合物并报告每种化合物的标记程度。可以在单一条件下进行分析，或者可以在多种条件之间比较同位素命运。选择哪种代谢物富集和使用哪种同位素标记是高度依赖于环境的，但是13 C-葡萄糖和13 C-谷氨酰胺经常被应用，因为它们提供了大量的代谢途径。X13 CMS是免费的。
Identification of previously unreported metabolites (so-called ‘unknowns’) in untargeted metabolomic data has become an increasingly active area of research. Considerably less attention, however, has been dedicated to identifying unknown metabolic pathways. Yet, for each unknown metabolite structure, there is potentially a yet-to-be-discovered chemical transformation. Elucidating these biochemical connections is essential to advancing our knowledge of cellular metabolism and can be achieved by tracking an isotopically labeled precursor to an unexpected product. In addition to their role in mapping metabolic fates, isotopic labels also provide critical insight into pathway dynamics (i.e., metabolic fluxes) that cannot be obtained from conventional label-free metabolomic analyses. When labeling is compared quantitatively between conditions, for example, isotopic tracers can enable relative pathway activities to be inferred. To discover unexpected chemical transformations or unanticipated differences in metabolic pathway activities, we have developed X13CMS, a platform for analyzing liquid chromatography/mass spectrometry (LC/MS) data at the systems level. After providing cells, animals, or patients with an isotopically enriched metabolite (e.g.,13C,15N, or2H), X13CMS identifies compounds that have incorporated the isotopic tracer and reports the extent of labeling for each. The analysis can be performed with a single condition, or isotopic fates can be compared between multiple conditions. The choice of which metabolite to enrich and which isotopic label to use is highly context dependent, but13C-glucose and13C-glutamine are often applied because they feed a large number of metabolic pathways. X13CMS is freely available.