3D molecular cartography using LC-MS facilitated by Optimus and 'ili software
3D molecular cartography using LC-MS facilitated by Optimus and 'ili software
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DOI：
10.1038/nprot.2017.122
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发表时间：
2018-01-01
期刊：
影响因子：
14.8
通讯作者：
Alexandrov, Theodore
中科院分区：
文献类型：
--
作者：
Protsyuk, Ivan;Melnik, Alexey V.;Alexandrov, Theodore
我们的皮肤，我们的物品，我们周围的世界，以及我们生活的环境都覆盖着分子痕迹。检测和表征这些分子痕迹对于了解环境对人类健康和疾病的影响，以及破译人类与其他物种，特别是微生物之间复杂的分子相互作用是必要的。我们最近引入了3D分子制图，用于绘制在各种表面（包括人体）上发现的小有机分子（包括代谢物，脂质和环境分子）。在这里，我们提供了一个协议和开源软件的三维分子制图。该方案包括样品收集和处理、基于液相色谱-质谱（LC-MS）的代谢组学、质量控制（QC）、使用MS/MS的分子鉴定、数据处理以及采样环境3D模型可视化的分步程序。LC-MS方法针对广泛的小有机分子进行了优化。我们使科学家能够重现我们以前获得的结果，并说明了我们的方法与迷迭香植物和ATM键盘的分子图谱后，输入PIN码的广泛用途。为了提高再现性，我们引入了制图快照：描述特定地图和可视化设置的文件，可以共享和加载以再现可视化。该协议使分子制图可以在任何质谱实验室进行，原则上，任何空间映射的数据。我们预计应用，特别是在医学，生态学，农业，生物技术和法医学。该方案需要78小时的100个点的分子图谱，不包括试剂设置。
Our skin, our belongings, the world surrounding us, and the environment we live in are covered with molecular traces. Detecting and characterizing these molecular traces is necessary to understand the environmental impact on human health and disease, and to decipher complex molecular interactions between humans and other species, particularly microbiota. We recently introduced 3D molecular cartography for mapping small organic molecules (including metabolites, lipids, and environmental molecules) found on various surfaces, including the human body. Here, we provide a protocol and open-source software for 3D molecular cartography. The protocol includes step-by-step procedures for sample collection and processing, liquid chromatography-mass spectrometry (LC-MS)-based metabolomics, quality control (QC), molecular identification using MS/MS, data processing, and visualization with 3D models of the sampled environment. The LC-MS method was optimized for a broad range of small organic molecules. We enable scientists to reproduce our previously obtained results, and illustrate the broad utility of our approach with molecular maps of a rosemary plant and an ATM keypad after a PIN code was entered. To promote reproducibility, we introduce cartographical snapshots: files that describe a particular map and visualization settings, and that can be shared and loaded to reproduce the visualization. The protocol enables molecular cartography to be performed in any mass spectrometry laboratory and, in principle, for any spatially mapped data. We anticipate applications, in particular, in medicine, ecology, agriculture, biotechnology, and forensics. The protocol takes 78 h for a molecular map of 100 spots, excluding the reagent setup.