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.

中文翻译：

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在Optimus和'ili软件的协助下，使用LC-MS进行3D分子制图。

我们的皮肤，财产，周围的世界以及我们所生活的环境都被分子痕迹覆盖。检测和表征这些分子的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（尤其是微生物群）之间复杂的分子相互作用是必不可少的。我们最近推出了3D分子制图技术，用于绘制在包括人体在内的各种表面上发现的有机小分子（包括代谢物，脂质和环境分子）的地图。在这里，我们提供了用于3D分子制图的协议和开源软件。该协议包括用于样品收集和处理的分步程序，基于液相色谱-质谱（LC-MS）的代谢组学，质量控制（QC），使用MS / MS进行分子鉴定，数据处理，以及使用采样环境的3D模型进行可视化。LC-MS方法针对各种小有机分子进行了优化。我们使科学家能够重现我们先前获得的结果，并在输入PIN码后用迷迭香植物和ATM小键盘的分子图来说明我们的方法的广泛用途。为了提高可重复性，我们引入了制图快照：描述特定地图和可视化设置的文件，可以共享和加载这些文件以重现可视化。该协议使分子制图可以在任何质谱实验室中进行，并且原则上可以对任何空间映射数据进行。我们预计将在医学，生态学，农业，生物技术和法证学等领域中广泛应用。