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3D Molecular Cartography Using LC-MS facilitated by Optimus and 'ili software

NCJ Number
Nature Protocols Volume: 13 Issue: 1 Dated: 2018 Pages: 134-154
Date Published
21 pages

The authors recently introduced 3D molecular cartography for mapping small organic molecules (including metabolites, lipids, and environmental molecules) found on various surfaces, including the human body; and in the current project, they provide a protocol and open-source software for 3D molecular cartography.


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. The protocol developed in the current project 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. With this protocol, scientists can reproduce the authors' previously obtained results, and illustrate the broad utility of their approach with molecular maps of a rosemary plant and an ATM keypad after a PIN code was entered. To promote reproducibility, this article introduces cartographical snapshots, i.e., 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. The authors 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. (publisher abstract modified)

Date Published: January 1, 2018