What does this strategy enable?
3D molecular cartography extends metabolomics beyond conventional bulk samples by attaching each extraction to a physical coordinate. LC-MS data are processed and annotated, then mapped onto photographs or 3D surface models so chemical distributions can be explored spatially. Cartographical snapshots preserve visualization settings for reproducibility.
Transferable workflow
Workflow
- 1
Define a spatial sampling scheme
Record coordinates for reproducible sampling across a surface, organism or object.
- 2
Extract and profile each location
Analyze spatially indexed extracts by LC-MS/MS with appropriate blanks and quality controls.
- 3
Process and annotate features
Generate a quantitative feature table and molecular annotations while preserving spatial sample identifiers.
- 4
Map molecular features onto the physical model
Join feature abundance to sampling coordinates and visualize the chemical distribution on a 2D image or 3D model.
- 5
Share cartographical snapshots
Preserve the mapped view and visualization settings so collaborators can reproduce the spatial interpretation.
Connected resources
Tools used in this strategy
Strategy profile
Related objectives
Environmental metabolomics, Molecular discovery
Components
Sample preparation, Chromatography, Data acquisition, Preprocessing and feature extraction, Annotation or identification, Data and workflow sharing
Biological context
Environmental, Plant, Human, Broadly applicable
Scope and considerations
Designed for
- Mapping extractable small molecules over complex surfaces at scales larger than pixel-based MSI.
- Environmental, ecological, built-environment and organism-surface chemistry.
Important requirements
- A reproducible coordinate system connecting each extraction to the mapped object.
- Sufficient sampling density for the spatial question.
Considerations
- Spatial resolution is determined by sampling geometry and is much coarser than many MSI methods.
- Observed distributions integrate extraction, LC-MS detectability and sampling effects.
Reusable resources
Publication
Protsyuk I, Melnik AV, Nothias L-F, et al. 3D molecular cartography using LC–MS facilitated by Optimus and 'ili software. Nature Protocols 13, 134–154 (2018).