MetaboAnalyst

Spatial Data Bridge

Converts the exports of other tools into the spot intensity and spot metadata tables of the spatial modules, derives regions of interest, merges sections, or pairs a section with a bulk LC-MS table; the result opens in Spatial MS Peaks or Spatial Compound Table.

Format

Files

Feature-intensity table:

Choose

Section files

Choose

Select all files at once (Ctrl/Cmd-click), or one ZIP containing them. 50 MB in total.

Options

m/z matching tolerance (ppm):

Matches a section to a bulk LC-MS (or GC-MS) table of the same tissue; matched features take the LC-MS identities and continue in Spatial Compound Table.

Spatial section

Intensity table:	Choose
Spatial metadata:	Choose

LC-MS table

Peak / compound table:

Choose

Matching

Ion mode:

Tolerance (ppm):

imzML / ibd files (Cardinal) and Seurat or SpaMTP objects are converted on your computer with the MetaboAnalystR package, which writes the two standard tables for upload here:

library(MetaboAnalystR)
ReadImzML2Spatial("section.imzML", outPrefix = "section")      # Cardinal is required
ReadSeurat2Spatial("spamtp_object.rds", assay = "SPM", outPrefix = "section")
# writes section_intensity.csv and section_meta.csv

Both functions take a region column (roiCol); see the package documentation.