Spatial Metabolomics Feature Annotation

Spatial Metabolomics Feature Annotation

Summary

Assign metabolite identities to mass-to-charge (m/z) features in spatial metabolomics datasets by matching observed m/z values against a reference database (e.g., LipidMaps, HMDB) within a specified mass error tolerance and adduct assumption. This skill enables interpretation of spatial MS imaging data by linking ion signals to known chemical structures.

When to use

Your spatial metabolomics dataset contains raw m/z features (e.g., from MALDI-MS imaging or LC-MS/MS) without metabolite annotations, and you have selected a reference database and adduct type appropriate for your ionization mode and biological sample. Apply this skill when you need to convert m/z-only feature matrices into interpretable metabolite annotations for downstream statistical analysis, visualization, or pathway inference.

When NOT to use

• Your reference database is incomplete or poorly curated for your sample type (e.g., plant metabolites when only animal lipids are in the database).
• You have not validated mass calibration on your MS instrument; systematic calibration drift will cause ppm-based matches to fail.
• You are working with small-molecule metabolites but only have lipid-focused databases available.

Inputs

• SpaMTP Seurat object with spatial metabolomics intensity matrix
• Reference metabolite database (LipidMaps_db or HMDB_db in RDS format)
• m/z feature list from spatial MS imaging experiment
• Mass calibration and ionization polarity metadata

Outputs

• Annotated SpaMTP Seurat object with metabolite identities in feature metadata
• Annotation summary table (m/z, metabolite name, chemical formula, adduct type)
• Count and proportion of successfully annotated features
• ppm error distribution for matched annotations

How to apply

Load your spatial metabolomics dataset (e.g., as a SpaMTP Seurat object from a CSV intensity matrix) and invoke the AnnotateSM function with three key parameters: the reference database (db = Lipidmaps_db or HMDB_db), the mass error tolerance in parts per million (ppm_error, typically 15 ppm for high-resolution MS), and the expected adduct type (adducts = 'M+K' for positive potassium adducts, or 'M+H' for protons). The function matches each observed m/z to the nearest database entry within the specified ppm window, returning a Seurat object with annotations stored in the feature metadata slot. Verify success by extracting the count of successfully annotated features and inspecting a summary table of m/z values and their corresponding metabolite identities; low annotation rates may indicate insufficient database coverage, incorrect adduct selection, or mass calibration issues.

Related tools

• SpaMTP (R package providing AnnotateSM function for m/z-to-metabolite matching in spatial metabolomics Seurat objects) — https://github.com/GenomicsMachineLearning/SpaMTP
• Seurat (Data container class (Seurat object) that stores intensity matrix, feature metadata, and annotation results)
• Cardinal (Underlying spatial mass spectrometry analysis framework inherited by SpaMTP for m/z feature handling) — https://github.com/Vitek-Lab/Cardinal3-vignettes
• R (Execution environment for AnnotateSM function calls and downstream metadata manipulation)

Examples

bladder_annotated <- AnnotateSM(bladder, db = Lipidmaps_db, ppm_error = 15, adducts = "M+K", polarity = "positive")

Evaluation signals

• Non-zero count of annotated features; typical thresholds depend on database coverage but >50% annotation success is expected for well-matched lipidomes.
• ppm error distribution is centered near zero and falls within specified tolerance window (e.g., 68–95% of matches within ±7.5 ppm for ppm_error=15).
• Annotated metabolites match known composition of the biological sample (e.g., lipid classes appropriate to bladder urine, liver tissue).
• Feature metadata slot contains non-NA metabolite names, chemical formulas, and adduct annotations for all matched m/z values.
• Reproducibility check: re-running AnnotateSM on the same object with identical parameters yields identical annotation results.

Limitations

• Annotation accuracy depends critically on reference database completeness and curation; underrepresented metabolite classes will show low match rates.
• Assumes a single dominant adduct per m/z feature; multiply charged or mixed-adduct ions may be misannotated or missed.
• ppm error tolerance is fixed globally across all m/z features; low m/z values and high m/z values have different absolute mass error ranges, which may cause over- or under-matching.
• No built-in filtering for biological plausibility; chemically valid matches that are absent in the sample will still be reported.
• The article indicates two planned refinement methods—'Pseudo MS/MS-Based Refinement' and 'Refinement with Paired Targeted Metabolic Data'—are marked 'To come!', implying current annotation lacks MS/MS confirmation and cannot yet be validated against targeted metabolomics.

Evidence

• [methods] Run AnnotateSM function with parameters: db=Lipidmaps_db, ppm_error=15, adducts='M+K', polarity='positive': "Run AnnotateSM function with parameters: db=Lipidmaps_db, ppm_error=15, adducts='M+K', polarity='positive'"
• [methods] Extract the count of successfully annotated m/z features from the returned SpaMTP object and verify that annotations are stored in the feature metadata slot: "Extract the count of successfully annotated m/z features from the returned SpaMTP object and verify that annotations are stored in the feature metadata slot"
• [methods] Generate a summary table showing the m/z values and their corresponding metabolite annotations from the Lipidmaps_db: "Generate a summary table showing the m/z values and their corresponding metabolite annotations from the Lipidmaps_db"
• [readme] m/z metabolite annotation, (2) various downstream statistical analysis including differential metabolite expression and pathway analysis: "(1) mass-to-charge ratio (m/z) metabolite annotation, (2) various downstream statistical analysis"
• [methods] ## 3) Pseudo MS/MS-Based Refinement

To come!

• Refinement with Paired Targeted Metabolic Data section marked as 'To come!': "## 3) Pseudo MS/MS-Based Refinement

To come!"