Metabolomics inputs and parameters
Data formats, normalization methods, annotation databases, and filter options for all metabolomics tools.
You provide a URI to your data — a raw mzML/mzXML file, a feature table, or a list of metabolite identifiers, depending on the stage. Which stage you start from most affects the result, since each tool takes the output of the one before it.
Metabolomics inputs and parameters
Common data formats
The metabolomics tools are async Modal jobs (2-30 minutes depending on stage). Each stage takes a URI to your data rather than an inline table:
| Tool | Input | Format |
|---|---|---|
metabolomics_preprocess | raw_data_uri | Raw LC-MS file (mzML/mzXML) |
metabolomics_annotate | feature_table_uri | Feature table (output of metabolomics_preprocess) |
metabolomics_differential | feature_table_uri + metadata_file_uri | Feature/intensity table plus a sample metadata CSV with a group column |
metabolomics_pathway | metabolite_list | Array of metabolite identifiers (HMDB, KEGG, or PubChem) |
Metabolomics Preprocess parameters
| Parameter | Type | Required | Default | Description |
|---|---|---|---|---|
raw_data_uri | string | Yes | -- | URI of the raw LC-MS data file (mzML/mzXML) |
method | string | No | "xcms" | Preprocessing software: "xcms", "mzmine", or "openms" |
polarity | string | No | -- | Ionization polarity: "positive" or "negative" |
ppm_tolerance | number | No | 10 | Mass accuracy tolerance in ppm |
Metabolomics Annotate parameters
| Parameter | Type | Required | Default | Description |
|---|---|---|---|---|
feature_table_uri | string | Yes | -- | URI of the feature table (from metabolomics_preprocess) |
databases | string | No | "all" | Database to match against: "hmdb", "lipidmaps", "kegg", or "all" |
mass_tolerance_ppm | number | No | 5 | Mass tolerance for matching, in ppm |
adducts | string[] | No | -- | Adduct types to consider (e.g., ["[M+H]+", "[M+Na]+"]) |
Supported databases
| Database | Code | Content |
|---|---|---|
| HMDB | hmdb | Human metabolites, endogenous and exogenous |
| LipidMaps | lipidmaps | Lipid structures and classifications |
| KEGG | kegg | KEGG compound entries |
Common adduct types
| Ion Mode | Adducts |
|---|---|
| Positive | [M+H]+, [M+Na]+, [M+K]+, [M+NH4]+, [M+2H]2+ |
| Negative | [M-H]-, [M+FA-H]-, [M+Cl]-, [M-2H]2-, [M+HAc-H]- |
Metabolomics Differential parameters
| Parameter | Type | Required | Default | Description |
|---|---|---|---|---|
feature_table_uri | string | Yes | -- | URI of the feature/intensity table |
metadata_file_uri | string | Yes | -- | URI of sample metadata file (CSV with sample, condition columns) |
contrast | string | Yes | -- | Contrast to test (e.g., "treated_vs_control") |
method | string | No | "limma" | Statistical method: "limma", "ttest", or "wilcoxon" |
fdr_threshold | number | No | 0.05 | FDR threshold for significance |
Only a single two-group contrast is supported per run — there's no multi-group (ANOVA/Kruskal-Wallis) or paired-design option.
Metabolomics Pathway parameters
| Parameter | Type | Required | Default | Description |
|---|---|---|---|---|
metabolite_list | string[] | Yes | -- | List of metabolite identifiers (HMDB, KEGG, or PubChem IDs) |
organism | string | No | "hsa" | KEGG organism code: "hsa" (human) or "mmu" (mouse) — no other organisms are supported |
analysis_type | string | No | "enrichment" | "enrichment" (over-representation) or "topology"-based analysis |
id_type | string | No | "hmdb" | Identifier type provided in metabolite_list: "hmdb", "kegg", or "pubchem" |
Pathway enrichment is against KEGG metabolic pathways only — SMPDB and Reactome are not supported by this tool.
Read next
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Metabolomics FAQ
Why annotation reports only putative_match confidence, why differential analysis takes one two-group contrast and no ANOVA, and what impact_score measures.
Interpreting metabolomics outputs
Preprocessed feature tables, annotated metabolites, differential results, and pathway enrichment scores.