---
title: Metabolomics inputs and parameters
description: >-
  Data formats, normalization methods, annotation databases, and filter options
  for all metabolomics tools.
tags:
  - metabolomics
  - inputs
---

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.

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