Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Workflow management and reproducibility

TidyMass

Connect LC-MS processing, quality control, annotation and interpretation through an R package ecosystem.

LC-MSR packageOpen source
Access toolSuggest an update

Overview

TidyMass uses shared objects and conventions to connect analysis stages while retaining data and processing context. Individual modules can also be used separately.

What can this tool do?

Provenance tracking

Common uses

  • Build a consistent workflow from LC-MS data to interpretation.
  • Track processing across coordinated R packages.

Scientific fit

Primary function

Workflow management and reproducibility

Data compatibility

Inputs

Mass spectra, Feature or peak table, Sample metadata

Outputs

Feature or peak table, Compound list or annotations, Statistical results, Human-readable report

Input formats

Other, LC-MS files or TidyMass data objects

Output formats

Other, TidyMass analysis objects and reports

Scope and considerations

Designed for

  • Build a consistent workflow from LC-MS data to interpretation.

Not designed for

  • Eliminating the need to evaluate preprocessing choices and annotation evidence.

Important requirements

  • R, compatible TidyMass package versions and module-specific data resources.

Considerations

  • The ecosystem includes older and newer package documentation; keep a consistent set of versions and record database snapshots.

Access and documentation

Primary access

Open R ecosystem; inspect component and reference-data licenses.

Evidence and review

Documentation-based editorial review on 7 September 2026. Scope and limitations summarize the linked official sources; software execution and developer verification were not assessed.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. Shen X, Yan H, Wang C, et al. TidyMass an object-oriented reproducible analysis framework for LC-MS data. Nat Commun 13, 4365 (2022). doi:10.1038/s41467-022-32155-w

Related tools

metIDComplementary to · Annotate LC-MS features using accurate mass, retention time and tandem mass spectra in R.

Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-09-08 · Entry update

    Audit core publications across existing tools

    View change · Entry at this revision
  2. 2026-09-07 · First committed entry

    Add 50 documented metabolomics resources

    View change · Entry at this revision

Full GitHub history