Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Preprocessing and feature extraction

SLAW

A scalable, containerized workflow for untargeted LC-MS preprocessing with automated parameter optimization, feature detection, alignment, gap filling, isotope/adduct grouping, and DDA MS/MS consolidation.

LC-MSUntargeted metabolomicsCommand lineOpen source
Access toolSuggest an update

Overview

SLAW is a containerized untargeted LC-MS processing workflow that wraps multiple peak-picking algorithms and optimizes processing parameters. It performs alignment, gap filling, ion grouping and consolidation of DDA tandem spectra for downstream analysis.

What can this tool do?

Peak or feature detectionRetention-time alignmentGap fillingAdduct and isotope groupingMS/MS processingContainer support

Common uses

  • Run reproducible preprocessing of large untargeted LC-MS studies.
  • Optimize peak picking, alignment, and gap-filling parameters using QC samples.
  • Produce feature tables and consolidated DDA MS/MS spectra for downstream analysis.

Scientific fit

Primary function

Preprocessing and feature extraction

Other functions

Workflow management and reproducibility, Quality control and filtering, Spectral processing and comparison

Analysis types

Untargeted metabolomics

MS level

MS1, MS/MS

Acquisition

Full-scan MS, Data-dependent acquisition (DDA)

Ion mobility

Not specified

Data compatibility

Inputs

Raw instrument data, Sample metadata

Outputs

Feature or peak table, Mass spectra

Input formats

mzML, CSV or TSV

Output formats

CSV or TSV, MGF

Scope and considerations

Designed for

  • Scalable untargeted LC-MS preprocessing from centroided mzML files.

Not designed for

  • DIA-MS2 deconvolution, direct processing of profile data or universal processing of mixed-polarity acquisitions.

Important requirements

  • Docker or a compatible Singularity workflow, centroided single-polarity mzML files and an edited parameters file; representative pooled QCs and an injection-order sample table are recommended.

Considerations

  • DIA-MS2 is skipped. If QCs are not specified, the workflow selects samples for optimization; the selected reference material affects optimized parameters.

Access and documentation

Primary accessDocumentation

GPL-2.0 code with a documented container distribution. Container execution and dependency versions should be recorded for reproducibility.

License: GPL-2.0

Evidence and review

Enveda intake rechecked against official README/documentation, repository access terms and primary publication metadata on 2026-10-27. Editorial source review only; no software execution or independent benchmarking. See docs/enveda-expansion-review-2026-10-27.md.

Core publications

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

  1. SLAW: A Scalable and Self-Optimizing Processing Workflow for Untargeted LC-MS. Analytical Chemistry (2021). doi:10.1021/acs.analchem.1c02687

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Entry history

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

  1. 2026-10-27 · First committed entry

    Add 27 source-reviewed tools from Enveda intake

    View change · Entry at this revision

Full GitHub history