Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Data acquisition and instrument control

MS2Planner

Plan precursor acquisition schedules from LC-MS survey features.

LC-MSUntargeted metabolomicsCommand lineFree for academic use
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Overview

MS2Planner computes acquisition paths from feature masses, retention times and signals. Companion scripts translate these paths into instrument inclusion lists.

What can this tool do?

Blank and contaminant filtering

Common uses

  • Plan precursor acquisition schedules from LC-MS survey features.

Scientific fit

Primary function

Data acquisition and instrument control

Analysis types

Untargeted metabolomics

Data compatibility

Inputs

Feature or peak table

Outputs

Feature or peak table, Human-readable report

Input formats

Prepared survey-feature table; optional MS1 mzML or mzTab for curve mode

Output formats

Text or CSV acquisition paths and a planning log

Scope and considerations

Designed for

  • MS2Planner computes acquisition paths from feature masses, retention times and signals. Companion scripts translate these paths into instrument inclusion lists.

Not designed for

  • Real-time instrument control or retrospective metabolite identification.

Important requirements

  • Survey features with sample/background information and a configured Python environment.
  • Instrument-compatible inclusion-list export, repeat injections and reproducible chromatography.

Considerations

  • Timing and isolation parameters must match the instrument; planned coverage does not guarantee usable MS/MS spectra.

Access and documentation

Primary accessDocumentation

Official license permits academic/nonprofit noncommercial internal research, with restrictions on redistribution and derivatives. Not an unrestricted open-source license.

From tool to strategy

Strategies using MS2Planner

Iterative optimized MS/MS acquisitionMetabolite annotation · Bioinformatics

Evidence and review

Enveda intake candidate checked against official documentation, license information and primary publication on 2026-10-21. Editorial review only; no execution or independent benchmark.

Core publications

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

  1. MS2Planner: improved fragmentation spectra coverage in untargeted mass spectrometry by iterative optimized data acquisition. Bioinformatics (2021). doi:10.1093/bioinformatics/btab279

Related tools

AutonoMSSimilar function · Automate ion-mobility metabolomic fingerprinting on a configured RapidFire system.BAGOSimilar function · BAGO is an open-source bioinformatics tool designed for the systematic optimization of LC gradient using the Bayesian optimization framework. It is particularly useful for optimizing LC gradients in LC-MS-based metabolomics, lipidomics, and exposomics.LipidCreatorSimilar function · Design targeted lipidomics assays and predicted fragment libraries for PRM and MRM experiments.ViMMSSimilar function · ViMMS simulates LC-MS/MS acquisition at scan level so researchers can prototype and compare fragmentation strategies.

Entry history

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

  1. 2026-10-21 · First committed entry

    Add nine reviewed Enveda tools and reconcile intake coverage

    View change · Entry at this revision

Full GitHub history