Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Data conversion and import

msconvert

Convert mass-spectrometry files into open formats for downstream analysis.

Multiple analytical platformsCommand lineDesktop graphical interfaceOpen source
Access toolSuggest an update

Overview

Part of ProteoWizard, msconvert provides command-line conversion and optional spectral filters. MSConvertGUI offers a graphical route through the same ecosystem.

What can this tool do?

Provenance tracking

Common uses

  • Prepare mzML files for MZmine, XCMS or other compatible processors.
  • Automate conversion across an acquisition batch.

Scientific fit

Primary function

Data conversion and import

Data compatibility

Inputs

Raw instrument data

Outputs

Mass spectra

Input formats

Vendor raw format, mzML, mzXML

Output formats

mzML, mzXML, MGF

Scope and considerations

Designed for

  • Prepare mzML files for MZmine, XCMS or other compatible processors.

Not designed for

  • Producing an aligned metabolite abundance table by conversion alone.

Important requirements

  • A supported reader for the instrument format; some vendor readers require Windows.

Considerations

  • Record centroiding and filtering choices, and retain original files: conversion settings can alter downstream results.

Access and documentation

Primary access

ProteoWizard is open source; vendor reader components have their own distribution and platform terms.

From tool to strategy

Strategies using msconvert

Iterative exclusion-list MS/MS acquisitionMetabolite annotation · Journal of the American Society for Mass Spectrometry

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. Kessner D, Chambers M, Burke R, et al. ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24, 2534-2536 (2008). doi:10.1093/bioinformatics/btn323

    Official ProteoWizard platform citation covering msconvert; not a standalone msconvert paper.

Related tools

MZmineComplementary to · A modular mass-spectrometry environment for raw-data import, feature detection/alignment, multimodal LC/IMS/GC/MSI processing, molecular networking, annotation, lipid analysis, visualization, normalization, statistics, and downstream exports.xcmsComplementary to · An open-source Bioconductor package for chromatographic mass spectrometry data preprocessing, feature detection, alignment, grouping, and visualization.IDBacComplementary to · Web-based MALDI-TOF mass spectrometry platform and community knowledgebase for bacterial identification, culture-collection analysis, and comparison of specialized-metabolite profiles.

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