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ms-format-conversion

Convert vendor-specific mass spectrometry files to mzML and mzXML formats.

7|Updated Apr 5, 2026
Search Tags:#pyopenms#batch-conversion#msconvert#mzml#mzxml#vendor-format#centroiding
One-click install
npx skills add https://github.com/dailycafi/metabolism-skills --skill ms-format-conversion
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ms-format-conversion
Source: https://github.com/dailycafi/metabolism-skills/tree/main/skills/ms-data-processing/format-conversion
Command: npx skills add https://github.com/dailycafi/metabolism-skills --skill ms-format-conversion

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Mass spectrometry instruments produce proprietary vendor files that block downstream analysis and sharing; this Skill provides reliable, reproducible conversion to open formats (mzML, mzXML) and tools to validate converted data for metabolomics pipelines.

Core Features & Use Cases

  • Vendor-to-open conversion: msConvert (ProteoWizard) guidance and Docker usage to convert Thermo RAW, AB SCIEX WIFF, Agilent .d, Waters .raw, and Bruker formats to mzML or mzXML.
  • Preprocessing choices: Centroiding (vendor-native or algorithmic), encoding precision selection (32/64-bit), and selective filtering (msLevel, rt window, m/z window).
  • Batch processing & validation: Example bash and Python batch scripts, pyopenms-based interconversion and validation routines to check centroid/profile status, spectrum counts, and RT ranges.

Quick Start

Convert all Thermo RAW files in /data/raw to centroided mzML files in /data/mzml using msConvert with vendor peak-picking (or run the provided Docker msConvert image on non-Windows systems).

Frequently Asked Questions about ms-format-conversion

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I convert Thermo RAW files to mzML using msConvert?▼

Convert Thermo RAW files to mzML using msConvert by running the ProteoWizard command-line tool or its Docker-wrapped image on non-Windows systems, specifying output format and optional vendor peak-picking for centroiding.

What's the best way to batch convert vendor mass-spec files to open formats?▼

Batch convert vendor mass-spec files to open formats using provided bash and Python batch scripts that process Thermo RAW, AB SCIEX WIFF, and Agilent .d files in bulk to mzML or mzXML outputs.

Does msConvert work with Bruker and Waters .raw files for metabolomics workflows?▼

msConvert supports Bruker formats and Waters .raw files for metabolomics workflows through Docker-wrapped vendor support, enabling conversion to open formats like mzML and mzXML.

Can I validate centroiding status and encoding precision after converting to mzML?▼

Validate centroiding status and encoding precision after converting to mzML using pyopenms-based validation routines that check centroid/profile status, spectrum counts, and RT ranges.

How do I convert between mzML and mzXML formats using pyopenms?▼

Convert between mzML and mzXML formats using pyopenms-based interconversion routines that handle format transformation while preserving spectrum data and metadata for metabolomics pipelines.

When do I need to choose vendor-native centroiding vs algorithmic centroiding for mass-spec conversion?▼

Choose vendor-native centroiding during msConvert conversion for instrument-specific peak-picking accuracy, or use algorithmic centroiding when vendor libraries are unavailable or cross-platform consistency is needed.

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