ms-format-conversion
CommunityConvert vendor mass-spec files to open formats
Authordailycafi
Version1.0.0
Installs0
System Documentation
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).
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: ms-format-conversion Download link: https://github.com/dailycafi/metabolism-skills/archive/main.zip#ms-format-conversion Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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