file_io

PyOpenMS supports multiple mass spectrometry file formats for reading and writing. This guide covers file handling strategies and format-specific operations.

Skills
Scientific
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A skill that teaches Claude Code to do scientific tasks well. It is packaged knowledge the model uses whenever it is relevant.

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Install (Claude Code)

mkdir -p .claude/skills/file-io && curl -fsSL https://doutorai.pt/data/lib/skills__file-io.md -o .claude/skills/file-io/SKILL.md

Paste this command into the terminal, in your project folder, and the component installs automatically.

Content

# File I/O and Data Formats

## Overview

PyOpenMS supports multiple mass spectrometry file formats for reading and writing. This guide covers file handling strategies and format-specific operations.

## Supported Formats

### Spectrum Data Formats

- **mzML**: Standard XML-based format for mass spectrometry data
- **mzXML**: Earlier XML-based format
- **mzData**: XML format (deprecated but supported)

### Identification Formats

- **idXML**: OpenMS native identification format
- **mzIdentML**: Standard XML format for identification data
- **pepXML**: X! Tandem format
- **protXML**: Protein id

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