# Maxquant Processor

> MaxQuant mass spectrometry skill for protein identification and quantification

- Skill: `a5c-ai/maxquant-processor` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/maxquant-processor`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/maxquant-processor/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/maxquant-processor

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# MaxQuant Processor Skill

## Purpose
Provide MaxQuant mass spectrometry analysis for protein identification and quantification.

## Capabilities
- Andromeda search engine execution
- Label-free quantification (LFQ)
- TMT/iTRAQ labeled quantification
- Match between runs
- FDR control and filtering
- PTM site localization

## Usage Guidelines
- Configure search parameters for experiment type
- Select appropriate quantification method
- Enable match between runs for improved quantification
- Apply FDR filtering at protein and peptide level
- Localize PTM sites accurately
- Document database and parameter versions

## Dependencies
- MaxQuant
- MSFragger
- Proteome Discoverer

## Process Integration
- Mass Spectrometry Proteomics Pipeline (ms-proteomics-pipeline)
- Multi-Omics Data Integration (multi-omics-integration)