MaxQuant Processor Skill

SkillDev tools

MaxQuant mass spectrometry skill for protein identification and quantification

Instructions available. Your AI can read the instructions. Execution depends on the setup they require.

Account requirements not reviewed. Check the skill instructions before use; ahel provides instructions and does not run this skill.

Add ahel to your AI once: Claude, ChatGPT, Cursor, Claude Code or Codex. Then ask it to use this.

Then ask your AI: use the MaxQuant Processor Skill skill

What this skill tells your AI

The instructions your AI receives, as published by a5c-ai/babysitter in library/specializations/domains/science/bioinformatics/skills/maxquant-processor/SKILL.md and read by ahel’s review.

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)

Signals

GitHub stars: 2k
Forks: 112
Last commit: Sep 2026

Advanced

Item type: skill
Key: maxquant-processor
Source: github.com/a5c-ai/babysitter

github.com/a5c-ai/babysitter