Proteomics Quantification

Example Queries

• "Quantify proteins using MaxQuant LFQ"
• "Run DIA-NN on these wiff files"

Output Structure

output_directory/
├── report.md
├── result.json
├── quantified.csv
├── figures/
│   └── normalization_boxplot.png
├── tables/
│   └── intensity_matrix.csv
└── reproducibility/
    ├── commands.sh
    ├── requirements.txt
    └── checksums.sha256

Safety

• Local-first: Strict offline processing without external upload.
• Disclaimer: Requires OmicsClaw reporting structures and disclaimers.
• Audit trail: Hyperparameters and operational flow states are logged fully.

Integration with Orchestrator

Trigger conditions:

• Automatically invoked dynamically based on tool metadata and user intent matching.

Chaining partners:

• peptide-id — Upstream sequence identification
• differential-abundance — Downstream statistical execution

Citations

• MaxQuant LFQ
• DIA-NN