📥 Proteomics Data Import

Import and convert proteomics data from various formats (MaxQuant, DIA-NN, Spectronaut output) into standardised tables.

CLI Reference

python omicsclaw.py run proteomics-data-import --demo
python omicsclaw.py run proteomics-data-import --input <proteinGroups.txt> --output <dir>

Why This Exists

• Without it: Each search engine (MaxQuant, DIA-NN, FragPipe) outputs completely different table structures
• With it: Raw vendor and search outputs are unified into a standard long-format intensity matrix
• Why OmicsClaw: Provides a single universal ingestion point before statistical testing

Workflow

1. Calculate: Parse header shapes and metadata dictionaries.
2. Execute: Melt and reshape raw search engine text files.
3. Assess: Perform basic missing value logic checks.
4. Generate: Output normalized H5AD or standard CSV objects.
5. Report: Tabulate key protein/peptide groups parsed.

Example Queries

• "Convert my MaxQuant proteinGroups.txt into a standard format"
• "Import DIA-NN evidence tables"

Output Structure

output_directory/
├── report.md
├── result.json
├── processed.csv
├── figures/
│   └── intensity_distribution.png
├── tables/
│   └── import_summary.csv
└── reproducibility/
    ├── commands.sh
    ├── environment.yml
    └── 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:

• ms-qc

  — Downstream quality profiling

• differential-abundance

  — Downstream statistical execution