CITATION.cff
LICENSE
MANIFEST.in
PRIVACY.md
README.md
manifest.json
mkdocs.yml
pyproject.toml
docs/index.md
docs/publishing.md
docs/reference.md
docs/prompt_examples/00_overview.md
docs/prompt_examples/01_table_inspection.md
docs/prompt_examples/02_spectrum_level.md
docs/prompt_examples/03_batch_prediction_and_scoring.md
docs/prompt_examples/04_dataset_aggregation.md
docs/prompt_examples/05_sdrf_and_metadata.md
docs/prompt_examples/06_conversion_and_export.md
docs/prompt_examples/07_rendering_and_dashboards.md
docs/prompt_examples/08_troubleshooting.md
docs/releases/v0.1.1.md
docs/releases/v0.1.2.md
docs/releases/v0.1.3.md
docs/releases/v0.1.4.md
docs/releases/v0.1.5.md
docs/releases/v0.1.6.md
docs/releases/v0.1.7.md
docs/releases/v0.1.8.md
src/proteomics_mcp/__init__.py
src/proteomics_mcp/cli.py
src/proteomics_mcp/config.py
src/proteomics_mcp/server.py
src/proteomics_mcp.egg-info/PKG-INFO
src/proteomics_mcp.egg-info/SOURCES.txt
src/proteomics_mcp.egg-info/dependency_links.txt
src/proteomics_mcp.egg-info/entry_points.txt
src/proteomics_mcp.egg-info/requires.txt
src/proteomics_mcp.egg-info/top_level.txt
src/proteomics_mcp/adapters/__init__.py
src/proteomics_mcp/adapters/casanovo.py
src/proteomics_mcp/adapters/fragpipe.py
src/proteomics_mcp/adapters/generic.py
src/proteomics_mcp/adapters/instanovo.py
src/proteomics_mcp/adapters/maxquant.py
src/proteomics_mcp/adapters/modifications.py
src/proteomics_mcp/adapters/proteome_discoverer.py
src/proteomics_mcp/adapters/table_io.py
src/proteomics_mcp/core/__init__.py
src/proteomics_mcp/core/acquisition.py
src/proteomics_mcp/core/annotation.py
src/proteomics_mcp/core/dataset.py
src/proteomics_mcp/core/instanovo_export.py
src/proteomics_mcp/core/ion_annotation.py
src/proteomics_mcp/core/metrics.py
src/proteomics_mcp/core/scoring.py
src/proteomics_mcp/core/sdrf.py
src/proteomics_mcp/core/spectrum_loader.py
src/proteomics_mcp/core/visualization.py
src/proteomics_mcp/models/__init__.py
src/proteomics_mcp/models/schemas.py
src/proteomics_mcp/predictors/__init__.py
src/proteomics_mcp/predictors/koina.py
src/proteomics_mcp/predictors/mock.py
src/proteomics_mcp/predictors/ms2pip.py
src/proteomics_mcp/resources/__init__.py
src/proteomics_mcp/resources/docs.py
src/proteomics_mcp/tools/__init__.py
src/proteomics_mcp/tools/workflows.py
tests/test_annotation.py
tests/test_casanovo_adapter.py
tests/test_cli_mcp_imports.py
tests/test_config_and_resources.py
tests/test_dataset.py
tests/test_fragpipe_adapter.py
tests/test_generic_adapter.py
tests/test_instanovo_adapter.py
tests/test_instanovo_export.py
tests/test_koina_predictor.py
tests/test_maxquant_adapter.py
tests/test_prediction_and_visualization.py
tests/test_proteome_discoverer_adapter.py
tests/test_release_metadata.py
tests/test_score_candidates_tool.py
tests/test_scoring.py
tests/test_sdrf.py
tests/test_spectrum_loader.py