├── .gitattributes ├── .github └── workflows │ ├── build_and_publish.yml │ └── test.yml ├── .gitignore ├── .readthedocs.yml ├── CITATION.cff ├── LICENSE ├── MANIFEST.in ├── README.rst ├── docs └── source │ ├── LICENSE.txt │ ├── _static │ └── css │ │ └── custom.css │ ├── api │ ├── ms2pip.constants.rst │ ├── ms2pip.correlation.rst │ ├── ms2pip.exceptions.rst │ ├── ms2pip.result.rst │ ├── ms2pip.rst │ ├── ms2pip.search-space.rst │ ├── ms2pip.spectrum-input.rst │ ├── ms2pip.spectrum-output.rst │ └── ms2pip.spectrum.rst │ ├── cli │ └── cli.rst │ ├── conf.py │ ├── index.rst │ ├── installation.rst │ ├── prediction-models.rst │ ├── usage.rst │ └── webserver-api.md ├── img ├── PGAQANPYSR-3-TMT.png ├── mirror-DVAQIFNNILR-2.png ├── mirror-DVAQIFNNILR-2.svg ├── ms2pip_logo_1000px.png └── ms2pip_logo_circle_color.svg ├── manuscripts ├── 2019 │ ├── MS2PIP_2019_manuscript_figures.html │ ├── MS2PIP_2019_manuscript_figures.ipynb │ └── style.css └── 2023 │ ├── MS2PIP_2023_manuscript_figures.html │ └── MS2PIP_2023_manuscript_figures.ipynb ├── ms2pip ├── __init__.py ├── __main__.py ├── _cython_modules │ ├── __init__.py │ ├── ms2pip_features_c.c │ ├── ms2pip_init_c.c │ ├── ms2pip_peaks_c.c │ └── ms2pip_pyx.pyx ├── _models_c │ ├── HCD-2019.h │ ├── HCD-2019 │ │ ├── model_20190107_HCD_train_B.c │ │ ├── model_20190107_HCD_train_B2.c │ │ ├── model_20190107_HCD_train_Y.c │ │ └── model_20190107_HCD_train_Y2.c │ ├── TMT.h │ └── TMT │ │ ├── model_20190107_TMT_train_B.c │ │ └── model_20190107_TMT_train_Y.c ├── _utils │ ├── cli.py │ ├── dlib.py │ ├── encoder.py │ ├── feature_names.py │ ├── ion_mobility.py │ ├── psm_input.py │ ├── retention_time.py │ └── xgb_models.py ├── constants.py ├── core.py ├── correlation.py ├── exceptions.py ├── plot.py ├── result.py ├── search_space.py ├── spectrum.py ├── spectrum_input.py └── spectrum_output.py ├── pyproject.toml ├── setup.py └── tests ├── test_core.py ├── test_data ├── config.toml ├── config.txt ├── crap_2015-01-30.fasta ├── easy_test.mgf ├── 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