├── .gitattributes ├── .gitignore ├── LICENSE ├── README.md ├── data ├── models │ ├── charge2 │ │ └── epoch_035.hdf5 │ ├── charge3 │ │ └── epoch_034.hdf5 │ ├── detectability │ │ └── epoch_004.hdf5 │ └── irt │ │ └── epoch_082.hdf5 └── peptides │ ├── Pan_human.peptide.csv │ ├── Pan_human_charge2.peptide.csv │ └── Pan_human_charge3.peptide.csv ├── docs ├── predict_detectability.md ├── predict_msms_irt.md ├── train_detectability.md └── train_msms_irt.md ├── misc └── SpectroMine_Report_Schema │ ├── FragmentReport.rs │ ├── PeptideReport.rs │ └── ProteinReport.rs └── src ├── assay ├── __init__.py ├── assay.py ├── assay2table.py ├── combine.py ├── consensus.py ├── modseq.py ├── rtcalibration.py ├── similarity.py ├── table2assay.py └── values.py ├── build_assays_from_prediction.py ├── common ├── __init__.py ├── options.py ├── preprocessing.py ├── split.py └── training.py ├── concat_text_libraries.py ├── convert_assays_to_Spectronaut_library.py ├── convert_assays_to_ions.py ├── digest_proteins.py ├── extract_detect_from_MaxQuant.py ├── extract_detect_from_SpectroMine.py ├── extract_im_from_MaxQuant.py ├── extract_im_from_SpectroMine.py ├── extract_ms2_from_MaxQuant.py ├── extract_ms2_from_SpectroMine.py ├── extract_rt_from_MaxQuant.py ├── extract_rt_from_SpectroMine.py ├── filter_assays.py ├── filter_peptide_by_detectability.py ├── formatting ├── generic │ ├── __init__.py │ ├── assay2ions.py │ ├── detect.py │ ├── ions2assay.py │ ├── mod.py │ └── table.py ├── maxquant │ ├── __assay.py │ ├── __init__.py │ ├── assay.py │ ├── mod.py │ └── table.py └── spectronaut │ ├── __init__.py │ ├── assay.py │ ├── mod.py │ └── table.py ├── pepdetect ├── __init__.py ├── hardnegative.py ├── modeling.py ├── options.py ├── predicting.py ├── preprocessing.py └── training.py ├── pepim └── __init__.py ├── pepmass ├── __init__.py ├── modinfo.py ├── modmass.py └── pepmass.py ├── pepms2 ├── __init__.py ├── modeling.py ├── options.py ├── predicting.py ├── preprocessing.py └── 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