├── .gitattributes ├── .github └── workflows │ ├── docs.yml │ ├── imspy-connector-publish.yml │ ├── imspy-publish.yml │ └── rust.yml ├── .gitignore ├── Cargo.toml ├── IMSJL ├── Manifest.toml ├── Project.toml ├── README.md └── src │ ├── Data.jl │ ├── DataHandle.jl │ ├── IMSJL.jl │ ├── RustCAPI.jl │ ├── Slice.jl │ └── Spectrum.jl ├── LICENSE ├── README.md ├── imsjl_connector ├── Cargo.toml ├── README.md └── src │ ├── frame.rs │ ├── handle.rs │ └── lib.rs ├── imspy ├── README.md ├── docs │ └── source │ │ ├── conf.py │ │ ├── imspy.algorithm.ccs.rst │ │ ├── imspy.algorithm.intensity.rst │ │ ├── imspy.algorithm.ionization.rst │ │ ├── imspy.algorithm.pretrained.rst │ │ ├── imspy.algorithm.rst │ │ ├── imspy.algorithm.rt.rst │ │ ├── imspy.chemistry.rst │ │ ├── imspy.data.rst │ │ ├── imspy.rst │ │ ├── imspy.simulation.rst │ │ ├── imspy.simulation.timsim.jobs.rst │ │ ├── imspy.simulation.timsim.rst │ │ ├── imspy.timstof.dbsearch.rst │ │ ├── imspy.timstof.rst │ │ ├── imspy.utility.rst │ │ ├── imspy.vis.rst │ │ ├── index.rst │ │ └── modules.rst ├── examples │ ├── imspy_dda.ipynb │ ├── timsim-configs │ │ ├── TIMSIM-DDA-HeLa-G15-10K-from-template.toml │ │ ├── TIMSIM-DDA-HeLa-G15-10K.toml │ │ ├── TIMSIM-DIA-HeLa-G15-10K-from-template.toml │ │ └── TIMSIM-DIA-HeLa-G15-10K.toml │ ├── timsimDDA.ipynb │ └── timsimDIA.ipynb ├── imspy │ ├── __init__.py │ ├── algorithm │ │ ├── __init__.py │ │ ├── ccs │ │ │ ├── __init__.py │ │ │ ├── model_std.py │ │ │ ├── predictors.py │ │ │ └── utility.py │ │ ├── hashing.py │ │ ├── intensity │ │ │ ├── __init__.py │ │ │ ├── predictors.py │ │ │ └── utility.py │ │ ├── ionization │ │ │ ├── __init__.py │ │ │ └── predictors.py │ │ ├── koina_models │ │ │ ├── __init__.py │ │ │ ├── access_models.py │ │ │ └── input_filters.py │ │ ├── mixture.py │ │ ├── pretrained │ │ │ ├── __init__.py │ │ │ ├── ccs │ │ │ │ ├── ionmob-24-05-2024.keras │ │ │ │ └── ionmob-std-20-01-2025.keras │ │ │ ├── charge │ │ │ │ └── chargepred-26-05-2024.keras │ │ │ ├── intensity │ │ │ │ └── Prosit2023TimsTOFPredictor │ │ │ │ │ ├── saved_model.pb │ │ │ │ │ └── variables │ │ │ │ │ ├── variables.data-00000-of-00001 │ │ │ │ │ └── variables.index │ │ │ ├── rt │ │ │ │ └── rtpred-26-05-2024.keras │ │ │ ├── tokenizer-ptm.json │ │ │ └── unimod-vocab.json │ │ ├── rescoring.py │ │ ├── rt │ │ │ ├── __init__.py │ │ │ └── predictors.py │ │ ├── utilities │ │ │ ├── hf_tokenizers.py │ │ │ └── tokenizers.py │ │ └── utility.py │ ├── chemistry │ │ ├── __init__.py │ │ ├── amino_acids.py │ │ ├── constants.py │ │ ├── elements.py │ │ ├── mobility.py │ │ ├── sum_formula.py │ │ ├── unimod.py │ │ └── utility.py │ ├── data │ │ ├── __init__.py │ │ ├── peptide.py │ │ └── spectrum.py │ ├── simulation │ │ ├── __init__.py │ │ ├── acquisition.py │ │ ├── annotation.py │ │ ├── experiment.py │ │ ├── feature.py │ │ ├── handle.py │ │ ├── isotopes.py │ │ ├── noise.py │ │ ├── proteome.py │ │ ├── resources │ │ │ ├── .DS_Store │ │ │ ├── NATIVE.d │ │ │ │ ├── analysis.tdf │ │ │ │ └── analysis.tdf_bin │ │ │ ├── configs │ │ │ │ ├── dia_ms_ms_windows.csv │ │ │ │ ├── diapasef.toml │ │ │ │ ├── dilution_factors.csv │ │ │ │ ├── midia_ms_ms_windows.csv │ │ │ │ ├── midiapasef.toml │ │ │ │ ├── slice_ms_ms_windows.csv │ │ │ │ ├── slicepasef.toml │ │ │ │ ├── synchro_ms_ms_windows.csv │ │ │ │ └── synchropasef.toml │ │ │ ├── docs │ │ │ │ └── documentation.md │ │ │ └── icons │ │ │ │ ├── info_icon.png │ │ │ │ ├── logo_2.png │ │ │ │ └── rustims_logo.png │ │ ├── tdf.py │ │ ├── timsim │ │ │ ├── __init__.py │ │ │ ├── configs │ │ │ │ ├── config.toml │ │ │ │ └── modifications.toml │ │ │ ├── jobs │ │ │ │ ├── __init__.py │ │ │ │ ├── add_noise_from_real_data.py │ │ │ │ ├── assemble_frames.py │ │ │ │ ├── build_acquisition.py │ │ │ │ ├── dda_selection_scheme.py │ │ │ │ ├── digest_fasta.py │ │ │ │ ├── simulate_charge_states.py │ │ │ │ ├── simulate_fragment_intensities.py │ │ │ │ ├── simulate_frame_distributions_emg.py │ │ │ │ ├── simulate_ion_mobilities.py │ │ │ │ ├── simulate_ion_mobilities_and_variance.py │ │ │ │ ├── simulate_occurrences.py │ │ │ │ ├── simulate_peptides.py │ │ │ │ ├── simulate_phosphorylation.py │ │ │ │ ├── simulate_precursor_spectra.py │ │ │ │ ├── simulate_proteins.py │ │ │ │ ├── simulate_retention_time.py │ │ │ │ ├── simulate_scan_distributions_with_variance.py │ │ │ │ └── utility.py │ │ │ ├── simulator.py │ │ │ └── timsim_gui.py │ │ └── utility.py │ ├── timstof │ │ ├── __init__.py │ │ ├── collision.py │ │ ├── data.py │ │ ├── dbsearch │ │ │ ├── __init__.py │ │ │ ├── configs │ │ │ │ ├── config_ccs.toml │ │ │ │ ├── config_hla.toml │ │ │ │ └── config_tryptic.toml │ │ │ ├── imspy_ccs.py │ │ │ ├── imspy_dda.py │ │ │ ├── imspy_rescore_sage.py │ │ │ ├── mgf.py │ │ │ ├── sage_output_utility.py │ │ │ └── utility.py │ │ ├── dda.py │ │ ├── dia.py │ │ ├── frame.py │ │ ├── quadrupole.py │ │ └── slice.py │ ├── utility │ │ ├── __init__.py │ │ ├── sequence.py │ │ └── utilities.py │ └── vis │ │ ├── __init__.py │ │ ├── frame_rendering.py │ │ └── pointcloud.py ├── pyproject.toml └── tests │ ├── __init__.py │ └── test_s_curve.py ├── imspy_connector ├── Cargo.toml ├── README.md ├── pyproject.toml └── src │ ├── lib.rs │ ├── py_amino_acids.rs │ ├── py_annotation.rs │ ├── py_chemistry.rs │ ├── py_constants.rs │ ├── py_dataset.rs │ ├── py_dda.rs │ ├── py_dia.rs │ ├── py_elements.rs │ ├── py_ml_utility.rs │ ├── py_mz_spectrum.rs │ ├── py_peptide.rs │ ├── py_quadrupole.rs │ ├── py_simulation.rs │ ├── py_sumformula.rs │ ├── py_tims_frame.rs │ ├── py_tims_slice.rs │ ├── py_unimod.rs │ └── py_utility.rs ├── mscore ├── Cargo.toml ├── README.md └── src │ ├── algorithm │ ├── isotope.rs │ ├── mod.rs │ ├── peptide.rs │ └── utility.rs │ ├── chemistry │ ├── amino_acid.rs │ ├── constants.rs │ ├── elements.rs │ ├── formulas.rs │ ├── mod.rs │ ├── sum_formula.rs │ ├── unimod.rs │ └── utility.rs │ ├── data │ ├── mod.rs │ ├── peptide.rs │ ├── smiles.rs │ └── spectrum.rs │ ├── lib.rs │ ├── main.rs │ ├── simulation │ ├── annotation.rs │ ├── mod.rs │ └── simulation.rs │ └── timstof │ ├── collision.rs │ ├── frame.rs │ ├── mod.rs │ ├── quadrupole.rs │ ├── slice.rs │ ├── spectrum.rs │ └── vec_utils.rs ├── rustdf ├── Cargo.toml ├── README.md └── src │ ├── data │ ├── acquisition.rs │ ├── dataset.rs │ ├── dda.rs │ ├── dia.rs │ ├── handle.rs │ ├── meta.rs │ ├── mod.rs │ ├── raw.rs │ └── utility.rs │ ├── lib.rs │ ├── main.rs │ └── sim │ ├── containers.rs │ ├── dda.rs │ ├── dia.rs │ ├── handle.rs │ ├── mod.rs │ ├── precursor.rs │ └── utility.rs ├── rustims_layout.png ├── rustims_logo.png └── rustms ├── .DS_Store ├── .idea ├── .gitignore ├── modules.xml ├── rustms.iml └── vcs.xml ├── Cargo.toml └── src ├── algorithm ├── isotope.rs ├── mod.rs └── peptide.rs ├── chemistry ├── constants.rs ├── element.rs ├── formula.rs ├── mod.rs ├── sum_formula.rs ├── unimod.rs └── utility.rs ├── lib.rs ├── ms ├── mod.rs └── spectrum.rs └── proteomics ├── amino_acid.rs ├── mod.rs └── peptide.rs /.gitattributes: -------------------------------------------------------------------------------- 1 | *.ipynb 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