Index

A

accumulated_intensity_cdf_numba() (in module imspy.simulation.utility) acquisition_mode (imspy.timstof.data.TimsDataset property) acquisition_mode_numeric (imspy.timstof.data.TimsDataset property) AcquisitionMode (class in imspy.timstof.data) add_mz_noise_normal() (imspy.data.spectrum.MzSpectrum method) add_mz_noise_uniform() (imspy.data.spectrum.MzSpectrum method) add_real_data_noise_to_frames() (in module imspy.simulation.timsim.jobs.add_noise_from_real_data) add_uniform_noise() (in module imspy.simulation.utility) all_transmitted() (imspy.timstof.quadrupole.TimsTofQuadrupoleDIA method) amino_acid_count (imspy.data.peptide.PeptideSequence property) annotations (imspy.simulation.annotation.MzSpectrumAnnotated property) (imspy.simulation.annotation.TimsFrameAnnotated property)

any_transmitted() (imspy.timstof.quadrupole.TimsTofQuadrupoleDIA method) append_table() (imspy.simulation.experiment.SyntheticExperimentDataHandle method) apply() (imspy.timstof.dbsearch.sage_output_utility.PatternReplacer method) apply_transmission() (imspy.timstof.quadrupole.TimsTofQuadrupoleDIA method) assemble_frames() (in module imspy.simulation.timsim.jobs.assemble_frames) associate_fragment_ion_series_with_prosit_intensities() (imspy.data.peptide.PeptideSequence method) atomic_composition (imspy.data.peptide.PeptideIon property) (imspy.data.peptide.PeptideSequence property) atomic_composition() (imspy.data.peptide.PeptideProductIon method) average_cycle_length (imspy.timstof.data.TimsDataset property) average_mz (imspy.timstof.dda.PrecursorDDA property)

B

baseline_noise() (in module imspy.simulation.noise) baseline_shot_noise() (in module imspy.simulation.noise) baseline_shot_noise_window() (in module imspy.simulation.noise) beta_score() (in module imspy.algorithm.intensity.utility) BinomialChargeStateDistributionModel (class in imspy.algorithm.ionization.predictors) break_into_equal_size_sets() (in module imspy.timstof.dbsearch.sage_output_utility) build() (imspy.algorithm.ccs.predictors.GRUCCSPredictor method) (imspy.algorithm.ccs.predictors.SquareRootProjectionLayer method) (imspy.algorithm.ionization.predictors.GRUChargeStatePredictor method) (imspy.algorithm.rt.predictors.GRURetentionTimePredictor method)

build_acquisition() (in module imspy.simulation.timsim.jobs.build_acquisition) build_frame() (imspy.simulation.experiment.TimsTofSyntheticFrameBuilderDIA method) build_frame_annotated() (imspy.simulation.experiment.TimsTofSyntheticFrameBuilderDIA method) build_frame_meta_row() (imspy.simulation.tdf.TDFWriter method) build_frames() (imspy.simulation.experiment.TimsTofSyntheticFrameBuilderDIA method) build_frames_annotated() (imspy.simulation.experiment.TimsTofSyntheticFrameBuilderDIA method) build_precursor_frame() (imspy.simulation.experiment.TimsTofSyntheticPrecursorFrameBuilder method) build_precursor_frame_annotated() (imspy.simulation.experiment.TimsTofSyntheticPrecursorFrameBuilder method) build_precursor_frames() (imspy.simulation.experiment.TimsTofSyntheticPrecursorFrameBuilder method) build_precursor_frames_annotated() (imspy.simulation.experiment.TimsTofSyntheticPrecursorFrameBuilder method) bytes_to_indexed_values() (imspy.timstof.data.TimsDataset method)

C

c_ions (imspy.data.peptide.PeptideProductIonSeries property) calculate_b_y_fragment_mz() (in module imspy.simulation.utility) calculate_b_y_ion_series_ims() (in module imspy.simulation.utility) calculate_bounds_numba() (in module imspy.simulation.utility) calculate_frame_types() (imspy.simulation.acquisition.TimsTofAcquisitionBuilder method) (imspy.simulation.acquisition.TimsTofAcquisitionBuilderDDA method) (imspy.simulation.acquisition.TimsTofAcquisitionBuilderDIA method) calculate_isotopic_product_ion_spectrum_annotated() (imspy.data.peptide.PeptideSequence method) calculate_isotopic_spectrum() (imspy.data.peptide.PeptideIon method) calculate_isotopic_spectrum_annotated() (imspy.data.peptide.PeptideIon method) calculate_keys() (imspy.algorithm.hashing.CosimHasher method) calculate_mobility_spacing() (in module imspy.simulation.utility) calculate_mono_isotopic_product_ion_spectrum() (imspy.data.peptide.PeptideSequence method) calculate_mono_isotopic_product_ion_spectrum_annotated() (imspy.data.peptide.PeptideSequence method) calculate_mz() (in module imspy.chemistry.utility) calculate_number_frames() (in module imspy.simulation.utility) calculate_product_ion_series() (imspy.data.peptide.PeptideSequence method) calculate_transmission_dependent_fragment_ion_isotope_distribution() (in module imspy.chemistry.utility) call() (imspy.algorithm.ccs.predictors.GRUCCSPredictor method) (imspy.algorithm.ccs.predictors.SquareRootProjectionLayer method) (imspy.algorithm.ionization.predictors.GRUChargeStatePredictor method) (imspy.algorithm.rt.predictors.GRURetentionTimePredictor method) ccs_to_one_over_k0() (in module imspy.chemistry.mobility) ccs_to_one_over_k0_par() (in module imspy.chemistry.mobility) charge (imspy.data.peptide.PeptideIon property) (imspy.data.peptide.PeptideProductIon property) (imspy.data.peptide.PeptideProductIonSeries property) (imspy.timstof.dda.PrecursorDDA property)

charge_state (imspy.simulation.annotation.SignalAttributes property) charge_state_distribution_from_sequence_rust() (in module imspy.algorithm.ionization.predictors) charge_state_distributions_from_sequences_rust() (in module imspy.algorithm.ionization.predictors) charge_states_first_only (imspy.simulation.annotation.TimsFrameAnnotated property) check_memory() (in module imspy.timstof.dbsearch.utility) check_path() (in module imspy.simulation.timsim.jobs.utility) close() (imspy.simulation.experiment.SyntheticExperimentDataHandle method) collision_energy (imspy.timstof.dda.FragmentDDA property) (imspy.timstof.dda.PrecursorDDA property) compress_frame() (imspy.simulation.tdf.TDFWriter method) compress_frames() (imspy.timstof.data.TimsDataset method) compress_zstd() (imspy.timstof.data.TimsDataset method) contributions (imspy.simulation.annotation.PeakAnnotation property) ContributionSource (class in imspy.simulation.annotation) cosim_from_dict() (in module imspy.timstof.dbsearch.sage_output_utility) CosimHasher (class in imspy.algorithm.hashing) count_number_transmissions() (imspy.simulation.experiment.TimsTofSyntheticFrameBuilderDIA method) count_number_transmissions_parallel() (imspy.simulation.experiment.TimsTofSyntheticFrameBuilderDIA method) create_database() (in module imspy.timstof.dbsearch.imspy_dda) create_table() (imspy.simulation.experiment.SyntheticExperimentDataHandle method) create_table_sql() (imspy.simulation.experiment.SyntheticExperimentDataHandle method) custom_cdf() (in module imspy.simulation.utility)

D

decompress_zstd() (imspy.timstof.data.TimsDataset method) DeepChargeStateDistribution (class in imspy.algorithm.ionization.predictors) DeepChromatographyApex (class in imspy.algorithm.rt.predictors) DeepPeptideIonMobilityApex (class in imspy.algorithm.ccs.predictors) description (imspy.simulation.annotation.SignalAttributes property) (imspy.timstof.data.TimsDataset property) detection_noise() (in module imspy.simulation.noise) df (imspy.data.spectrum.IndexedMzSpectrum property) (imspy.data.spectrum.MzSpectrum property) (imspy.data.spectrum.TimsSpectrum property) (imspy.simulation.annotation.TimsFrameAnnotated property) (imspy.timstof.frame.TimsFrame property) (imspy.timstof.frame.TimsFrameVectorized property) (imspy.timstof.slice.TimsPlane property) (imspy.timstof.slice.TimsSlice property) (imspy.timstof.slice.TimsSliceVectorized property)

dia_ms_ms_info (imspy.timstof.dia.TimsDatasetDIA property) dia_ms_ms_windows (imspy.timstof.dia.TimsDatasetDIA property) digest_fasta() (in module imspy.simulation.timsim.jobs.digest_fasta)

E

exp_distribution() (in module imspy.utility.utilities) exp_gaussian() (in module imspy.utility.utilities)

ExponentialGaussianDistribution (class in imspy.utility.utilities) extract_timstof_dda_data() (in module imspy.timstof.dbsearch.utility)

F

filter() (imspy.data.spectrum.IndexedMzSpectrum method) (imspy.data.spectrum.MzSpectrum method) (imspy.data.spectrum.TimsSpectrum method) (imspy.simulation.annotation.MzSpectrumAnnotated method) (imspy.simulation.annotation.TimsFrameAnnotated method) (imspy.timstof.frame.TimsFrame method) (imspy.timstof.frame.TimsFrameVectorized method) (imspy.timstof.slice.TimsSlice method) (imspy.timstof.slice.TimsSliceVectorized method) filter_by_type() (imspy.timstof.slice.TimsSlice method) find_series() (imspy.data.peptide.PeptideProductIonSeriesCollection method) fine_tune_model() (imspy.algorithm.ccs.predictors.DeepPeptideIonMobilityApex method) (imspy.algorithm.rt.predictors.DeepChromatographyApex method) first_frame_id (imspy.timstof.slice.TimsSlice property) (imspy.timstof.slice.TimsSliceVectorized property) flat_intensity_to_sparse() (in module imspy.simulation.utility) flatten_prosit_array() (in module imspy.simulation.utility) FragmentDDA (class in imspy.timstof.dda) fragments (imspy.timstof.slice.TimsSlice property) (imspy.timstof.slice.TimsSliceVectorized property) fragments_to_dict() (in module imspy.timstof.dbsearch.sage_output_utility) frame_count (imspy.timstof.data.TimsDataset property) frame_id (imspy.data.spectrum.TimsSpectrum property) (imspy.simulation.annotation.TimsFrameAnnotated property) (imspy.timstof.dda.FragmentDDA property) (imspy.timstof.dda.PrecursorDDA property) (imspy.timstof.frame.TimsFrame property) (imspy.timstof.frame.TimsFrameVectorized property) frame_ids (imspy.timstof.slice.TimsPlane property) frame_to_window_group() (imspy.timstof.quadrupole.TimsTofQuadrupoleDIA method) frames (imspy.timstof.slice.TimsSlice property) (imspy.timstof.slice.TimsSliceVectorized property) from_config() (imspy.algorithm.ccs.predictors.GRUCCSPredictor class method) (imspy.algorithm.ccs.predictors.SquareRootProjectionLayer class method) (imspy.algorithm.ionization.predictors.GRUChargeStatePredictor class method) (imspy.algorithm.rt.predictors.GRURetentionTimePredictor class method) (imspy.simulation.acquisition.TimsTofAcquisitionBuilderDIA static method)

from_existing() (imspy.simulation.acquisition.TimsTofAcquisitionBuilder class method) (imspy.simulation.acquisition.TimsTofAcquisitionBuilderDIA class method) from_frames() (imspy.timstof.slice.TimsSlice class method) from_jsons() (imspy.data.spectrum.MzSpectrum class method) from_mz_spectra_list() (imspy.data.spectrum.MzSpectrum class method) from_py_ptr() (imspy.data.peptide.PeptideIon class method) (imspy.data.peptide.PeptideProductIon class method) (imspy.data.peptide.PeptideProductIonSeries class method) (imspy.data.peptide.PeptideProductIonSeriesCollection class method) (imspy.data.peptide.PeptideSequence class method) (imspy.data.spectrum.IndexedMzSpectrum class method) (imspy.data.spectrum.MzSpectrum class method) (imspy.data.spectrum.MzSpectrumVectorized class method) (imspy.data.spectrum.TimsSpectrum class method) (imspy.simulation.annotation.ContributionSource class method) (imspy.simulation.annotation.MzSpectrumAnnotated class method) (imspy.simulation.annotation.PeakAnnotation class method) (imspy.simulation.annotation.RustWrapperObject class method) (imspy.simulation.annotation.SignalAttributes class method) (imspy.simulation.annotation.SourceType class method) (imspy.simulation.annotation.TimsFrameAnnotated class method) (imspy.simulation.experiment.TimsTofSyntheticFrameBuilderDIA class method) (imspy.simulation.experiment.TimsTofSyntheticPrecursorFrameBuilder class method) (imspy.timstof.data.AcquisitionMode class method) (imspy.timstof.dda.FragmentDDA class method) (imspy.timstof.dda.PrecursorDDA class method) (imspy.timstof.dda.TimsDatasetDDA class method) (imspy.timstof.dia.TimsDatasetDIA class method) (imspy.timstof.frame.TimsFrame class method) (imspy.timstof.frame.TimsFrameVectorized class method) from_py_tims_plane() (imspy.timstof.slice.TimsPlane class method) from_py_tims_slice() (imspy.timstof.slice.TimsSlice class method) from_tims_spectra() (imspy.timstof.frame.TimsFrame class method) from_vectorized_py_tims_slice() (imspy.timstof.slice.TimsSliceVectorized class method) from_windows() (imspy.timstof.frame.TimsFrame class method)

G

gaussian() (in module imspy.utility.utilities) generate_balanced_im_dataset() (in module imspy.timstof.dbsearch.utility) generate_balanced_rt_dataset() (in module imspy.timstof.dbsearch.utility) generate_events() (in module imspy.simulation.utility) generate_frame_table() (imspy.simulation.acquisition.TimsTofAcquisitionBuilder method) generate_frame_to_window_group_table() (imspy.simulation.acquisition.TimsTofAcquisitionBuilderDIA method) generate_isotopic_spectrum() (imspy.data.peptide.PeptideProductIonSeriesCollection method) generate_isotopic_spectrum_annotated() (imspy.data.peptide.PeptideProductIonSeriesCollection method) generate_noise_peak() (in module imspy.simulation.noise) generate_prosit_intensity_prediction_dataset() (in module imspy.algorithm.intensity.utility) generate_scan_table() (imspy.simulation.acquisition.TimsTofAcquisitionBuilder method) generate_tf_ds_inference() (imspy.algorithm.rt.predictors.DeepChromatographyApex method) generate_tf_ds_train() (imspy.algorithm.rt.predictors.DeepChromatographyApex method) generate_training_data() (in module imspy.timstof.dbsearch.sage_output_utility) (in module imspy.timstof.dbsearch.utility) get_aa_num_proforma_sequence() (in module imspy.utility.utilities) get_acquisition_builder_resource_path() (in module imspy.simulation.utility) get_arrays_at_index() (imspy.timstof.frame.TimsFrameVectorized method) get_collision_energies() (imspy.simulation.experiment.TimsTofSyntheticFrameBuilderDIA method) (imspy.timstof.collision.TimsTofCollisionEnergy method) (imspy.timstof.collision.TimsTofCollisionEnergyDIA method) get_collision_energy() (imspy.simulation.experiment.TimsTofSyntheticFrameBuilderDIA method) (imspy.timstof.collision.TimsTofCollisionEnergy method) (imspy.timstof.collision.TimsTofCollisionEnergyDIA method) get_collision_energy_calibration_factor() (in module imspy.algorithm.intensity.predictors) get_compressible_data() (in module imspy.simulation.utility) get_config() (imspy.algorithm.ccs.predictors.GRUCCSPredictor method) (imspy.algorithm.ccs.predictors.SquareRootProjectionLayer method) (imspy.algorithm.ionization.predictors.GRUChargeStatePredictor method) (imspy.algorithm.rt.predictors.GRURetentionTimePredictor method) get_dilution_factors() (in module imspy.simulation.utility) get_fasta_file_paths() (in module imspy.simulation.utility) get_frame_meta_data() (imspy.simulation.tdf.TDFWriter method) get_frame_to_window_group() (imspy.simulation.experiment.SyntheticExperimentDataHandleDIA method) get_frames_numba() (in module imspy.simulation.utility) get_inverse_mobility_along_scan_marginal() (imspy.timstof.frame.TimsFrame method) get_ion_transmission_matrix() (imspy.simulation.experiment.TimsTofSyntheticFrameBuilderDIA method) get_mobility_mean_and_variance() (imspy.timstof.frame.TimsFrame method) get_model_path() (in module imspy.algorithm.utility) get_ms_ms_window_layout_resource_path() (in module imspy.simulation.utility) get_native_dataset_path() (in module imspy.simulation.utility) get_pasef_fragments() (imspy.timstof.dda.TimsDatasetDDA method) get_peak_cnts() (in module imspy.simulation.utility) get_peak_integral() (in module imspy.data.spectrum) get_precursor_frames() (imspy.timstof.dda.TimsDatasetDDA method) get_prosit_intensity_flat_labels() (in module imspy.algorithm.intensity.utility) get_py_ptr() (imspy.data.peptide.PeptideIon method) (imspy.data.peptide.PeptideProductIon method) (imspy.data.peptide.PeptideProductIonSeries method) (imspy.data.peptide.PeptideProductIonSeriesCollection method) (imspy.data.peptide.PeptideSequence method) (imspy.data.spectrum.IndexedMzSpectrum method) (imspy.data.spectrum.MzSpectrum method) (imspy.data.spectrum.MzSpectrumVectorized method) (imspy.data.spectrum.TimsSpectrum method) (imspy.simulation.annotation.ContributionSource method) (imspy.simulation.annotation.MzSpectrumAnnotated method) (imspy.simulation.annotation.PeakAnnotation method) (imspy.simulation.annotation.RustWrapperObject method) (imspy.simulation.annotation.SignalAttributes method) (imspy.simulation.annotation.SourceType method) (imspy.simulation.annotation.TimsFrameAnnotated method) (imspy.simulation.experiment.TimsTofSyntheticFrameBuilderDIA method) (imspy.simulation.experiment.TimsTofSyntheticPrecursorFrameBuilder method) (imspy.simulation.handle.TimsTofSyntheticsDataHandleRust method) (imspy.timstof.data.AcquisitionMode method) (imspy.timstof.dda.FragmentDDA method) (imspy.timstof.dda.PrecursorDDA method) (imspy.timstof.dda.TimsDatasetDDA method) (imspy.timstof.dia.TimsDatasetDIA method) (imspy.timstof.frame.TimsFrame method) (imspy.timstof.frame.TimsFrameVectorized method) (imspy.timstof.slice.TimsSliceVectorized method)

get_realdata() (in module imspy.simulation.utility) get_realdata_loop() (in module imspy.simulation.utility) get_rt_prediction_set() (in module imspy.algorithm.rt.predictors) get_rt_train_set() (in module imspy.algorithm.rt.predictors) get_sage_processed_precursors() (imspy.timstof.dda.TimsDatasetDDA method) get_scans_numba() (in module imspy.simulation.utility) get_searchable_spec() (in module imspy.timstof.dbsearch.utility) get_selected_precursors() (imspy.timstof.dda.TimsDatasetDDA method) get_sqrt_slopes_and_intercepts() (in module imspy.algorithm.ccs.predictors) get_table() (imspy.simulation.experiment.SyntheticExperimentDataHandle method) (imspy.timstof.data.TimsDataset method) get_tensor_repr() (imspy.timstof.frame.TimsFrameVectorized method) (imspy.timstof.slice.TimsSliceVectorized method) get_tims_frame() (imspy.timstof.data.TimsDataset method) get_tims_planes() (imspy.timstof.slice.TimsSlice method) get_tims_slice() (imspy.timstof.data.TimsDataset method) get_transmission_set() (imspy.timstof.quadrupole.TimsTofQuadrupoleDIA method) get_transmitted_ions() (imspy.simulation.handle.TimsTofSyntheticsDataHandleRust method) get_window_group_settings() (imspy.simulation.experiment.SyntheticExperimentDataHandleDIA method) get_z_score_for_percentile() (in module imspy.simulation.utility) GRUCCSPredictor (class in imspy.algorithm.ccs.predictors) GRUChargeStatePredictor (class in imspy.algorithm.ionization.predictors) GRURetentionTimePredictor (class in imspy.algorithm.rt.predictors)

H

highest_intensity_mz (imspy.timstof.dda.PrecursorDDA property)

I

im_lower (imspy.timstof.data.TimsDataset property) im_upper (imspy.timstof.data.TimsDataset property) imspy module imspy.algorithm module imspy.algorithm.ccs module imspy.algorithm.ccs.predictors module imspy.algorithm.hashing module imspy.algorithm.intensity module imspy.algorithm.intensity.predictors module imspy.algorithm.intensity.utility module imspy.algorithm.ionization module imspy.algorithm.ionization.predictors module imspy.algorithm.pretrained module imspy.algorithm.rt module imspy.algorithm.rt.predictors module imspy.algorithm.utility module imspy.chemistry module imspy.chemistry.amino_acids module imspy.chemistry.constants module imspy.chemistry.elements module imspy.chemistry.mobility module imspy.chemistry.unimod module imspy.chemistry.utility module imspy.data module imspy.data.peptide module imspy.data.spectrum module imspy.simulation module imspy.simulation.acquisition module imspy.simulation.annotation module imspy.simulation.experiment module imspy.simulation.handle module imspy.simulation.noise module imspy.simulation.proteome module imspy.simulation.tdf module imspy.simulation.timsim module imspy.simulation.timsim.jobs module imspy.simulation.timsim.jobs.add_noise_from_real_data module imspy.simulation.timsim.jobs.assemble_frames module imspy.simulation.timsim.jobs.build_acquisition module imspy.simulation.timsim.jobs.digest_fasta module imspy.simulation.timsim.jobs.simulate_charge_states module imspy.simulation.timsim.jobs.simulate_fragment_intensities module imspy.simulation.timsim.jobs.simulate_frame_distributions module

imspy.simulation.timsim.jobs.simulate_frame_distributions_emg module imspy.simulation.timsim.jobs.simulate_ion_mobilities module imspy.simulation.timsim.jobs.simulate_occurrences module imspy.simulation.timsim.jobs.simulate_retention_time module imspy.simulation.timsim.jobs.simulate_scan_distributions module imspy.simulation.timsim.jobs.utility module imspy.simulation.utility module imspy.timstof module imspy.timstof.collision module imspy.timstof.data module imspy.timstof.dbsearch module imspy.timstof.dbsearch.imspy_dda module imspy.timstof.dbsearch.imspy_rescore_sage module imspy.timstof.dbsearch.sage_output_utility module imspy.timstof.dbsearch.utility module imspy.timstof.dda module imspy.timstof.dia module imspy.timstof.frame module imspy.timstof.quadrupole module imspy.timstof.slice module imspy.utility module imspy.utility.sequence module imspy.utility.utilities module imspy.vis module index (imspy.data.spectrum.IndexedMzSpectrum property) (imspy.data.spectrum.TimsSpectrum property) indexed_values_to_compressed_bytes() (imspy.timstof.data.TimsDataset method) IndexedMzSpectrum (class in imspy.data.spectrum) indices (imspy.data.spectrum.MzSpectrumVectorized property) (imspy.timstof.frame.TimsFrameVectorized property) InMemoryCheckpoint (class in imspy.algorithm.utility) intensities (imspy.timstof.slice.TimsPlane property) intensity (imspy.data.peptide.PeptideIon property) (imspy.data.peptide.PeptideProductIon property) (imspy.data.spectrum.IndexedMzSpectrum property) (imspy.data.spectrum.MzSpectrum property) (imspy.data.spectrum.TimsSpectrum property) (imspy.simulation.annotation.MzSpectrumAnnotated property) (imspy.simulation.annotation.TimsFrameAnnotated property) (imspy.timstof.frame.TimsFrame property) (imspy.timstof.frame.TimsFrameVectorized property) intensity_contribution (imspy.simulation.annotation.ContributionSource property) inv_mobility (imspy.simulation.annotation.TimsFrameAnnotated property) inv_mobility_to_scan() (imspy.simulation.tdf.TDFWriter method) inverse_ion_mobility (imspy.timstof.dda.PrecursorDDA property) inverse_mobility_to_scan() (imspy.timstof.data.TimsDataset method) IonIntensityPredictor (class in imspy.algorithm.intensity.predictors) irt_to_rts_numba() (in module imspy.simulation.utility) is_amd64() (in module imspy.timstof.data) is_precursor() (imspy.timstof.quadrupole.TimsTofQuadrupoleDIA method) is_transmitted() (imspy.timstof.quadrupole.TimsTofQuadrupoleDIA method) is_unimod_end() (in module imspy.utility.utilities) is_unimod_start() (in module imspy.utility.utilities) isolation_mz (imspy.timstof.dda.PrecursorDDA property) isolation_width (imspy.timstof.dda.PrecursorDDA property) isotope_distribution() (imspy.data.peptide.PeptideProductIon method) isotope_peak (imspy.simulation.annotation.SignalAttributes property) isotope_peaks_first_only (imspy.simulation.annotation.TimsFrameAnnotated property) isotopes_transmitted() (imspy.timstof.quadrupole.TimsTofQuadrupoleDIA method)

J

json_string_to_python_list() (in module imspy.simulation.utility)

jsons (imspy.utility.utilities.TokenSequence property)

K

kind (imspy.data.peptide.PeptideProductIon property)

L

last_frame_id (imspy.timstof.slice.TimsSlice property) (imspy.timstof.slice.TimsSliceVectorized property) linear_map() (in module imspy.timstof.dbsearch.utility) list_columns() (imspy.simulation.experiment.SyntheticExperimentDataHandle method) list_tables() (imspy.simulation.experiment.SyntheticExperimentDataHandle method) list_to_semicolon_string() (in module imspy.timstof.dbsearch.utility)

load_config() (in module imspy.timstof.dbsearch.imspy_dda) load_deep_ccs_predictor() (in module imspy.algorithm.ccs.predictors) load_deep_charge_state_predictor() (in module imspy.algorithm.ionization.predictors) load_deep_retention_time_predictor() (in module imspy.algorithm.rt.predictors) load_prosit_2023_timsTOF_predictor() (in module imspy.algorithm.intensity.predictors) load_tokenizer_from_resources() (in module imspy.algorithm.utility)

M

main() (in module imspy.timstof.dbsearch.imspy_dda) (in module imspy.timstof.dbsearch.imspy_rescore_sage) map_to_domain() (in module imspy.timstof.dbsearch.utility) merge_dicts_with_merge_dict() (in module imspy.timstof.dbsearch.utility) mobilities (imspy.timstof.slice.TimsPlane property) mobility (imspy.data.spectrum.TimsSpectrum property) (imspy.timstof.frame.TimsFrame property) (imspy.timstof.frame.TimsFrameVectorized property) mode (imspy.timstof.data.AcquisitionMode property) modify_tofs() (in module imspy.simulation.utility) module imspy imspy.algorithm imspy.algorithm.ccs imspy.algorithm.ccs.predictors imspy.algorithm.hashing imspy.algorithm.intensity imspy.algorithm.intensity.predictors imspy.algorithm.intensity.utility imspy.algorithm.ionization imspy.algorithm.ionization.predictors imspy.algorithm.pretrained imspy.algorithm.rt imspy.algorithm.rt.predictors imspy.algorithm.utility imspy.chemistry imspy.chemistry.amino_acids imspy.chemistry.constants imspy.chemistry.elements imspy.chemistry.mobility imspy.chemistry.unimod imspy.chemistry.utility imspy.data imspy.data.peptide imspy.data.spectrum imspy.simulation imspy.simulation.acquisition imspy.simulation.annotation imspy.simulation.experiment imspy.simulation.handle imspy.simulation.noise imspy.simulation.proteome imspy.simulation.tdf imspy.simulation.timsim imspy.simulation.timsim.jobs imspy.simulation.timsim.jobs.add_noise_from_real_data imspy.simulation.timsim.jobs.assemble_frames imspy.simulation.timsim.jobs.build_acquisition imspy.simulation.timsim.jobs.digest_fasta imspy.simulation.timsim.jobs.simulate_charge_states imspy.simulation.timsim.jobs.simulate_fragment_intensities imspy.simulation.timsim.jobs.simulate_frame_distributions imspy.simulation.timsim.jobs.simulate_frame_distributions_emg imspy.simulation.timsim.jobs.simulate_ion_mobilities imspy.simulation.timsim.jobs.simulate_occurrences imspy.simulation.timsim.jobs.simulate_retention_time imspy.simulation.timsim.jobs.simulate_scan_distributions imspy.simulation.timsim.jobs.utility imspy.simulation.utility imspy.timstof imspy.timstof.collision imspy.timstof.data imspy.timstof.dbsearch imspy.timstof.dbsearch.imspy_dda imspy.timstof.dbsearch.imspy_rescore_sage imspy.timstof.dbsearch.sage_output_utility imspy.timstof.dbsearch.utility imspy.timstof.dda imspy.timstof.dia imspy.timstof.frame imspy.timstof.quadrupole imspy.timstof.slice imspy.utility imspy.utility.sequence imspy.utility.utilities imspy.vis

mono_isotopic_mass (imspy.data.peptide.PeptideProductIon property) (imspy.data.peptide.PeptideSequence property) mono_mz (imspy.timstof.dda.PrecursorDDA property) ms_type (imspy.data.spectrum.TimsSpectrum property) (imspy.simulation.annotation.TimsFrameAnnotated property) (imspy.timstof.frame.TimsFrame property) (imspy.timstof.frame.TimsFrameVectorized property) ms_type_as_string (imspy.timstof.frame.TimsFrame property) ms_type_numeric (imspy.simulation.annotation.TimsFrameAnnotated property) mu_function_normal_default() (in module imspy.simulation.noise) mu_function_poisson_default() (in module imspy.simulation.noise) mz (imspy.data.peptide.PeptideIon property) (imspy.data.peptide.PeptideProductIon property) (imspy.data.spectrum.IndexedMzSpectrum property) (imspy.data.spectrum.MzSpectrum property) (imspy.data.spectrum.TimsSpectrum property) (imspy.simulation.annotation.MzSpectrumAnnotated property) (imspy.simulation.annotation.TimsFrameAnnotated property) (imspy.timstof.frame.TimsFrame property) mz_lower (imspy.timstof.data.TimsDataset property) mz_mean (imspy.timstof.slice.TimsPlane property) mz_spectrum (imspy.data.spectrum.TimsSpectrum property) mz_std (imspy.timstof.slice.TimsPlane property) mz_to_tof() (imspy.simulation.tdf.TDFWriter method) (imspy.timstof.data.TimsDataset method) mz_upper (imspy.timstof.data.TimsDataset property) MzSpectrum (class in imspy.data.spectrum) MzSpectrumAnnotated (class in imspy.simulation.annotation) MzSpectrumVectorized (class in imspy.data.spectrum)

N

n_ions (imspy.data.peptide.PeptideProductIonSeries property) normal_pdf() (in module imspy.utility.utilities) NormalDistribution (class in imspy.utility.utilities)

np_zip() (in module imspy.simulation.utility) num_points (imspy.timstof.slice.TimsPlane property) num_scans (imspy.timstof.data.TimsDataset property)

O

on_epoch_end() (imspy.algorithm.utility.InMemoryCheckpoint method) on_train_begin() (imspy.algorithm.utility.InMemoryCheckpoint method)

on_train_end() (imspy.algorithm.utility.InMemoryCheckpoint method) one_over_k0_to_ccs() (in module imspy.chemistry.mobility) one_over_k0_to_ccs_par() (in module imspy.chemistry.mobility)

P

parse_string_list() (in module imspy.timstof.dbsearch.utility) parse_to_tims2rescore() (in module imspy.timstof.dbsearch.utility) PatternReplacer (class in imspy.timstof.dbsearch.sage_output_utility) PeakAnnotation (class in imspy.simulation.annotation) peptide_id (imspy.data.peptide.PeptideIon property) (imspy.data.peptide.PeptideSequence property) (imspy.simulation.annotation.SignalAttributes property) peptide_ids_first_only (imspy.simulation.annotation.TimsFrameAnnotated property) peptide_length() (in module imspy.timstof.dbsearch.utility) PeptideChargeStateDistribution (class in imspy.algorithm.ionization.predictors) PeptideChromatographyApex (class in imspy.algorithm.rt.predictors) PeptideDigest (class in imspy.simulation.proteome) PeptideIon (class in imspy.data.peptide) PeptideIonMobilityApex (class in imspy.algorithm.ccs.predictors) PeptideProductIon (class in imspy.data.peptide) PeptideProductIonSeries (class in imspy.data.peptide)

PeptideProductIonSeriesCollection (class in imspy.data.peptide) PeptideSequence (class in imspy.data.peptide) phosphorylation_sizes() (in module imspy.simulation.timsim.jobs.utility) plot_summary() (in module imspy.timstof.dbsearch.sage_output_utility) post_process_predicted_fragment_spectra() (in module imspy.algorithm.intensity.utility) precuror_total_intensity (imspy.timstof.dda.PrecursorDDA property) precursor_id (imspy.timstof.dda.FragmentDDA property) (imspy.timstof.dda.PrecursorDDA property) PrecursorDDA (class in imspy.timstof.dda) precursors (imspy.timstof.slice.TimsSlice property) (imspy.timstof.slice.TimsSliceVectorized property) predict_intensities() (imspy.algorithm.intensity.predictors.Prosit2023TimsTofWrapper method) predict_intensities_prosit() (in module imspy.algorithm.intensity.predictors) predict_inverse_ion_mobility() (in module imspy.algorithm.ccs.predictors) predict_retention_time() (in module imspy.algorithm.rt.predictors) Prosit2023TimsTofWrapper (class in imspy.algorithm.intensity.predictors) python_list_to_json_string() (in module imspy.simulation.utility)

R

random_subsample_frame() (imspy.timstof.frame.TimsFrame method) re_index_indices() (in module imspy.utility.utilities) re_score_psms() (in module imspy.timstof.dbsearch.sage_output_utility) read_acquisition_config() (in module imspy.simulation.utility) read_compressed_data_full() (imspy.timstof.dia.TimsDatasetDIA method) remove_substrings() (in module imspy.timstof.dbsearch.sage_output_utility) remove_unimod_annotation() (in module imspy.algorithm.intensity.predictors)

resolution (imspy.data.spectrum.MzSpectrumVectorized property) retention_time (imspy.data.spectrum.TimsSpectrum property) (imspy.simulation.annotation.TimsFrameAnnotated property) (imspy.timstof.frame.TimsFrame property) (imspy.timstof.frame.TimsFrameVectorized property) retention_times (imspy.timstof.slice.TimsPlane property) row_to_fragment() (in module imspy.timstof.dbsearch.sage_output_utility) RustWrapperObject (class in imspy.simulation.annotation)

S

sample_fragment_signal() (imspy.timstof.dia.TimsDatasetDIA method) sample_parameters_rejection() (in module imspy.simulation.timsim.jobs.simulate_frame_distributions_emg) sample_precursor_signal() (imspy.timstof.dia.TimsDatasetDIA method) sanitize_charge() (in module imspy.timstof.dbsearch.utility) sanitize_mz() (in module imspy.timstof.dbsearch.utility) scan (imspy.data.spectrum.TimsSpectrum property) (imspy.simulation.annotation.TimsFrameAnnotated property) (imspy.timstof.frame.TimsFrame property) (imspy.timstof.frame.TimsFrameVectorized property) scan_to_inv_mobility() (imspy.simulation.tdf.TDFWriter method) scan_to_inverse_mobility() (imspy.timstof.data.TimsDataset method) scans (imspy.timstof.slice.TimsPlane property) selected_fragment (imspy.timstof.dda.FragmentDDA property) seq_to_index() (in module imspy.algorithm.intensity.utility) sequence (imspy.data.peptide.PeptideIon property) (imspy.data.peptide.PeptideProductIon property) (imspy.data.peptide.PeptideSequence property) sequence_to_all_ions() (in module imspy.simulation.utility) sequence_to_numpy() (in module imspy.simulation.utility) sequences_to_all_ions() (in module imspy.simulation.utility) series (imspy.data.peptide.PeptideProductIonSeriesCollection property) set_percentage_to_zero() (in module imspy.simulation.utility) sigma_function_normal_default() (in module imspy.simulation.noise) signal_attributes (imspy.simulation.annotation.ContributionSource property) SignalAttributes (class in imspy.simulation.annotation) simulate_charge_state_distribution_pandas() (imspy.algorithm.ionization.predictors.BinomialChargeStateDistributionModel method) (imspy.algorithm.ionization.predictors.DeepChargeStateDistribution method) (imspy.algorithm.ionization.predictors.PeptideChargeStateDistribution method) simulate_charge_states() (in module imspy.simulation.timsim.jobs.simulate_charge_states) simulate_fragment_intensities() (in module imspy.simulation.timsim.jobs.simulate_fragment_intensities)

simulate_frame_distributions() (in module imspy.simulation.timsim.jobs.simulate_frame_distributions) simulate_frame_distributions_emg() (in module imspy.simulation.timsim.jobs.simulate_frame_distributions_emg) simulate_ion_intensities() (imspy.algorithm.intensity.predictors.IonIntensityPredictor method) (imspy.algorithm.intensity.predictors.Prosit2023TimsTofWrapper method) simulate_ion_intensities_pandas() (imspy.algorithm.intensity.predictors.IonIntensityPredictor method) (imspy.algorithm.intensity.predictors.Prosit2023TimsTofWrapper method) simulate_ion_intensities_pandas_batched() (imspy.algorithm.intensity.predictors.Prosit2023TimsTofWrapper method) simulate_ion_mobilities() (imspy.algorithm.ccs.predictors.DeepPeptideIonMobilityApex method) (imspy.algorithm.ccs.predictors.PeptideIonMobilityApex method) (in module imspy.simulation.timsim.jobs.simulate_ion_mobilities) simulate_ion_mobilities_pandas() (imspy.algorithm.ccs.predictors.DeepPeptideIonMobilityApex method) (imspy.algorithm.ccs.predictors.PeptideIonMobilityApex method) simulate_ionizations() (imspy.algorithm.ionization.predictors.BinomialChargeStateDistributionModel method) (imspy.algorithm.ionization.predictors.DeepChargeStateDistribution method) (imspy.algorithm.ionization.predictors.PeptideChargeStateDistribution method) simulate_peptide_occurrences() (in module imspy.simulation.timsim.jobs.simulate_occurrences) simulate_retention_times() (in module imspy.simulation.timsim.jobs.simulate_retention_time) simulate_scan_distributions() (in module imspy.simulation.timsim.jobs.simulate_scan_distributions) simulate_separation_times() (imspy.algorithm.rt.predictors.DeepChromatographyApex method) (imspy.algorithm.rt.predictors.PeptideChromatographyApex method) simulate_separation_times_pandas() (imspy.algorithm.rt.predictors.DeepChromatographyApex method) (imspy.algorithm.rt.predictors.PeptideChromatographyApex method) source_type (imspy.simulation.annotation.ContributionSource property) (imspy.simulation.annotation.SourceType property) SourceType (class in imspy.simulation.annotation) split_dataframe_randomly() (in module imspy.timstof.dbsearch.sage_output_utility) split_fasta() (in module imspy.timstof.dbsearch.utility) split_psms() (in module imspy.timstof.dbsearch.utility) SquareRootProjectionLayer (class in imspy.algorithm.ccs.predictors) SyntheticExperimentDataHandle (class in imspy.simulation.experiment) SyntheticExperimentDataHandleDIA (class in imspy.simulation.experiment)

T

TDFWriter (class in imspy.simulation.tdf) TimsDataset (class in imspy.timstof.data) TimsDatasetDDA (class in imspy.timstof.dda) TimsDatasetDIA (class in imspy.timstof.dia) TimsFrame (class in imspy.timstof.frame) TimsFrameAnnotated (class in imspy.simulation.annotation) TimsFrameVectorized (class in imspy.timstof.frame) TimsHasher (class in imspy.algorithm.hashing) TimsPlane (class in imspy.timstof.slice) TimsSlice (class in imspy.timstof.slice) TimsSliceVectorized (class in imspy.timstof.slice) TimsSpectrum (class in imspy.data.spectrum) TimsTofAcquisitionBuilder (class in imspy.simulation.acquisition) TimsTofAcquisitionBuilderDDA (class in imspy.simulation.acquisition) TimsTofAcquisitionBuilderDIA (class in imspy.simulation.acquisition) TimsTofCollisionEnergy (class in imspy.timstof.collision) TimsTofCollisionEnergyDIA (class in imspy.timstof.collision) TimsTofQuadrupoleDIA (class in imspy.timstof.quadrupole) TimsTofSyntheticFrameBuilderDIA (class in imspy.simulation.experiment) TimsTofSyntheticPrecursorFrameBuilder (class in imspy.simulation.experiment) TimsTofSyntheticsDataHandleRust (class in imspy.simulation.handle) to_centroided() (imspy.data.spectrum.MzSpectrum method) (imspy.data.spectrum.MzSpectrumVectorized method) to_dense_windows() (imspy.timstof.frame.TimsFrame method) (imspy.timstof.slice.TimsSlice method) to_indexed_mz_spectrum() (imspy.timstof.frame.TimsFrame method) to_json() (imspy.data.peptide.PeptideIon method) (imspy.data.peptide.PeptideProductIon method) (imspy.data.peptide.PeptideProductIonSeries method) (imspy.data.peptide.PeptideProductIonSeriesCollection method) (imspy.data.peptide.PeptideSequence method)

to_jsons() (imspy.data.spectrum.MzSpectrum method) to_noise_annotated_tims_frame() (imspy.timstof.frame.TimsFrame method) to_prosit_tensor() (in module imspy.algorithm.intensity.utility) to_resolution() (imspy.data.spectrum.MzSpectrum method) (imspy.timstof.frame.TimsFrame method) (imspy.timstof.slice.TimsSlice method) to_sage_precursor() (imspy.timstof.dda.PrecursorDDA method) to_sage_representation() (imspy.data.peptide.PeptideSequence method) to_tims_spectra() (imspy.timstof.frame.TimsFrame method) to_tokens() (imspy.data.peptide.PeptideSequence method) to_windows() (imspy.data.spectrum.MzSpectrum method) (imspy.timstof.frame.TimsFrame method) (imspy.timstof.slice.TimsSlice method) tof (imspy.simulation.annotation.TimsFrameAnnotated property) (imspy.timstof.frame.TimsFrame property) (imspy.timstof.frame.TimsFrameVectorized property) tof_mean (imspy.timstof.slice.TimsPlane property) tof_std (imspy.timstof.slice.TimsPlane property) tof_to_mz() (imspy.simulation.tdf.TDFWriter method) (imspy.timstof.data.TimsDataset method) tokenize_proforma_sequence() (in module imspy.utility.utilities) tokenize_unimod_sequence() (in module imspy.utility.sequence) tokenizer_from_json() (in module imspy.utility.utilities) tokenizer_to_json() (in module imspy.utility.utilities) TokenSequence (class in imspy.utility.utilities) transform_psm_to_pin() (in module imspy.timstof.dbsearch.utility) transmit_frame() (imspy.timstof.quadrupole.TimsTofQuadrupoleDIA method) transmit_ion() (imspy.timstof.quadrupole.TimsTofQuadrupoleDIA method) transmit_spectrum() (imspy.timstof.quadrupole.TimsTofQuadrupoleDIA method)

U

unpack_dict() (in module imspy.algorithm.intensity.utility)

V

values (imspy.data.spectrum.MzSpectrumVectorized property) vectorized() (imspy.data.spectrum.MzSpectrum method) (imspy.timstof.frame.TimsFrame method) (imspy.timstof.slice.TimsSlice method)

W

write_dia_ms_ms_info() (imspy.simulation.tdf.TDFWriter method) write_dia_ms_ms_windows() (imspy.simulation.tdf.TDFWriter method)

write_frame() (imspy.simulation.tdf.TDFWriter method) write_frame_meta_data() (imspy.simulation.tdf.TDFWriter method) write_psms_binary() (in module imspy.timstof.dbsearch.utility)