Index

_

_convertConformerFeatureToTransitionGroupFeatures() (massdash.peakPickers.ConformerPeakPicker method) _get_actual_column() (massdash.loaders.access.TransitionTSVDataAccess method) _load() (massdash.loaders.access.TransitionPQPDataAccess method) (massdash.loaders.access.TransitionTSVDataAccess method)

_resolve_column_names() (massdash.loaders.access.TransitionTSVDataAccess method) _validate_columns() (massdash.loaders.access.TransitionPQPDataAccess method) (massdash.loaders.access.TransitionTSVDataAccess method) _validate_model() (massdash.peakPickers.ConformerPeakPicker method)

A

adjust_length() (massdash.structs.Chromatogram method) (massdash.structs.Data1D method) (massdash.structs.Mobilogram method) (massdash.structs.Spectrum method) (massdash.structs.TransitionGroup method)

aggregate_mslevels (massdash.plotting.PlotConfig attribute) areaIntensity (massdash.structs.TransitionGroupFeature attribute)

B

BokehSnapshotExtension (class in massdash.testing)

C

c (massdash.loaders.access.OSWDataAccess attribute) (massdash.loaders.access.TransitionPQPDataAccess attribute) check_ion_mobility() (massdash.loaders.access.MzMLDataAccess method) Chromatogram (class in massdash.structs) compare_json() (massdash.testing.BokehSnapshotExtension static method) (massdash.testing.PlotlySnapshotExtension static method) computeCV() (massdash.loaders.ResultsLoader method) config (massdash.plotting.InteractivePlotter attribute) (massdash.plotting.InteractiveThreeDimensionPlotter attribute) (massdash.plotting.InteractiveTwoDimensionPlotter attribute)

ConformerPeakPicker (class in massdash.peakPickers) conn (massdash.loaders.access.OSWDataAccess attribute) (massdash.loaders.access.TransitionPQPDataAccess attribute) consensusApex (massdash.structs.TransitionGroupFeature attribute) consensusApexIM (massdash.structs.TransitionGroupFeature attribute) consensusApexIntensity (massdash.structs.TransitionGroupFeature attribute) context (massdash.plotting.PlotConfig attribute) create_heatmap_plot() (massdash.plotting.InteractiveTwoDimensionPlotter method)

D

data (massdash.loaders.access.TransitionPQPDataAccess attribute) (massdash.loaders.access.TransitionTSVDataAccess attribute) (massdash.loaders.SpectralLibraryLoader attribute) Data1D (class in massdash.structs) dataFiles (massdash.loaders.GenericChromatogramLoader attribute) (massdash.loaders.GenericSpectrumLoader attribute) (massdash.loaders.MzMLDataLoader attribute) (massdash.loaders.ResultsLoader attribute)

detectResultsType() (massdash.loaders.access.ResultsTSVDataAccess method) df (massdash.plotting.InteractiveThreeDimensionPlotter attribute) (massdash.plotting.InteractiveTwoDimensionPlotter attribute)

E

empty() (massdash.structs.Data1D method) (massdash.structs.FeatureMap method) (massdash.structs.TransitionGroup method)

exp (massdash.loaders.access.MzMLDataAccess attribute) extract_bokeh_json() (massdash.testing.BokehSnapshotExtension method)

F

feature_df (massdash.structs.FeatureMap attribute) FeatureMap (class in massdash.structs) FeatureMapCollection (class in massdash.structs) filename (massdash.loaders.access.MzMLDataAccess attribute) (massdash.loaders.access.TransitionTSVDataAccess attribute)

filter() (massdash.structs.Data1D method) filter_for_target_transition_list() (massdash.loaders.SpectralLibraryLoader method) filter_single_spectrum() (massdash.loaders.access.MzMLDataAccess method) find_peak_boundaries() (massdash.peakPickers.pyMRMTransitionGroupPicker method) flatten() (massdash.structs.TransitionGroup method)

G

generate_annotation() (massdash.loaders.access.TransitionTSVDataAccess method), [1] GenericChromatogramLoader (class in massdash.loaders) GenericFeature (class in massdash.structs) GenericPeakPicker (class in massdash.peakPickers) GenericPlotter (class in massdash.plotting) GenericResultsAccess (class in massdash.loaders.access) GenericSpectrumLoader (class in massdash.loaders) GenericStructCollection (class in massdash.structs) get_axis_titles() (massdash.plotting.InteractiveTwoDimensionPlotter method) get_fragment_library_intensity() (massdash.loaders.SpectralLibraryLoader method) get_im_upper_lower() (massdash.structs.TargetedDIAConfig method) get_peptide_fragment_annotation_list() (massdash.loaders.SpectralLibraryLoader method) get_peptide_ion_mobility() (massdash.loaders.SpectralLibraryLoader method) get_peptide_library_intensity() (massdash.loaders.SpectralLibraryLoader method) get_peptide_precursor_mz() (massdash.loaders.SpectralLibraryLoader method) get_peptide_product_charge_list() (massdash.loaders.SpectralLibraryLoader method) get_peptide_product_mz_list() (massdash.loaders.SpectralLibraryLoader method) get_peptide_retention_time() (massdash.loaders.SpectralLibraryLoader method) get_plot_parameters() (massdash.plotting.InteractiveTwoDimensionPlotter method) get_precursor_chromatograms() (massdash.structs.FeatureMap method) get_precursor_mobilograms() (massdash.structs.FeatureMap method) get_precursor_spectra() (massdash.structs.FeatureMap method) get_rt_upper_lower() (massdash.structs.TargetedDIAConfig method) get_score_distribution() (massdash.loaders.access.OSWDataAccess method) get_score_table_contexts() (massdash.loaders.access.OSWDataAccess method) get_score_tables() (massdash.loaders.access.OSWDataAccess method) get_spectra_rt_list() (massdash.loaders.access.MzMLDataAccess method), [1] get_target_ms_level_indices() (massdash.loaders.access.MzMLDataAccess method), [1] get_top_rank_precursor_feature() (massdash.loaders.access.OSWDataAccess method) get_top_rank_precursor_features_across_runs() (massdash.loaders.access.OSWDataAccess method) (massdash.loaders.access.ResultsTSVDataAccess method) get_transition_chromatograms() (massdash.structs.FeatureMap method) get_transition_mobilograms() (massdash.structs.FeatureMap method) get_transition_spectra() (massdash.structs.FeatureMap method) get_unique_charge_states_per_peptide() (massdash.loaders.SpectralLibraryLoader method) get_unique_peptides_per_protein() (massdash.loaders.SpectralLibraryLoader method) get_unique_proteins() (massdash.loaders.SpectralLibraryLoader method) get_upper_lower_tol() (massdash.structs.TargetedDIAConfig method) getAllTopTransitionGroupFeaturesDf() (massdash.loaders.access.OSWDataAccess method) getBoundaries() (massdash.structs.GenericFeature method) (massdash.structs.TransitionFeature method) (massdash.structs.TransitionGroupFeature method) getChromatogramDfFromSequenceAndCharge() (massdash.loaders.access.OpenSwathXICParquetAccess method) getChromatogramsFromSequenceAndCharge() (massdash.loaders.access.OpenSwathXICParquetAccess method) getDataForChromatograms() (massdash.loaders.access.SqMassDataAccess method) getDataForChromatogramsDf() (massdash.loaders.access.SqMassDataAccess method) getDataForChromatogramsFromNativeIds() (massdash.loaders.access.SqMassDataAccess method)

getDataForChromatogramsFromNativeIdsDf() (massdash.loaders.access.SqMassDataAccess method) getExactRunName() (massdash.loaders.access.ResultsTSVDataAccess method) getExperimentSummary() (massdash.loaders.access.GenericResultsAccess method) getIdentifiedPeptides() (massdash.loaders.access.GenericResultsAccess method) (massdash.loaders.access.OSWDataAccess method) (massdash.loaders.access.OSWPQResultsAccess method) (massdash.loaders.access.ResultsTSVDataAccess method) getIdentifiedPrecursorIntensities() (massdash.loaders.access.GenericResultsAccess method) (massdash.loaders.access.OSWDataAccess method) (massdash.loaders.access.OSWPQResultsAccess method) (massdash.loaders.access.ResultsTSVDataAccess method) getIdentifiedPrecursors() (massdash.loaders.access.GenericResultsAccess method) (massdash.loaders.access.OSWDataAccess method) (massdash.loaders.access.OSWPQResultsAccess method) (massdash.loaders.access.ResultsTSVDataAccess method) getIdentifiedProteins() (massdash.loaders.access.GenericResultsAccess method) (massdash.loaders.access.OSWDataAccess method) (massdash.loaders.access.OSWPQResultsAccess method) (massdash.loaders.access.ResultsTSVDataAccess method) getNumIdentifiedPeptides() (massdash.loaders.access.GenericResultsAccess method) getNumIdentifiedPrecursors() (massdash.loaders.access.GenericResultsAccess method) getNumIdentifiedProteins() (massdash.loaders.access.GenericResultsAccess method) getOSWAccessPtr() (massdash.loaders.ResultsLoader method) getPeptideTable() (massdash.loaders.access.OSWDataAccess method) getPeptideTableFromProteinID() (massdash.loaders.access.OSWDataAccess method) getPeptideTransitionInfo() (massdash.loaders.access.OSWDataAccess method) getPrecursorCharges() (massdash.loaders.access.OSWDataAccess method) getPrecursorChromIDs() (massdash.loaders.access.SqMassDataAccess method) getPrecursorCVs() (massdash.loaders.access.GenericResultsAccess method) getPrecursorID() (massdash.loaders.access.OSWPQResultsAccess method) getPrettyParameters() (massdash.peakPickers.MRMTransitionGroupPicker method) getProteinTable() (massdash.loaders.access.OSWDataAccess method) getRunNames() (massdash.loaders.access.OSWDataAccess method) (massdash.loaders.access.ResultsTSVDataAccess method) getScoreTable() (massdash.loaders.access.OSWDataAccess method) getSoftware() (massdash.loaders.access.OSWPQResultsAccess method) getTopTransitionGroupFeature() (massdash.loaders.access.OSWPQResultsAccess method) (massdash.loaders.access.ResultsTSVDataAccess method) getTopTransitionGroupFeatureDf() (massdash.loaders.access.OSWPQResultsAccess method) (massdash.loaders.access.ResultsTSVDataAccess method) getTransitionData() (massdash.loaders.access.XICParquetDataAccess method) getTransitionDataDf() (massdash.loaders.access.XICParquetDataAccess method) getTransitionGroupFeatures() (massdash.loaders.access.OSWPQResultsAccess method) (massdash.loaders.access.ResultsTSVDataAccess method) getTransitionGroupFeaturesDf() (massdash.loaders.access.OSWPQResultsAccess method) (massdash.loaders.access.ResultsTSVDataAccess method) getTransitionIDAnnotationFromSequence() (massdash.loaders.access.OSWDataAccess method) getTransitionList() (massdash.loaders.access.TransitionPQPDataAccess method), [1]

H

has_im (massdash.loaders.access.MzMLDataAccess attribute) (massdash.loaders.access.OSWPQResultsAccess property) (massdash.structs.FeatureMap attribute)

hide_legends (massdash.plotting.PlotConfig attribute)

I

im_window (massdash.structs.TargetedDIAConfig attribute) in_file (massdash.loaders.SpectralLibraryLoader attribute) include_ms1 (massdash.plotting.PlotConfig attribute) include_ms2 (massdash.plotting.PlotConfig attribute)

integrate_intensity_across_two_dimensions() (massdash.structs.FeatureMap static method) InteractivePlotter (class in massdash.plotting) InteractiveThreeDimensionPlotter (class in massdash.plotting) InteractiveTwoDimensionPlotter (class in massdash.plotting) is_mz_in_product_mz_tol_window() (massdash.structs.TargetedDIAConfig method)

L

leftBoundary (massdash.structs.TransitionGroupFeature attribute) libraryFile (massdash.loaders.GenericSpectrumLoader attribute) (massdash.loaders.MzMLDataLoader attribute) load() (massdash.loaders.access.TransitionPQPDataAccess method) (massdash.loaders.access.TransitionTSVDataAccess method) (massdash.loaders.SpectralLibraryLoader method) load_data() (massdash.loaders.access.MzMLDataAccess method), [1] (massdash.loaders.access.OSWDataAccess method) load_model() (massdash.peakPickers.ConformerPeakPicker method), [1] load_spectrum() (massdash.loaders.access.MzMLDataAccess method) loadData() (massdash.loaders.access.ResultsTSVDataAccess method) loadExperimentSummary() (massdash.loaders.ResultsLoader method) loadFeatureMaps() (massdash.loaders.GenericSpectrumLoader method) (massdash.loaders.MzMLDataLoader method) loadIdentifiedPeptides() (massdash.loaders.ResultsLoader method) loadIdentifiedPrecursors() (massdash.loaders.ResultsLoader method) loadIdentifiedProteins() (massdash.loaders.ResultsLoader method) loadNumIdentifiedPeptides() (massdash.loaders.ResultsLoader method) loadNumIdentifiedPrecursors() (massdash.loaders.ResultsLoader method)

loadNumIdentifiedProteins() (massdash.loaders.ResultsLoader method) loadQuantificationMatrix() (massdash.loaders.ResultsLoader method) loadScoreDistribution() (massdash.loaders.ResultsLoader method) loadTopTransitionGroupFeature() (massdash.loaders.ResultsLoader method) loadTopTransitionGroupFeatureDf() (massdash.loaders.ResultsLoader method) loadTransitionGroupFeatures() (massdash.loaders.ResultsLoader method) loadTransitionGroupFeaturesDf() (massdash.loaders.ResultsLoader method) loadTransitionGroups() (massdash.loaders.GenericChromatogramLoader method) (massdash.loaders.GenericSpectrumLoader method) (massdash.loaders.MzMLDataLoader method) (massdash.loaders.OpenSwathXICParquetLoader method) (massdash.loaders.SqMassLoader method) (massdash.loaders.XICParquetDataLoader method) loadTransitionGroupsDf() (massdash.loaders.GenericChromatogramLoader method) (massdash.loaders.GenericSpectrumLoader method) (massdash.loaders.MzMLDataLoader method) (massdash.loaders.OpenSwathXICParquetLoader method) (massdash.loaders.SqMassLoader method) (massdash.loaders.XICParquetDataLoader method) loadValidScores() (massdash.loaders.ResultsLoader method)

M

massdash.loaders module massdash.loaders.access module massdash.peakPickers module massdash.plotting module massdash.structs module massdash.testing module matches() (massdash.testing.BokehSnapshotExtension method) (massdash.testing.NumpySnapshotExtension method) (massdash.testing.PandasSnapshotExtension method) (massdash.testing.PlotlySnapshotExtension method) max() (massdash.structs.Data1D method) (massdash.structs.TransitionGroup method) median() (massdash.structs.Data1D method) (massdash.structs.TransitionGroup method)

meta_data (massdash.loaders.access.MzMLDataAccess attribute) Mobilogram (class in massdash.structs) mode (massdash.loaders.access.OSWDataAccess attribute) (massdash.loaders.GenericChromatogramLoader attribute) (massdash.loaders.ResultsLoader attribute) module massdash.loaders massdash.loaders.access massdash.peakPickers massdash.plotting massdash.structs massdash.testing MRMTransitionGroupPicker (class in massdash.peakPickers) ms1_mz_tol (massdash.structs.TargetedDIAConfig attribute) msExperimentToFeatureMap() (massdash.loaders.access.MzMLDataAccess method) mslevel (massdash.structs.TargetedDIAConfig attribute) mz_tol (massdash.structs.TargetedDIAConfig attribute) MzMLDataAccess (class in massdash.loaders.access) MzMLDataLoader (class in massdash.loaders)

N

normalization_dict (massdash.plotting.PlotConfig attribute)

num_plot_columns (massdash.plotting.PlotConfig attribute) NumpySnapshotExtension (class in massdash.testing)

O

onnx_session (massdash.peakPickers.ConformerPeakPicker attribute) OpenSwathXICParquetAccess (class in massdash.loaders.access)

OpenSwathXICParquetLoader (class in massdash.loaders) OSWDataAccess (class in massdash.loaders.access) OSWPQResultsAccess (class in massdash.loaders.access)

P

PandasSnapshotExtension (class in massdash.testing) pick() (massdash.peakPickers.ConformerPeakPicker method), [1] (massdash.peakPickers.GenericPeakPicker method) (massdash.peakPickers.MRMTransitionGroupPicker method) (massdash.peakPickers.pyMRMTransitionGroupPicker method) plot() (massdash.plotting.InteractivePlotter method) (massdash.plotting.InteractiveThreeDimensionPlotter method) (massdash.plotting.InteractiveTwoDimensionPlotter method) (massdash.structs.TransitionGroup method) plot_3d_scatter() (massdash.plotting.InteractiveThreeDimensionPlotter method) plot_3d_vline() (massdash.plotting.InteractiveThreeDimensionPlotter method) plot_aggregated_heatmap() (massdash.plotting.InteractiveTwoDimensionPlotter method) plot_chromatogram() (massdash.plotting.InteractivePlotter method) plot_individual_3d_mesh_cube() (massdash.plotting.InteractiveThreeDimensionPlotter method) plot_individual_3d_surface() (massdash.plotting.InteractiveThreeDimensionPlotter method) plot_individual_heatmaps() (massdash.plotting.InteractiveTwoDimensionPlotter method) plot_mobilogram() (massdash.plotting.InteractivePlotter method) plot_spectra() (massdash.plotting.InteractivePlotter method) plotChromatogram() (massdash.loaders.GenericChromatogramLoader method) (massdash.loaders.GenericSpectrumLoader method)

PlotConfig (class in massdash.plotting) plotCV() (massdash.loaders.ResultsLoader method) plotIdentifications() (massdash.loaders.ResultsLoader method) PlotlySnapshotExtension (class in massdash.testing) plotQuantifications() (massdash.loaders.ResultsLoader method) plotUpset() (massdash.loaders.ResultsLoader method) populateTransitionGroupFeature() (massdash.loaders.access.OSWPQResultsAccess method) (massdash.loaders.SpectralLibraryLoader method) populateTransitionGroupFeatures() (massdash.loaders.SpectralLibraryLoader method) precursor_charge (massdash.structs.TransitionGroupFeature attribute) precursor_mz (massdash.structs.TransitionGroupFeature attribute) prediction_threshold (massdash.peakPickers.ConformerPeakPicker attribute) prediction_type (massdash.peakPickers.ConformerPeakPicker attribute) prepare_array() (massdash.plotting.InteractiveTwoDimensionPlotter method) pretrained_model_file (massdash.peakPickers.ConformerPeakPicker attribute) process_chrom() (massdash.plotting.InteractivePlotter method) process_mobilo() (massdash.plotting.InteractivePlotter method) process_spectra() (massdash.plotting.InteractivePlotter method) product_annotations (massdash.structs.TransitionGroupFeature attribute) product_mz (massdash.structs.TransitionGroupFeature attribute) pyMRMTransitionGroupPicker (class in massdash.peakPickers)

Q

qvalue (massdash.structs.TransitionGroupFeature attribute)

R

readOptions (massdash.loaders.access.MzMLDataAccess attribute) reduce_spectra() (massdash.loaders.access.MzMLDataAccess method) ResultsLoader (class in massdash.loaders) ResultsTSVDataAccess (class in massdash.loaders.access) rightBoundary (massdash.structs.TransitionGroupFeature attribute)

rsltsFile (massdash.loaders.GenericChromatogramLoader attribute) (massdash.loaders.GenericSpectrumLoader attribute) (massdash.loaders.MzMLDataLoader attribute) (massdash.loaders.ResultsLoader attribute) rt_window (massdash.structs.TargetedDIAConfig attribute)

S

save() (massdash.loaders.SpectralLibraryLoader method) scale_intensity (massdash.plotting.PlotConfig attribute) sequence (massdash.structs.TransitionGroupFeature attribute) serialize() (massdash.testing.BokehSnapshotExtension method) (massdash.testing.NumpySnapshotExtension method) (massdash.testing.PandasSnapshotExtension method) (massdash.testing.PlotlySnapshotExtension method) setDefaults() (massdash.peakPickers.MRMTransitionGroupPicker method) setGeneralParameters() (massdash.peakPickers.MRMTransitionGroupPicker method) setSmoother() (massdash.peakPickers.MRMTransitionGroupPicker method)

show() (massdash.plotting.InteractivePlotter method) (massdash.plotting.InteractiveThreeDimensionPlotter method) (massdash.plotting.InteractiveTwoDimensionPlotter method) smoothing_dict (massdash.plotting.PlotConfig attribute) SpectralLibraryLoader (class in massdash.loaders) Spectrum (class in massdash.structs) SqMassDataAccess (class in massdash.loaders.access) SqMassLoader (class in massdash.loaders) subtitle (massdash.plotting.PlotConfig attribute) sum() (massdash.structs.Data1D method) (massdash.structs.TransitionGroup method)

T

TargetedDIAConfig (class in massdash.structs) title (massdash.plotting.PlotConfig attribute) to_chromatograms() (massdash.structs.FeatureMap method) (massdash.structs.FeatureMapCollection method) to_mobilograms() (massdash.structs.FeatureMap method) (massdash.structs.FeatureMapCollection method) to_pyopenms() (massdash.structs.Chromatogram method) (massdash.structs.TransitionGroup method) to_spectra() (massdash.structs.FeatureMap method) (massdash.structs.FeatureMapCollection method) toPandasDf() (massdash.structs.TransitionFeature static method) (massdash.structs.TransitionGroup method) (massdash.structs.TransitionGroupCollection method) (massdash.structs.TransitionGroupFeature static method)

toPandasDfHelper_() (massdash.structs.Data1D method) TopTransitionGroupFeatureCollection (class in massdash.structs) transition_group (massdash.peakPickers.ConformerPeakPicker attribute) TransitionFeature (class in massdash.structs) TransitionGroup (class in massdash.structs) TransitionGroupCollection (class in massdash.structs) TransitionGroupFeature (class in massdash.structs) TransitionGroupFeatureCollection (class in massdash.structs) TransitionPQPDataAccess (class in massdash.loaders.access) TransitionTSVDataAccess (class in massdash.loaders.access) type_of_3d_plot (massdash.plotting.PlotConfig attribute) type_of_comparison (massdash.plotting.PlotConfig attribute) type_of_heatmap (massdash.plotting.PlotConfig attribute)

U

update() (massdash.plotting.PlotConfig method) (massdash.structs.TargetedDIAConfig method), [1]

V

validateSQL() (massdash.loaders.access.OSWDataAccess method) verbose (massdash.loaders.access.OSWDataAccess attribute) (massdash.loaders.GenericChromatogramLoader attribute) (massdash.loaders.ResultsLoader attribute) (massdash.plotting.InteractivePlotter attribute)

W

window_size (massdash.peakPickers.ConformerPeakPicker attribute)

X

x_axis_label (massdash.plotting.PlotConfig attribute) x_range (massdash.plotting.PlotConfig attribute)

XICParquetDataAccess (class in massdash.loaders.access) XICParquetDataLoader (class in massdash.loaders)

Y

y_axis_label (massdash.plotting.PlotConfig attribute)

y_range (massdash.plotting.PlotConfig attribute)