Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | Y A aa_match() (proteobench.score.denovoscores.DenovoScores method) aa_match_prefix() (proteobench.score.denovoscores.DenovoScores method) add() (proteobench.validation.report.ValidationReport method) (proteobench.validation.ValidationReport method) add_current_data_point() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.quant.quant_base_module.QuantModule method) add_error() (proteobench.validation.report.ValidationReport method) (proteobench.validation.ValidationReport method) add_features() (proteobench.io.parsing.parse_settings.ParseSettingsDeNovo method) add_fixed_mod() (in module proteobench.io.parsing.utils) add_info() (proteobench.validation.report.ValidationReport method) (proteobench.validation.ValidationReport method) add_maxquant_fixed_modifications() (in module proteobench.io.parsing.utils) add_modification_parser() (proteobench.io.parsing.parse_settings.ParseSettingsDeNovo method) (proteobench.io.parsing.parse_settings.ParseSettingsEntrapment method) (proteobench.io.parsing.parse_settings.ParseSettingsQuant method) add_record() (in module proteobench.io.params.maxquant) add_warning() (proteobench.validation.report.ValidationReport method) (proteobench.validation.ValidationReport method) additional_params_json (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) aggregate_modification_column() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform) aggregate_modification_sites_column() (in module proteobench.io.parsing.parse_ion) all_datapoints (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) all_datapoints_submission (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) all_datapoints_submitted (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) allowed_miscleavages (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] alpha_warning (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) archived_warning (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) available_profiles() (in module proteobench.validation) (in module proteobench.validation.profiles) B benchmarking() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.denovo.denovo_DDA_HCD.DDAHCDDeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.entrapment.entrapment_ion_DIA_Astral.DIAEntrapmentIonModuleAstral method) (proteobench.modules.quant.quant_base_module.QuantModule method) (proteobench.modules.quant.quant_lfq_ion_DDA_Astral.DDAQuantIonAstralModule method) (proteobench.modules.quant.quant_lfq_ion_DDA_QExactive.DDAQuantIonModuleQExactive method) (proteobench.modules.quant.quant_lfq_ion_DIA_AIF.DIAQuantIonModuleAIF method) (proteobench.modules.quant.quant_lfq_ion_DIA_Astral.DIAQuantIonModuleAstral method) (proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF.DIAQuantIonModulediaPASEF method) (proteobench.modules.quant.quant_lfq_ion_DIA_lowinput.DIAQuantIonModulediaSC method) (proteobench.modules.quant.quant_lfq_ion_DIA_Plasma.DIAQuantIonModulePlasma method) (proteobench.modules.quant.quant_lfq_ion_DIA_ZenoTOF.DIAQuantIonModuleZenoTOF method) (proteobench.modules.quant.quant_lfq_peptidoform_DDA.DDAQuantPeptidoformModule method) (proteobench.modules.quant.quant_lfq_peptidoform_DIA.DIAQuantPeptidoformModule method) benchmarking_2() (proteobench.modules.quant.quant_lfq_ion_DDA_Astral.DDAQuantIonAstralModule method) beta_warning (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) build_parser() (proteobench.io.parsing.parse_settings.ParseSettingsBuilder method) build_Series_from_records() (in module proteobench.io.params.maxquant) button_submission_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) C calculate_fdp_at_fdr_thresholds() (proteobench.score.entrapmentscores.EntrapmentScores method) calculate_lower_bound_fdp() (proteobench.score.entrapmentscores.EntrapmentScores static method) calculate_metrics() (proteobench.score.entrapmentscores.EntrapmentScores method) calculate_paired_fdp() (proteobench.score.entrapmentscores.EntrapmentScores static method) calculate_prc() (in module proteobench.datapoint.denovo_datapoint) calculate_reported_fdr() (proteobench.score.entrapmentscores.EntrapmentScores static method) calculate_upper_bound_combined_fdp() (proteobench.score.entrapmentscores.EntrapmentScores static method) categorise_metric() (proteobench.score.entrapmentscores.EntrapmentScores static method) category_combined (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute) category_paired (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute) charge_column (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] Check (class in proteobench.validation) (class in proteobench.validation.profiles) check (proteobench.validation.report.ValidationIssue attribute), [1] (proteobench.validation.ValidationIssue attribute), [1] check_charge_range() (in module proteobench.validation.checks) check_enzyme() (in module proteobench.validation.checks) check_fdr_psm() (in module proteobench.validation.checks) check_mass_tolerances() (in module proteobench.validation.checks) check_max_modifications() (in module proteobench.validation.checks) check_modifications() (in module proteobench.validation.checks) check_names (proteobench.validation.profiles.ValidationProfile property) (proteobench.validation.ValidationProfile property) check_new_unique_hash() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.quant.quant_base_module.QuantModule method) check_peptide_length() (in module proteobench.validation.checks) check_protein_ids() (in module proteobench.validation.checks) check_run_consistency() (in module proteobench.validation.checks) check_submission (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) check_submission_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) CheckFunc (in module proteobench.validation.profiles) checkpoint (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) checks (proteobench.validation.profiles.ValidationProfile attribute), [1] (proteobench.validation.ValidationProfile attribute), [1] clean_line() (in module proteobench.io.params.alphadia) clean_text() (in module proteobench.io.params.peaks) (in module proteobench.io.params.spectronaut) clean_up_parameters() (in module proteobench.io.params.alphadia) clone() (proteobench.github.gh.GithubProteobotRepo static method) clone_pr() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.quant.quant_base_module.QuantModule method) clone_repo() (proteobench.github.gh.GithubProteobotRepo method) clone_repo_anonymous() (proteobench.github.gh.GithubProteobotRepo method) clone_repo_pr() (proteobench.github.gh.GithubProteobotRepo method) code (proteobench.validation.report.ValidationIssue attribute), [1] (proteobench.validation.ValidationIssue attribute), [1] collapse_aa_scores() (in module proteobench.datapoint.denovo_datapoint) colorblind_mode_selector_indepth_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) colorblind_mode_selector_submitted_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) colorblind_mode_selector_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) combined_FDP (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] comment (proteobench.io.params.fragger.Parameter attribute) comments (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] comments_submission_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) commit() (proteobench.github.gh.GithubProteobotRepo method) compute_condition_stats() (proteobench.score.QuantScoresHYE static method) (proteobench.score.quantscoresHYE.QuantScoresHYE static method) compute_epsilon() (proteobench.score.QuantScoresHYE static method) (proteobench.score.quantscoresHYE.QuantScoresHYE static method) compute_roc_auc() (in module proteobench.datapoint.quant_datapoint) compute_roc_auc_directional() (in module proteobench.datapoint.quant_datapoint) config (proteobench.validation.context.ValidationContext attribute), [1] (proteobench.validation.ValidationContext attribute), [1] contains() (proteobench.validation.fasta.FastaReference method) (proteobench.validation.FastaReference method) contains_any() (proteobench.validation.fasta.FastaReference method) (proteobench.validation.FastaReference method) contaminant_column (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] contaminant_flag (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] convert_peptidoform() (proteobench.score.denovoscores.DenovoScores method) convert_replicate_to_raw() (proteobench.score.QuantScoresHYE static method) (proteobench.score.quantscoresHYE.QuantScoresHYE static method) convert_to_proforma() (proteobench.io.parsing.parse_settings.ParseModificationSettings method) convert_to_standard_format() (proteobench.io.parsing.parse_settings.ParseSettingsDeNovo method) (proteobench.io.parsing.parse_settings.ParseSettingsEntrapment method) (proteobench.io.parsing.parse_settings.ParseSettingsQuant method) ConvertStandardFormatError count_chars() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform) create_branch() (proteobench.github.gh.GithubProteobotRepo method) create_pull_request() (proteobench.github.gh.GithubProteobotRepo method) D DatapointAppendError DatapointBase (class in proteobench.datapoint) (class in proteobench.datapoint.datapoint_base) DatapointGenerationError dataset_folder_exists() (in module proteobench.utils.server_io) dataset_selection_indepth (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Help attribute) dataset_selector_id_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) DatasetAlreadyExistsOnServerError DDAHCDDeNovoModule (class in proteobench.modules.denovo.denovo_DDA_HCD) DDAQuantIonAstralModule (class in proteobench.modules.quant.quant_lfq_ion_DDA_Astral) DDAQuantIonModuleQExactive (class in proteobench.modules.quant.quant_lfq_ion_DDA_QExactive) DDAQuantPeptidoformModule (class in proteobench.modules.quant.quant_lfq_peptidoform_DDA) decoding_strategy (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) decoy_prefixes (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] DEFAULT_DECOY_PREFIXES (in module proteobench.validation.config) default_evaluation (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) DEFAULT_GROUP_SEPARATORS (in module proteobench.validation.protein_ids) default_level (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) default_val_slider (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) DEFAULT_VALIDATION_PROFILE (in module proteobench.validation.config) DenovoDatapoint (class in proteobench.datapoint.denovo_datapoint) DeNovoModule (class in proteobench.modules.denovo.denovo_base) DeNovoPlotGenerator (class in proteobench.plotting.plot_generator_denovo) DenovoScores (class in proteobench.score.denovoscores) description (proteobench.validation.Check attribute), [1] (proteobench.validation.profiles.Check attribute), [1] (proteobench.validation.profiles.ValidationProfile attribute), [1] (proteobench.validation.ValidationProfile attribute), [1] description_files_md (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) description_input_file_md (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) description_module_md (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) description_radios_md (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) description_results_md (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) description_slider_md (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) description_submission_md (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) description_table_md (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) detect_newer_version() (in module proteobench.io.params.alphadia) df_head (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) DIAEntrapmentIonModuleAstral (class in proteobench.modules.entrapment.entrapment_ion_DIA_Astral) DIAQuantIonModuleAIF (class in proteobench.modules.quant.quant_lfq_ion_DIA_AIF) DIAQuantIonModuleAstral (class in proteobench.modules.quant.quant_lfq_ion_DIA_Astral) DIAQuantIonModulediaPASEF (class in proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF) DIAQuantIonModulediaSC (class in proteobench.modules.quant.quant_lfq_ion_DIA_lowinput) DIAQuantIonModulePlasma (class in proteobench.modules.quant.quant_lfq_ion_DIA_Plasma) DIAQuantIonModuleZenoTOF (class in proteobench.modules.quant.quant_lfq_ion_DIA_ZenoTOF) DIAQuantPeptidoformModule (class in proteobench.modules.quant.quant_lfq_peptidoform_DIA) doc_url (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.debug_session_state_variables.Variables attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) documentation_description (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) download_file() (in module proteobench.utils.server_io) download_selector_id_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) dynamic_range_human_plasma (proteobench.datapoint.quant_datapoint.QuantDatapointPYE attribute), [1] E enable_match_between_runs (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] enable_pmultiqc (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) EntrapmentDatapoint (class in proteobench.datapoint.entrapment_datapoint) EntrapmentError EntrapmentModule (class in proteobench.modules.entrapment.entrapment_base_module) EntrapmentPlotGenerator (class in proteobench.plotting.plot_generator_entrapment) EntrapmentScores (class in proteobench.score.entrapmentscores) enzyme (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] ERROR (proteobench.validation.report.Severity attribute) (proteobench.validation.Severity attribute) errors (proteobench.validation.report.ValidationReport property) (proteobench.validation.ValidationReport property) evaluate_match() (proteobench.score.denovoscores.DenovoScores method) evaluate_ptm() (proteobench.datapoint.denovo_datapoint.DenovoDatapoint static method) evaluation_mode_toggle_tab3_features (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) evaluation_mode_toggle_tab3_species (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) examples (proteobench.validation.report.ValidationIssue attribute), [1] (proteobench.validation.ValidationIssue attribute), [1] expected (proteobench.validation.report.ValidationIssue attribute), [1] (proteobench.validation.ValidationIssue attribute), [1] extend() (proteobench.validation.report.ValidationReport method) (proteobench.validation.ValidationReport method) extend_tuple() (in module proteobench.io.params.maxquant) extend_tuples_with_none() (in module proteobench.io.params.maxquant) extract_calibration_method() (in module proteobench.io.params.spectronaut) extract_cfg_parameter() (in module proteobench.io.params.diann) extract_identifiers() (in module proteobench.validation.protein_ids) extract_mass_tolerance() (in module proteobench.io.params.peaks) (in module proteobench.io.params.spectronaut) extract_modifications() (in module proteobench.io.params.diann) extract_params() (in module proteobench.io.params.adanovo) (in module proteobench.io.params.alphadia) (in module proteobench.io.params.alphapept) (in module proteobench.io.params.casanovo) (in module proteobench.io.params.contranovo) (in module proteobench.io.params.deepnovo) (in module proteobench.io.params.diann) (in module proteobench.io.params.fragger) (in module proteobench.io.params.i2masschroq) (in module proteobench.io.params.instanovo) (in module proteobench.io.params.maxquant) (in module proteobench.io.params.metamorpheus) (in module proteobench.io.params.msaid) (in module proteobench.io.params.msangel) (in module proteobench.io.params.peaks) (in module proteobench.io.params.pihelixnovo) (in module proteobench.io.params.piprimenovo) (in module proteobench.io.params.pointnovo) (in module proteobench.io.params.proline) (in module proteobench.io.params.quantms) (in module proteobench.io.params.sage) (in module proteobench.io.params.wombat) EXTRACT_PARAMS_DICT (proteobench.modules.denovo.denovo_base.DeNovoModule attribute) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule attribute) (proteobench.modules.quant.quant_base_module.QuantModule attribute) extract_params_mascot_specific() (in module proteobench.io.params.msangel) extract_params_xtandem_specific() (in module proteobench.io.params.msangel) extract_scan_id() (proteobench.io.parsing.parse_settings.ParseSettingsDeNovo method) extract_search_engine() (in module proteobench.io.params.msangel) extract_tolerances() (in module proteobench.io.params.spectronaut) extract_tolerances_with_regex() (in module proteobench.io.params.spectronaut) extract_value() (in module proteobench.io.params.peaks) (in module proteobench.io.params.spectronaut) extract_value_regex() (in module proteobench.io.params.peaks) (in module proteobench.io.params.spectronaut) extract_values_from_nested_lines() (in module proteobench.io.params.alphadia) extract_with_regex() (in module proteobench.io.params.diann) extras (proteobench.validation.context.ValidationContext attribute), [1] (proteobench.validation.ValidationContext attribute), [1] F fasta (proteobench.validation.context.ValidationContext attribute), [1] (proteobench.validation.ValidationContext attribute), [1] fasta_filename (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] fasta_url (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] FastaReference (class in proteobench.validation) (class in proteobench.validation.fasta) fdp_curve (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute) field (proteobench.validation.report.ValidationIssue attribute), [1] (proteobench.validation.ValidationIssue attribute), [1] fig_cv (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) fig_logfc (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) fig_ma_plot (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) fig_metric (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) fig_metric_submitted (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) fig_prefix (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) fig_ptm_overview (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) fig_ptm_specific (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) fig_species_overview (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) fig_spectrum_feature (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) fill_none() (proteobench.io.params.ProteoBenchParameters method) filter_data_point() (proteobench.modules.denovo.denovo_base.DeNovoModule static method) (proteobench.modules.quant.quant_base_module.QuantModule static method) filter_df_numquant_epsilon() (in module proteobench.datapoint.quant_datapoint) filter_df_numquant_nr_feature() (in module proteobench.datapoint.quant_datapoint) find_charge() (in module proteobench.io.params.proline) find_cmdline_string() (in module proteobench.io.params.diann) find_min_pep_length() (in module proteobench.io.params.proline) first_new_plot (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) flatten_dict_of_dicts() (in module proteobench.io.params.maxquant) flatten_results_column() (in module proteobench.plotting.plot_generator_denovo) format_scores() (proteobench.io.parsing.parse_settings.ParseSettingsDeNovo method) format_sequence() (proteobench.io.parsing.parse_settings.ParseSettingsDeNovo method) format_tolerances() (in module proteobench.io.params.metamorpheus) fragment_mass_tolerance (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] from_bytes() (proteobench.validation.fasta.FastaReference class method) (proteobench.validation.FastaReference class method) from_identifiers() (proteobench.validation.fasta.FastaReference class method) (proteobench.validation.FastaReference class method) from_parse_settings() (proteobench.validation.config.ModuleValidationConfig class method) (proteobench.validation.ModuleValidationConfig class method) from_path() (proteobench.validation.fasta.FastaReference class method) (proteobench.validation.FastaReference class method) from_text() (proteobench.validation.fasta.FastaReference class method) (proteobench.validation.FastaReference class method) from_url() (proteobench.validation.fasta.FastaReference class method) (proteobench.validation.FastaReference class method) func (proteobench.validation.Check attribute), [1] (proteobench.validation.profiles.Check attribute), [1] G generate_datapoint() (proteobench.datapoint.datapoint_base.DatapointBase static method) (proteobench.datapoint.DatapointBase static method) (proteobench.datapoint.denovo_datapoint.DenovoDatapoint static method) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint static method) (proteobench.datapoint.quant_datapoint.QuantDatapointHYE static method) (proteobench.datapoint.quant_datapoint.QuantDatapointPYE static method) (proteobench.datapoint.QuantDatapointHYE static method) generate_id() (proteobench.datapoint.datapoint_base.DatapointBase method) (proteobench.datapoint.DatapointBase method) (proteobench.datapoint.denovo_datapoint.DenovoDatapoint method) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint method) (proteobench.datapoint.quant_datapoint.QuantDatapointHYE method) (proteobench.datapoint.QuantDatapointHYE method) generate_in_depth_plots() (proteobench.plotting.LFQHYEPlotGenerator method) (proteobench.plotting.plot_generator_base.PlotGeneratorBase method) (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) (proteobench.plotting.plot_generator_entrapment.EntrapmentPlotGenerator method) (proteobench.plotting.plot_generator_lfq_HYE.LFQHYEPlotGenerator method) (proteobench.plotting.plot_generator_lfq_PYE.LFQPYEPlotGenerator method) (proteobench.plotting.PlotGeneratorBase method) generate_intermediate() (proteobench.score.denovoscores.DenovoScores method) (proteobench.score.entrapmentscores.EntrapmentScores method) (proteobench.score.QuantScoresHYE method) (proteobench.score.quantscoresHYE.QuantScoresHYE method) (proteobench.score.quantscoresPYE.QuantScoresPYE method) (proteobench.score.score_base.ScoreBase method) (proteobench.score.ScoreBase method) get_charges() (in module proteobench.io.params.msangel) get_cv_metrics() (proteobench.datapoint.quant_datapoint.QuantDatapointHYE static method) (proteobench.datapoint.QuantDatapointHYE static method) get_epsilon_metrics() (proteobench.datapoint.quant_datapoint.QuantDatapointHYE static method) (proteobench.datapoint.QuantDatapointHYE static method) get_homepage_tour_steps() (in module webinterface.pages.base_pages.tour_steps) get_in_depth_plot_descriptions() (proteobench.plotting.LFQHYEPlotGenerator method) (proteobench.plotting.plot_generator_base.PlotGeneratorBase method) (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) (proteobench.plotting.plot_generator_entrapment.EntrapmentPlotGenerator method) (proteobench.plotting.plot_generator_lfq_HYE.LFQHYEPlotGenerator method) (proteobench.plotting.plot_generator_lfq_PYE.LFQPYEPlotGenerator method) (proteobench.plotting.PlotGeneratorBase method) get_in_depth_plot_layout() (proteobench.plotting.LFQHYEPlotGenerator method) (proteobench.plotting.plot_generator_base.PlotGeneratorBase method) (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) (proteobench.plotting.plot_generator_entrapment.EntrapmentPlotGenerator method) (proteobench.plotting.plot_generator_lfq_HYE.LFQHYEPlotGenerator method) (proteobench.plotting.plot_generator_lfq_PYE.LFQPYEPlotGenerator method) (proteobench.plotting.PlotGeneratorBase method) get_incomplete_upload_warning() (in module proteobench.io.params.metamorpheus) get_indepth_metrics() (proteobench.datapoint.denovo_datapoint.DenovoDatapoint method) get_items_between() (in module proteobench.io.params.peaks) get_length_peptidoform_with_nterm() (proteobench.io.parsing.parse_settings.ParseSettingsDeNovo method) get_merged_json() (in module proteobench.utils.server_io) get_metrics() (proteobench.datapoint.datapoint_base.DatapointBase static method) (proteobench.datapoint.DatapointBase static method) (proteobench.datapoint.denovo_datapoint.DenovoDatapoint method) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint static method) (proteobench.datapoint.quant_datapoint.QuantDatapointHYE static method) (proteobench.datapoint.QuantDatapointHYE static method) get_modification_scores() (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator static method) get_open_source_tools() (in module proteobench.io.parsing.parse_settings) get_plot_generator() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.entrapment.entrapment_ion_DIA_Astral.DIAEntrapmentIonModuleAstral method) (proteobench.modules.quant.quant_base_module.QuantModule method) (proteobench.modules.quant.quant_lfq_ion_DDA_Astral.DDAQuantIonAstralModule method) (proteobench.modules.quant.quant_lfq_ion_DDA_QExactive.DDAQuantIonModuleQExactive method) (proteobench.modules.quant.quant_lfq_ion_DIA_AIF.DIAQuantIonModuleAIF method) (proteobench.modules.quant.quant_lfq_ion_DIA_Astral.DIAQuantIonModuleAstral method) (proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF.DIAQuantIonModulediaPASEF method) (proteobench.modules.quant.quant_lfq_ion_DIA_lowinput.DIAQuantIonModulediaSC method) (proteobench.modules.quant.quant_lfq_ion_DIA_Plasma.DIAQuantIonModulePlasma method) (proteobench.modules.quant.quant_lfq_peptidoform_DDA.DDAQuantPeptidoformModule method) (proteobench.modules.quant.quant_lfq_peptidoform_DIA.DIAQuantPeptidoformModule method) get_prc_curve() (in module proteobench.datapoint.denovo_datapoint) get_precision_metrics() (proteobench.datapoint.quant_datapoint.QuantDatapointHYE static method) (proteobench.datapoint.QuantDatapointHYE static method) get_profile() (in module proteobench.validation) (in module proteobench.validation.profiles) get_proforma_bracketed() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform) get_ptm_metrics() (proteobench.datapoint.denovo_datapoint.DenovoDatapoint method) get_quant_tour_steps() (in module webinterface.pages.base_pages.tour_steps) get_raw_data() (in module proteobench.utils.server_io) get_remote_url_anon() (proteobench.github.gh.GithubProteobotRepo method) get_species_metrics() (proteobench.datapoint.denovo_datapoint.DenovoDatapoint method) get_spectrum_metrics() (proteobench.datapoint.denovo_datapoint.DenovoDatapoint method) get_stripped_seq() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform) get_submission_dict() (in module proteobench.utils.submission) get_token_mass() (proteobench.score.denovoscores.DenovoScores method) get_token_str() (proteobench.score.denovoscores.DenovoScores method) get_upload_info() (proteobench.io.parsing.parse_settings.ParseSettingsBuilder method) github_link_pr (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) GithubProteobotRepo (class in proteobench.github.gh) graphical_abstract (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) H handle_benchmarking_error() (in module proteobench.modules.quant.benchmarking) has_errors (proteobench.validation.report.ValidationReport property) (proteobench.validation.ValidationReport property) highlight_list (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) highlight_list_submitted (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) homepage_title (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) homogenize_modification_string() (in module proteobench.io.params.alphadia) I id (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] ident_fdr_peptide (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] ident_fdr_protein (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] ident_fdr_psm (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] identifiers (proteobench.validation.fasta.FastaReference property) (proteobench.validation.FastaReference property) identify_file_type() (in module proteobench.io.params.metamorpheus) INFO (proteobench.validation.report.Severity attribute) (proteobench.validation.Severity attribute) infos (proteobench.validation.report.ValidationReport property) (proteobench.validation.ValidationReport property) initial_parameters (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) initial_results (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) initialize_default_parameters() (in module proteobench.io.params.alphadia) input_df (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) input_df_submission (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) input_file (webinterface.pages.texts.generic_texts.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.Help attribute) input_format (proteobench.validation.context.ValidationContext attribute), [1] (proteobench.validation.ValidationContext attribute), [1] (webinterface.pages.texts.generic_texts.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.Help attribute) intermediate_hash (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] IntermediateFormatGenerationError is_decoy_or_contaminant() (in module proteobench.validation.protein_ids) is_implemented() (in module proteobench.modules.rescoring.module_rescoring) (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.denovo.denovo_DDA_HCD.DDAHCDDeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.entrapment.entrapment_ion_DIA_Astral.DIAEntrapmentIonModuleAstral method) (proteobench.modules.quant.quant_base_module.QuantModule method) (proteobench.modules.quant.quant_lfq_ion_DDA_Astral.DDAQuantIonAstralModule method) (proteobench.modules.quant.quant_lfq_ion_DDA_QExactive.DDAQuantIonModuleQExactive method) (proteobench.modules.quant.quant_lfq_ion_DIA_AIF.DIAQuantIonModuleAIF method) (proteobench.modules.quant.quant_lfq_ion_DIA_Astral.DIAQuantIonModuleAstral method) (proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF.DIAQuantIonModulediaPASEF method) (proteobench.modules.quant.quant_lfq_ion_DIA_lowinput.DIAQuantIonModulediaSC method) (proteobench.modules.quant.quant_lfq_ion_DIA_Plasma.DIAQuantIonModulePlasma method) (proteobench.modules.quant.quant_lfq_ion_DIA_ZenoTOF.DIAQuantIonModuleZenoTOF method) (proteobench.modules.quant.quant_lfq_peptidoform_DDA.DDAQuantPeptidoformModule method) (proteobench.modules.quant.quant_lfq_peptidoform_DIA.DIAQuantPeptidoformModule method) is_temporary (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] isotope_error_range (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) issues (proteobench.validation.report.ValidationReport attribute), [1] (proteobench.validation.ValidationReport attribute), [1] K keywords (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.debug_session_state_variables.Variables attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) L legal_notice (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) LFQHYEPlotGenerator (class in proteobench.plotting) (class in proteobench.plotting.plot_generator_lfq_HYE) LFQPYEPlotGenerator (class in proteobench.plotting.plot_generator_lfq_PYE) load_files() (in module proteobench.io.params.metamorpheus) (in module proteobench.io.params.quantms) load_input_file() (in module proteobench.io.parsing.parse_denovo) (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform) load_params_file() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.quant.quant_base_module.QuantModule method) load_parsed_sdrf() (in module proteobench.io.params.quantms) load_versions() (in module proteobench.io.params.quantms) lower_bound_FDP (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] M make_submission() (in module proteobench.utils.server_io) map_keys_to_desired_format() (in module proteobench.io.params.alphadia) mass_diff() (proteobench.score.denovoscores.DenovoScores method) match_brackets() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform) max_intensity (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) max_mz (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) max_nr_observed (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) max_peptide_length (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] max_plausible_dalton (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] max_plausible_ppm (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] max_precursor_charge (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) MAX_PROTEIN_EXAMPLES (in module proteobench.validation.checks) MAX_ROW_EXAMPLES (in module proteobench.validation.checks) mean_abs_epsilon (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) mean_abs_epsilon_eq_species (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] mean_abs_epsilon_global (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] mean_abs_epsilon_precision_eq_species (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] mean_abs_epsilon_precision_global (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] median_abs_epsilon (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) median_abs_epsilon_eq_species (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] median_abs_epsilon_global (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] median_abs_epsilon_human_plasma (proteobench.datapoint.quant_datapoint.QuantDatapointPYE attribute), [1] median_abs_epsilon_precision_eq_species (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] median_abs_epsilon_precision_global (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] median_abs_log2_fc_error_spike_ins (proteobench.datapoint.quant_datapoint.QuantDatapointPYE attribute), [1] message (proteobench.validation.report.ValidationIssue attribute), [1] (proteobench.validation.ValidationIssue attribute), [1] meta_data (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) meta_data_file (webinterface.pages.texts.generic_texts.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.Help attribute) meta_data_text (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) meta_file_uploader_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) metric_calc_approach_selector_indepth_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) metric_calc_approach_selector_submitted_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) metric_calc_approach_selector_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) metric_plot_labels (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) metric_selector_indepth_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) metric_selector_submitted_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) metric_selector_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) min_intensity (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) min_mz (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) min_peptide_length (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] min_precursor_charge (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) module proteobench proteobench.datapoint proteobench.datapoint.datapoint_base proteobench.datapoint.denovo_datapoint proteobench.datapoint.entrapment_datapoint proteobench.datapoint.quant_datapoint proteobench.exceptions proteobench.github proteobench.github.gh proteobench.io proteobench.io.params proteobench.io.params.adanovo proteobench.io.params.alphadia proteobench.io.params.alphapept proteobench.io.params.casanovo proteobench.io.params.contranovo proteobench.io.params.deepnovo proteobench.io.params.diann proteobench.io.params.fragger proteobench.io.params.i2masschroq proteobench.io.params.instanovo proteobench.io.params.maxquant proteobench.io.params.metamorpheus proteobench.io.params.msaid proteobench.io.params.msangel proteobench.io.params.peaks proteobench.io.params.pihelixnovo proteobench.io.params.piprimenovo proteobench.io.params.pointnovo proteobench.io.params.proline proteobench.io.params.quantms proteobench.io.params.sage proteobench.io.params.spectronaut proteobench.io.params.wombat proteobench.io.parsing proteobench.io.parsing.parse_denovo proteobench.io.parsing.parse_ion proteobench.io.parsing.parse_peptidoform proteobench.io.parsing.parse_settings proteobench.io.parsing.utils proteobench.modules proteobench.modules.constants proteobench.modules.denovo proteobench.modules.denovo.denovo_base proteobench.modules.denovo.denovo_DDA_HCD proteobench.modules.entrapment proteobench.modules.entrapment.entrapment_base_module proteobench.modules.entrapment.entrapment_ion_DIA_Astral proteobench.modules.quant proteobench.modules.quant.benchmarking proteobench.modules.quant.quant_base_module proteobench.modules.quant.quant_lfq_ion_DDA_Astral proteobench.modules.quant.quant_lfq_ion_DDA_QExactive proteobench.modules.quant.quant_lfq_ion_DIA_AIF proteobench.modules.quant.quant_lfq_ion_DIA_Astral proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF proteobench.modules.quant.quant_lfq_ion_DIA_lowinput proteobench.modules.quant.quant_lfq_ion_DIA_Plasma proteobench.modules.quant.quant_lfq_ion_DIA_ZenoTOF proteobench.modules.quant.quant_lfq_peptidoform_DDA proteobench.modules.quant.quant_lfq_peptidoform_DIA proteobench.modules.rescoring proteobench.modules.rescoring.module_rescoring proteobench.plotting proteobench.plotting.plot_generator_base proteobench.plotting.plot_generator_denovo proteobench.plotting.plot_generator_entrapment proteobench.plotting.plot_generator_lfq_HYE proteobench.plotting.plot_generator_lfq_PYE proteobench.score proteobench.score.denovoscores proteobench.score.entrapmentscores proteobench.score.quantscoresHYE proteobench.score.quantscoresPYE proteobench.score.score_base proteobench.utils proteobench.utils.server_io proteobench.utils.submission proteobench.validation proteobench.validation.checks proteobench.validation.config proteobench.validation.context proteobench.validation.exceptions proteobench.validation.fasta proteobench.validation.profiles proteobench.validation.protein_ids proteobench.validation.report proteobench.validation.validator webinterface webinterface.pages webinterface.pages.base_pages webinterface.pages.base_pages.tour_steps webinterface.pages.base_pages.utils webinterface.pages.future_pages webinterface.pages.markdown_files webinterface.pages.markdown_files.DeNovo webinterface.pages.markdown_files.DeNovo.DDA webinterface.pages.markdown_files.Entrapment webinterface.pages.markdown_files.Entrapment.DIA webinterface.pages.markdown_files.Entrapment.DIA.ion webinterface.pages.markdown_files.Entrapment.DIA.ion.Astral webinterface.pages.markdown_files.Quant webinterface.pages.markdown_files.Quant.lfq webinterface.pages.markdown_files.Quant.lfq.DDA webinterface.pages.markdown_files.Quant.lfq.DDA.ion webinterface.pages.markdown_files.Quant.lfq.DDA.ion.Astral webinterface.pages.markdown_files.Quant.lfq.DDA.ion.QExactive webinterface.pages.markdown_files.Quant.lfq.DDA.peptidoform webinterface.pages.markdown_files.Quant.lfq.DIA webinterface.pages.markdown_files.Quant.lfq.DIA.ion webinterface.pages.markdown_files.Quant.lfq.DIA.ion.AIF webinterface.pages.markdown_files.Quant.lfq.DIA.ion.Astral webinterface.pages.markdown_files.Quant.lfq.DIA.ion.diaPASEF webinterface.pages.markdown_files.Quant.lfq.DIA.ion.lowinput webinterface.pages.markdown_files.Quant.lfq.DIA.ion.ZenoTOF webinterface.pages.pages_variables webinterface.pages.pages_variables.DeNovo webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables webinterface.pages.pages_variables.Entrapment webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables webinterface.pages.pages_variables.Quant webinterface.pages.pages_variables.Quant.debug_session_state_variables webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables webinterface.pages.texts webinterface.pages.texts.generic_texts webinterface.pages.texts.generic_texts_denovo webinterface.pages.texts.generic_texts_dia webinterface.pages.utils module_id (proteobench.modules.denovo.denovo_DDA_HCD.DDAHCDDeNovoModule attribute) (proteobench.modules.entrapment.entrapment_ion_DIA_Astral.DIAEntrapmentIonModuleAstral attribute), [1] (proteobench.modules.quant.quant_lfq_ion_DDA_Astral.DDAQuantIonAstralModule attribute), [1] (proteobench.modules.quant.quant_lfq_ion_DDA_QExactive.DDAQuantIonModuleQExactive attribute), [1] (proteobench.modules.quant.quant_lfq_ion_DIA_AIF.DIAQuantIonModuleAIF attribute), [1] (proteobench.modules.quant.quant_lfq_ion_DIA_Astral.DIAQuantIonModuleAstral attribute), [1] (proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF.DIAQuantIonModulediaPASEF attribute), [1] (proteobench.modules.quant.quant_lfq_ion_DIA_lowinput.DIAQuantIonModulediaSC attribute), [1] (proteobench.modules.quant.quant_lfq_ion_DIA_Plasma.DIAQuantIonModulePlasma attribute), [1] (proteobench.modules.quant.quant_lfq_ion_DIA_ZenoTOF.DIAQuantIonModuleZenoTOF attribute), [1] (proteobench.modules.quant.quant_lfq_peptidoform_DDA.DDAQuantPeptidoformModule attribute), [1] (proteobench.modules.quant.quant_lfq_peptidoform_DIA.DIAQuantPeptidoformModule attribute), [1] ModuleValidationConfig (class in proteobench.validation) (class in proteobench.validation.config) N n_beams (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) n_peaks (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) name (proteobench.io.params.fragger.Parameter attribute) (proteobench.validation.Check attribute), [1] (proteobench.validation.profiles.Check attribute), [1] (proteobench.validation.profiles.ValidationProfile attribute), [1] (proteobench.validation.ValidationProfile attribute), [1] no_results (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) normalize() (proteobench.io.params.ProteoBenchParameters method) normalize_dataframe_columns() (in module proteobench.io.params) normalize_enzyme() (in module proteobench.io.params.diann) nr_feature (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] nr_id_features (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] nr_quantified_spike_ins (proteobench.datapoint.quant_datapoint.QuantDatapointPYE attribute), [1] O observed (proteobench.validation.report.ValidationIssue attribute), [1] (proteobench.validation.ValidationIssue attribute), [1] obtain_all_data_points() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.quant.quant_base_module.QuantModule method) P paired_FDP (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] Parameter (class in proteobench.io.params.fragger) parameters (proteobench.validation.context.ValidationContext attribute), [1] (proteobench.validation.ValidationContext attribute), [1] parameters_additional (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) params_file_dict (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) params_json_dict (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) parse_button (webinterface.pages.texts.generic_texts.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.Help attribute) parse_cmdline_string() (in module proteobench.io.params.diann) parse_fasta_header() (in module proteobench.validation.fasta) parse_key_value() (in module proteobench.io.params.alphadia) parse_modifications() (in module proteobench.io.params.metamorpheus) parse_params() (in module proteobench.io.params.fragger) parse_phi_report_filters() (in module proteobench.io.params.fragger) parse_predictors_library() (in module proteobench.io.params.diann) parse_protein_inference_method() (in module proteobench.io.params.diann) parse_quantification_strategy() (in module proteobench.io.params.diann) parse_setting() (in module proteobench.io.params.diann) parse_settings_dir (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) ParseError ParseModificationSettings (class in proteobench.io.parsing.parse_settings) ParseSettingsBuilder (class in proteobench.io.parsing.parse_settings) ParseSettingsDeNovo (class in proteobench.io.parsing.parse_settings) ParseSettingsEntrapment (class in proteobench.io.parsing.parse_settings) ParseSettingsError ParseSettingsQuant (class in proteobench.io.parsing.parse_settings) passed (proteobench.validation.report.ValidationReport property) (proteobench.validation.ValidationReport property) placeholder_dataset_selection_container (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) placeholder_downloads_container (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) placeholder_fig_compare (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) placeholder_slider (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) placeholder_slider_submitted (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) placeholder_table (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) placeholder_table_submitted (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) plot_category_strip() (proteobench.plotting.plot_generator_entrapment.EntrapmentPlotGenerator method) plot_fdp_id_scatter() (proteobench.plotting.plot_generator_entrapment.EntrapmentPlotGenerator method) plot_fdp_ratio() (proteobench.plotting.plot_generator_entrapment.EntrapmentPlotGenerator method) plot_forest() (proteobench.plotting.plot_generator_entrapment.EntrapmentPlotGenerator method) plot_main_metric() (proteobench.plotting.LFQHYEPlotGenerator method) (proteobench.plotting.plot_generator_base.PlotGeneratorBase method) (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) (proteobench.plotting.plot_generator_entrapment.EntrapmentPlotGenerator method) (proteobench.plotting.plot_generator_lfq_HYE.LFQHYEPlotGenerator method) (proteobench.plotting.plot_generator_lfq_PYE.LFQPYEPlotGenerator method) (proteobench.plotting.PlotGeneratorBase method) plot_ptm_overview() (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) plot_ptm_specific() (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) plot_species_overview() (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) plot_species_specific() (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) plot_spectrum_feature() (proteobench.plotting.plot_generator_denovo.DeNovoPlotGenerator method) PlotError PlotGeneratorBase (class in proteobench.plotting) (class in proteobench.plotting.plot_generator_base) precision_aa (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) precision_peptide (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) precursor_column_name (proteobench.modules.entrapment.entrapment_ion_DIA_Astral.DIAEntrapmentIonModuleAstral attribute) (proteobench.modules.quant.quant_lfq_ion_DDA_Astral.DDAQuantIonAstralModule attribute) (proteobench.modules.quant.quant_lfq_ion_DDA_QExactive.DDAQuantIonModuleQExactive attribute) (proteobench.modules.quant.quant_lfq_ion_DIA_AIF.DIAQuantIonModuleAIF attribute) (proteobench.modules.quant.quant_lfq_ion_DIA_Astral.DIAQuantIonModuleAstral attribute) (proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF.DIAQuantIonModulediaPASEF attribute) (proteobench.modules.quant.quant_lfq_ion_DIA_ZenoTOF.DIAQuantIonModuleZenoTOF attribute) (proteobench.modules.quant.quant_lfq_peptidoform_DDA.DDAQuantPeptidoformModule attribute) (proteobench.modules.quant.quant_lfq_peptidoform_DIA.DIAQuantPeptidoformModule attribute) precursor_mass_tolerance (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] precursor_name (proteobench.modules.quant.quant_lfq_ion_DIA_lowinput.DIAQuantIonModulediaSC attribute) (proteobench.modules.quant.quant_lfq_ion_DIA_Plasma.DIAQuantIonModulePlasma attribute) prefix_params (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) privacy_notice (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) process_fragment_mz() (in module proteobench.io.params.alphadia) process_key_value_line() (in module proteobench.io.params.alphadia) process_precursor_charge() (in module proteobench.io.params.alphadia) process_precursor_len() (in module proteobench.io.params.alphadia) process_precursor_mz() (in module proteobench.io.params.alphadia) proforma_column (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] protein_column (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] protein_group_separators (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] proteobench module proteobench.datapoint module proteobench.datapoint.datapoint_base module proteobench.datapoint.denovo_datapoint module proteobench.datapoint.entrapment_datapoint module proteobench.datapoint.quant_datapoint module proteobench.exceptions module proteobench.github module proteobench.github.gh module proteobench.io module proteobench.io.params module proteobench.io.params.adanovo module proteobench.io.params.alphadia module proteobench.io.params.alphapept module proteobench.io.params.casanovo module proteobench.io.params.contranovo module proteobench.io.params.deepnovo module proteobench.io.params.diann module proteobench.io.params.fragger module proteobench.io.params.i2masschroq module proteobench.io.params.instanovo module proteobench.io.params.maxquant module proteobench.io.params.metamorpheus module proteobench.io.params.msaid module proteobench.io.params.msangel module proteobench.io.params.peaks module proteobench.io.params.pihelixnovo module proteobench.io.params.piprimenovo module proteobench.io.params.pointnovo module proteobench.io.params.proline module proteobench.io.params.quantms module proteobench.io.params.sage module proteobench.io.params.spectronaut module proteobench.io.params.wombat module proteobench.io.parsing module proteobench.io.parsing.parse_denovo module proteobench.io.parsing.parse_ion module proteobench.io.parsing.parse_peptidoform module proteobench.io.parsing.parse_settings module proteobench.io.parsing.utils module proteobench.modules module proteobench.modules.constants module proteobench.modules.denovo module proteobench.modules.denovo.denovo_base module proteobench.modules.denovo.denovo_DDA_HCD module proteobench.modules.entrapment module proteobench.modules.entrapment.entrapment_base_module module proteobench.modules.entrapment.entrapment_ion_DIA_Astral module proteobench.modules.quant module proteobench.modules.quant.benchmarking module proteobench.modules.quant.quant_base_module module proteobench.modules.quant.quant_lfq_ion_DDA_Astral module proteobench.modules.quant.quant_lfq_ion_DDA_QExactive module proteobench.modules.quant.quant_lfq_ion_DIA_AIF module proteobench.modules.quant.quant_lfq_ion_DIA_Astral module proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF module proteobench.modules.quant.quant_lfq_ion_DIA_lowinput module proteobench.modules.quant.quant_lfq_ion_DIA_Plasma module proteobench.modules.quant.quant_lfq_ion_DIA_ZenoTOF module proteobench.modules.quant.quant_lfq_peptidoform_DDA module proteobench.modules.quant.quant_lfq_peptidoform_DIA module proteobench.modules.rescoring module proteobench.modules.rescoring.module_rescoring module proteobench.plotting module proteobench.plotting.plot_generator_base module proteobench.plotting.plot_generator_denovo module proteobench.plotting.plot_generator_entrapment module proteobench.plotting.plot_generator_lfq_HYE module proteobench.plotting.plot_generator_lfq_PYE module proteobench.score module proteobench.score.denovoscores module proteobench.score.entrapmentscores module proteobench.score.quantscoresHYE module proteobench.score.quantscoresPYE module proteobench.score.score_base module proteobench.utils module proteobench.utils.server_io module proteobench.utils.submission module proteobench.validation module proteobench.validation.checks module proteobench.validation.config module proteobench.validation.context module proteobench.validation.exceptions module proteobench.validation.fasta module proteobench.validation.profiles module proteobench.validation.protein_ids module proteobench.validation.report module proteobench.validation.validator module proteobench_version (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] ProteoBenchError ProteobenchError ProteoBenchParameters (class in proteobench.io.params) ptm_overview (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Description attribute) ptm_specific (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Description attribute) pull_req (webinterface.pages.texts.generic_texts.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Help attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.Help attribute) Q QuantDatapointHYE (class in proteobench.datapoint) (class in proteobench.datapoint.quant_datapoint) QuantDatapointPYE (class in proteobench.datapoint.quant_datapoint) QuantificationError QuantModule (class in proteobench.modules.quant.quant_base_module) QuantScoresHYE (class in proteobench.score) (class in proteobench.score.quantscoresHYE) QuantScoresPYE (class in proteobench.score.quantscoresPYE) R radio_evaluation (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Help attribute) radio_evaluation_id_indepth_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) radio_evaluation_id_submitted_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) radio_evaluation_id_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) radio_level (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Help attribute) radio_level_id_indepth_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) radio_level_id_submitted_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) radio_level_id_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) raise_if_errors() (proteobench.validation.report.ValidationReport method) (proteobench.validation.ValidationReport method) raw_data_url (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) read_file() (in module proteobench.io.params.maxquant) read_file_lines() (in module proteobench.io.params.alphadia) read_fragpipe_workflow() (in module proteobench.io.params.fragger) read_reference_database() (proteobench.validation.config.ModuleValidationConfig static method) (proteobench.validation.ModuleValidationConfig static method) read_results_json_repo() (proteobench.github.gh.GithubProteobotRepo method) read_results_json_repo_single_file() (proteobench.github.gh.GithubProteobotRepo method) read_spectronaut_settings() (in module proteobench.io.params.spectronaut) read_xml_record() (in module proteobench.io.params.maxquant) recall_aa (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) recall_peptide (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) recommended_max_fdr_psm (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] record_proportions_to_results_feature() (proteobench.datapoint.denovo_datapoint.DenovoDatapoint static method) reference (proteobench.validation.context.ValidationContext attribute), [1] (proteobench.validation.ValidationContext attribute), [1] register_profile() (in module proteobench.validation) (in module proteobench.validation.profiles) remove_precursor_tol (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) reported_fdr_parsed_from_input (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] result_perf (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) result_performance_submission (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) result_plot_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) result_submitted_plot_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) results (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] run() (proteobench.validation.Check method) (proteobench.validation.profiles.Check method) run_benchmarking() (in module proteobench.modules.quant.benchmarking) run_benchmarking_with_timing() (in module proteobench.modules.quant.benchmarking) run_instructions (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) S ScoreBase (class in proteobench.score) (class in proteobench.score.score_base) search_engine (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] search_engine_version (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] selectbox_id_indepth_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) selectbox_id_submitted_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) selectbox_id_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) sequence_column (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] Severity (class in proteobench.validation) (class in proteobench.validation.report) severity (proteobench.validation.report.ValidationIssue attribute), [1] (proteobench.validation.ValidationIssue attribute), [1] shallow_clone() (proteobench.github.gh.GithubProteobotRepo static method) sidebar_category (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.debug_session_state_variables.Variables attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) sidebar_label (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.debug_session_state_variables.Variables attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) sidebar_path (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.debug_session_state_variables.Variables attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) slider_id_indepth_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) slider_id_submitted_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) slider_id_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) software_name (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] software_version (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute), [1] (proteobench.datapoint.entrapment_datapoint.EntrapmentDatapoint attribute), [1] (proteobench.datapoint.quant_datapoint.QuantDatapointHYE attribute), [1] (proteobench.datapoint.QuantDatapointHYE attribute), [1] species (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Description attribute) species_dict() (proteobench.io.parsing.parse_settings.ParseSettingsQuant method) species_expected_ratio() (proteobench.io.parsing.parse_settings.ParseSettingsQuant method) species_flags (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] spectrum_features_overview (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.Description attribute) split_protein_groups() (in module proteobench.validation.protein_ids) standard_df (proteobench.validation.context.ValidationContext attribute), [1] (proteobench.validation.ValidationContext attribute), [1] submission_processing_warning (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) submission_result_description (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) SubmissionValidationError, [1] submit (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) summary() (proteobench.validation.report.ValidationReport method) (proteobench.validation.ValidationReport method) T table_id_uuid (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) table_new_results_uuid (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) texts (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) title (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) (webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables.VariablesDIAEntrapmentAstral attribute) (webinterface.pages.pages_variables.Quant.debug_session_state_variables.Variables attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute) (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) to_dict() (proteobench.validation.report.ValidationIssue method) (proteobench.validation.report.ValidationReport method) (proteobench.validation.ValidationIssue method) (proteobench.validation.ValidationReport method) to_lowercase() (in module proteobench.io.parsing.parse_ion) (in module proteobench.io.parsing.parse_peptidoform) tokens (proteobench.datapoint.denovo_datapoint.DenovoDatapoint attribute) U unregister_profile() (in module proteobench.validation) (in module proteobench.validation.profiles) uploaded_id (webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables.VariablesDDADeNovo attribute) V VALIDATE_FILES_DICT (proteobench.modules.quant.quant_base_module.QuantModule attribute) validate_params_files() (proteobench.modules.quant.quant_base_module.QuantModule method) validate_submission() (in module proteobench.validation) (in module proteobench.validation.validator) validation_profile (proteobench.validation.config.ModuleValidationConfig attribute), [1] (proteobench.validation.ModuleValidationConfig attribute), [1] ValidationContext (class in proteobench.validation) (class in proteobench.validation.context) ValidationError ValidationIssue (class in proteobench.validation) (class in proteobench.validation.report) ValidationProfile (class in proteobench.validation) (class in proteobench.validation.profiles) ValidationReport (class in proteobench.validation) (class in proteobench.validation.report) value (proteobench.io.params.fragger.Parameter attribute) Variables (class in webinterface.pages.pages_variables.Quant.debug_session_state_variables) VariablesDDADeNovo (class in webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables) VariablesDDAQuant (class in webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables) (class in webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables) VariablesDDAQuantAstral (class in webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables) VariablesDIAEntrapmentAstral (class in webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables) VariablesDIAQuant (class in webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables) VariablesDIAQuantAstral (class in webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables) VariablesDIAQuantdiaPASEF (class in webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables) VariablesDIAQuantLI (class in webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables) VariablesDIAQuantPlasma (class in webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables) VariablesDIAQuantZenoTOF (class in webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables) W WARNING (proteobench.validation.report.Severity attribute) (proteobench.validation.Severity attribute) warning_alpha (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) warning_archived (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) warning_beta (webinterface.pages.texts.generic_texts.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_denovo.WebpageTexts.ShortMessages attribute) (webinterface.pages.texts.generic_texts_dia.WebpageTexts.ShortMessages attribute) warnings (proteobench.validation.report.ValidationReport property) (proteobench.validation.ValidationReport property) webinterface module webinterface.pages module webinterface.pages.base_pages module webinterface.pages.base_pages.tour_steps module webinterface.pages.base_pages.utils module webinterface.pages.future_pages module webinterface.pages.markdown_files module webinterface.pages.markdown_files.DeNovo module webinterface.pages.markdown_files.DeNovo.DDA module webinterface.pages.markdown_files.Entrapment module webinterface.pages.markdown_files.Entrapment.DIA module webinterface.pages.markdown_files.Entrapment.DIA.ion module webinterface.pages.markdown_files.Entrapment.DIA.ion.Astral module webinterface.pages.markdown_files.Quant module webinterface.pages.markdown_files.Quant.lfq module webinterface.pages.markdown_files.Quant.lfq.DDA module webinterface.pages.markdown_files.Quant.lfq.DDA.ion module webinterface.pages.markdown_files.Quant.lfq.DDA.ion.Astral module webinterface.pages.markdown_files.Quant.lfq.DDA.ion.QExactive module webinterface.pages.markdown_files.Quant.lfq.DDA.peptidoform module webinterface.pages.markdown_files.Quant.lfq.DIA module webinterface.pages.markdown_files.Quant.lfq.DIA.ion module webinterface.pages.markdown_files.Quant.lfq.DIA.ion.AIF module webinterface.pages.markdown_files.Quant.lfq.DIA.ion.Astral module webinterface.pages.markdown_files.Quant.lfq.DIA.ion.diaPASEF module webinterface.pages.markdown_files.Quant.lfq.DIA.ion.lowinput module webinterface.pages.markdown_files.Quant.lfq.DIA.ion.ZenoTOF module webinterface.pages.pages_variables module webinterface.pages.pages_variables.DeNovo module webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables module webinterface.pages.pages_variables.Entrapment module webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables module webinterface.pages.pages_variables.Quant module webinterface.pages.pages_variables.Quant.debug_session_state_variables module webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables module webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables module webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables module webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables module webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables module webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables module webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables module webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables module webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables module webinterface.pages.texts module webinterface.pages.texts.generic_texts module webinterface.pages.texts.generic_texts_denovo module webinterface.pages.texts.generic_texts_dia module webinterface.pages.utils module WebpageTexts (class in webinterface.pages.texts.generic_texts) (class in webinterface.pages.texts.generic_texts_denovo) (class in webinterface.pages.texts.generic_texts_dia) WebpageTexts.Description (class in webinterface.pages.texts.generic_texts_denovo) WebpageTexts.Help (class in webinterface.pages.texts.generic_texts) (class in webinterface.pages.texts.generic_texts_denovo) (class in webinterface.pages.texts.generic_texts_dia) WebpageTexts.ShortMessages (class in webinterface.pages.texts.generic_texts) (class in webinterface.pages.texts.generic_texts_denovo) (class in webinterface.pages.texts.generic_texts_dia) write_intermediate_raw() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.quant.quant_base_module.QuantModule method) write_json_local_development() (proteobench.modules.denovo.denovo_base.DeNovoModule method) (proteobench.modules.entrapment.entrapment_base_module.EntrapmentModule method) (proteobench.modules.quant.quant_base_module.QuantModule method) Y y_axis_title (proteobench.modules.quant.quant_base_module.QuantModule attribute) (proteobench.modules.quant.quant_lfq_ion_DIA_Plasma.DIAQuantIonModulePlasma attribute) (proteobench.modules.quant.quant_lfq_peptidoform_DDA.DDAQuantPeptidoformModule attribute) (proteobench.modules.quant.quant_lfq_peptidoform_DIA.DIAQuantPeptidoformModule attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_Astral_variables.VariablesDDAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DDA_peptidoform_variables.VariablesDDAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_AIF_variables.VariablesDIAQuant attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Astral_variables.VariablesDIAQuantAstral attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables.VariablesDIAQuantdiaPASEF attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables.VariablesDIAQuantLI attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_Plasma_variables.VariablesDIAQuantPlasma attribute) (webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables.VariablesDIAQuantZenoTOF attribute)
