All modules for which code is available

• proteobench.datapoint.datapoint_base
• proteobench.datapoint.denovo_datapoint
• proteobench.datapoint.entrapment_datapoint
• proteobench.datapoint.quant_datapoint
• proteobench.exceptions
• proteobench.github.gh
• 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.parse_denovo
• proteobench.io.parsing.parse_ion
• proteobench.io.parsing.parse_peptidoform
• proteobench.io.parsing.parse_settings
• proteobench.io.parsing.utils
• proteobench.modules.denovo.denovo_DDA_HCD
• proteobench.modules.denovo.denovo_base
• proteobench.modules.entrapment.entrapment_base_module
• proteobench.modules.entrapment.entrapment_ion_DIA_Astral
• 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_Plasma
• proteobench.modules.quant.quant_lfq_ion_DIA_ZenoTOF
• proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF
• proteobench.modules.quant.quant_lfq_ion_DIA_lowinput
• proteobench.modules.quant.quant_lfq_peptidoform_DDA
• proteobench.modules.quant.quant_lfq_peptidoform_DIA
• proteobench.modules.rescoring.module_rescoring
• 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.denovoscores
• proteobench.score.entrapmentscores
• proteobench.score.quantscoresHYE
• proteobench.score.quantscoresPYE
• proteobench.score.score_base
• proteobench.utils.server_io
• proteobench.utils.submission
• 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.pages.base_pages.tour_steps
• webinterface.pages.pages_variables.DeNovo.DDA_HCD_variables
• webinterface.pages.pages_variables.Entrapment.Entrapment_DIA_ion_Astral_variables
• 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_Plasma_variables
• webinterface.pages.pages_variables.Quant.lfq_DIA_ion_ZenoTOF_variables
• webinterface.pages.pages_variables.Quant.lfq_DIA_ion_diaPASEF_variables
• webinterface.pages.pages_variables.Quant.lfq_DIA_ion_lowinput_variables
• webinterface.pages.texts.generic_texts
• webinterface.pages.texts.generic_texts_denovo
• webinterface.pages.texts.generic_texts_dia