Documentation for AlphaPeptDeep (PeptDeep)# The deep learning framework for MS proteomics. For more information, see AlphaPeptDeep on GitHub. Tutorials and Notebooks Tutorial: building new models from scratch Tutorial: Predicting Spectral Library from Fasta Translate spectral libraries Tutorial: HLA prediction Tutorial: using ModelManager Building your own models for RT prediction Building your own models for CCS prediction peptdeep.protein peptdeep.protein.fasta peptdeep.pipeline_api peptdeep.pretrained_models ModelManager clear_error_modloss_intensities() count_mods() download_models() is_model_zip() load_models() load_models_by_model_type_in_zip() load_phos_models() psm_sampling_with_important_mods() peptdeep.model peptdeep.model.generic_property_prediction peptdeep.model.model_interface peptdeep.model.building_block peptdeep.model.featurize peptdeep.model.ms2 peptdeep.model.rt peptdeep.model.ccs peptdeep.settings add_user_defined_modifications() global_settings load_global_settings() update_all_mod_features() update_global_settings() update_modifications() update_settings() peptdeep.rescore peptdeep.rescore.fdr peptdeep.rescore.feature_extractor peptdeep.rescore.percolator peptdeep.spec_lib peptdeep.spec_lib.predict_lib peptdeep.spec_lib.library_factory peptdeep.spec_lib.translate alphabase.mass_spec peptdeep.mass_spec.mass_calibration peptdeep.mass_spec.match peptdeep.mass_spec.ms_reader