Documentation for AlphaPeptDeep (PeptDeep)

The deep learning framework for MS proteomics. For more information, see AlphaPeptDeep on GitHub.

• Tutorials and Notebooks
  • Using peptdeep for MHC class I immunopeptidomics
  • Tutorial: building new models from scratch
  • Tutorial: Predicting Spectral Library from Fasta
  • Translate spectral libraries
  • 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
  • generate_library()
  • get_median_pccs_for_dia_psms()
  • import_psm_df()
  • match_psms()
  • transfer_learn()
• peptdeep.pretrained_models
  • ModelManager
  • clear_error_modloss_intensities()
  • count_mods()
  • download_models()
  • get_local_model_zip_name()
  • get_model_download_instructions()
  • get_model_url()
  • get_model_zip_file_path()
  • get_pretrain_dir()
  • 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