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
• 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
• 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