Documentation for AlphaBase

The infrastructure of AlphaX ecosystem for MS proteomics. For more information, see AlphaBase on GitHub.

• Tutorials and Notebooks
  • Tutorial for Dev: Basic Definations
  • Tutorial for Dev: Peptide and Fragment DataFrames
  • Tutorial for Dev: Spectral Libraries
  • SpecLibFasta usage
  • PSM readers
  • Library reader with fragments
• alphabase.protein
  • alphabase.protein.fasta
  • alphabase.protein.protein_level_decoy
• alphabase.spectral_library
  • alphabase.spectral_library.base
  • alphabase.spectral_library.flat
  • alphabase.spectral_library.decoy
  • alphabase.spectral_library.reader
  • alphabase.spectral_library.translate
• alphabase.peptide
  • alphabase.peptide.precursor
  • alphabase.peptide.fragment
  • alphabase.peptide.mass_calc
  • alphabase.peptide.mobility
• alphabase.constants
  • alphabase.constants.atom
  • alphabase.constants.aa
  • alphabase.constants.modification
  • alphabase.constants.isotope
• alphabase.io
  • alphabase.io.hdf
• alphabase.psm_reader
  • alphabase.psm_reader.psm_reader
  • alphabase.psm_reader.alphapept_reader
  • alphabase.psm_reader.pfind_reader
  • alphabase.psm_reader.maxquant_reader
  • alphabase.psm_reader.msfragger_reader
  • alphabase.psm_reader.dia_psm_reader
• alphabase.scoring
  • alphabase.scoring.fdr
  • alphabase.scoring.feature_extraction_base
  • alphabase.scoring.ml_scoring
• alphabase.statistics
  • alphabase.statistics.regression