Welcome to masskit’s documentation!

Contents:

• Use of the spectrum object
  • Spectrum properties
  • Spectrum mass tolerance information
  • Operations on spectra
  • Operations on pairs of spectra
    • Cosine score between two spectra
    • Cosine score between mz subranges
    • Merge two spectra, first by creating a filter spectrum
      • Then merge with previous spectrum
• Tables of spectra
  • Pandas dataframes
    • Load a pandas dataframe from the parquet version of a spectral library
    • Take the top 10 lines of the dataframe and display in html
    • List columns
    • Iterating through a dataframe
    • Query on the dataframe to return a dataframe containing rows that match the query, then display the new dataframe
  • Select one spectrum from the new dataframe, filter out low m/z peaks, normalize the base intensity to 1.0
    • Input/output
      • MSP
      • MGF
      • PKL (python pickle)
      • CSV
• Recipes
  • Library generation
    • Protein sequences to peptide library
      • An example command line to convert uniprot.fasta to uniprot_peptides.parquet
  • Library import
    • SDF Molfiles to small molecule libraries
      • SDF files with incorrect encoding or pre-v2000 format
    • CSV file to small molecule libraries
      • Example of reading in a headerless tab delimited file with the SMILES in the second column
  • Modification specification

Indices and tables

• Index

• Module Index

• Search Page