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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

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  • Welcome to masskit’s documentation!
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  • masskit 1.2.0 documentation »
  • Welcome to masskit’s documentation!