SugarPy Parameters

SugarPy is devided into a run and a results class. Some parameters are shared by both, while others are specific to the respective class.

General Parameters

  • charges (list):
    list of charge states that are quantified
  • max_tree_length (int):
    maximum number of monosaccharides in one combination
  • min_spec_number (int):
    defines the minimum number of spectra for one matched formula.
  • monosaccharides(dict):
    dictionary containing name and chemical composition of monosaccharides
  • ms_level:
    MS level for which quantification should be performed
  • mzml_file (str):
    path to the mzML file used for the quantification

Run Parameters

For an example on how to use these parameters, refer to

  • ident_file (str):
    Path to the Ursgal result .csv file. This file should only include (potential) glycopeptides, i.e. it should be filtered.
  • min_tree_length (int):
    minimum number of monosaccharides per glycan
  • params (dict):
    pyQms parameters (see pyQms manual for further information)
  • pkl_name (str):
    name of the result pickle containing the pyQms results
  • rt_window (dict):
    optional argument to define a retention time window in which the molecules are quantified (use ‘min’ and ‘max’ as keys in the dict)
  • spectra (list):
    optional list of spectrum IDs that should be quantified
  • unimod_glycans_incl_in_search (list):
    List of Unimod PSI-MS names corresponding to glycans that were included in the database search as modification (will be removed from the peptide).

Results Parameters

For an example on how to use these parameters, refer to

  • output_file (str):
    output file name
  • max_trees_per_spec (int):
    maximum number of glycan compositions returned for one spectrum
  • min_sugarpy_score (float):
    minimum SugarPy score (glycan compositions with lower scores are not returned)
  • min_sub_cov (float):
    minimum subtree coverage (glycan compositions with sub_cov are not returned)