General Structure

SugarPy is comprised by a run and a results class. The run class includes all major functions to identify glycopeptides from IS-CID mass spectrometry measurements, while the results class can be used to generate different output files.


The main functionalities of the SugarPy run class include

  1. parsing protein database search result files to extract peptide sequences, retention times, etc.
  2. building all theoretical combinations for a set of peptide sequences, monosaccharides and a given glycan length
  3. searching MS1 spectra for isotope envelopes of all theoretical glycopeptides (using pyQms)
  4. reassambling intact glycopeptides by combining subtrees, calculating SugarPy scores, etc.


A variety of output files can be generated using the SugarPy results class, including

  1. output .csv file
  2. glycopeptide elution profiles
  3. annotated spectra

Furthermore, the results class can be used to validate identified glycopeptides through non-IS-fragmenting MS runs. The corresponding .mzML files can be searched for glycopeptides on different levels

  1. isotope envelope on MS1 level
  2. selection for fragmentation by HCD
  3. presence of glycopeptide specific fragment ions on MS2 level