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
- parsing protein database search result files to extract peptide sequences, retention times, etc.
- building all theoretical combinations for a set of peptide sequences, monosaccharides and a given glycan length
- searching MS1 spectra for isotope envelopes of all theoretical glycopeptides (using pyQms)
- reassambling intact glycopeptides by combining subtrees, calculating SugarPy scores, etc.
A variety of output files can be generated using the SugarPy results class, including
- output .csv file
- glycopeptide elution profiles
- 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
- isotope envelope on MS1 level
- selection for fragmentation by HCD
- presence of glycopeptide specific fragment ions on MS2 level