Contents:

• Installing
  • Installing from PyPI
  • Installing From Source
  • For PyInstaller
• Command Line Applications
  • Database Building
    • Building a Combinatorial Glycan Hypothesis
    • Building a Glycan Hypothesis from a Text File
    • Building a Glycan Hypothesis from glySpace
    • Building a Glycan Composition Graph
    • Building a Glycopeptide Hypothesis from a FASTA File
  • Search and Analysis
    • LC-MS/MS Data Preprocessing and Deconvolution
    • Searching a Processed Sample with a Glycan Database
    • Searching a Processed Sample with a Glycopeptide Database
    • (Deprecated) Modeling Glycopeptide Chromatographic Retention Times
  • Output and Exporting
    • Export Glycopeptide Search Results
    • Export Glycan Search Results
    • Export Hypotheses
• Tutorials
  • High Energy Glycopeptide Search Tutorial
    • Preparing the Data
    • Building the Search Space
    • Search the Data
  • Stepped Collision Energy Glycopeptide Search Tutorial
    • Preparing the Data
    • Building the Search Space
    • Searching the Data
    • Build a Glycosite Smoothing Model
    • Build a Fragmentation Model
• Topics
  • IUPAClite Glycan Syntax
  • Peptide Modifications
    • UNIMOD
    • Targeting Rules
  • Glycan Composition Classes
    • Class Names