DrawGlycan-SNFG & gpAnnotate: Rendering glycans and annotating glycopeptide mass spectra.
basic_science · Level V
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- Record sourced from PubMed, PMID 31710658.
- Also identified by DOI 10.1093/bioinformatics/btz819 and PMC identifier 10251767.
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Abstract
This manuscript describes an open-source program, DrawGlycan-SNFG (version 2), that accepts IUPAC (International Union of Pure & Applied Chemist)-condensed inputs to render Symbol Nomenclature For Glycans (SNFG) drawings. A wide range of local and global options enable display of various glycan/peptide modifications including bond breakages, adducts, repeat structures, ambiguous identifications, etc. These facilities make DrawGlycan-SNFG ideal for integration into various glycoinformatics software, including glycomics and glycoproteomics mass spectrometry applications. As a demonstration of such usage, we incorporated DrawGlycan-SNFG into gpAnnotate, a standalone application to score and annotate individual MS/MS glycopeptide spectrum in different fragmentation modes. DrawGlycan-SNFG and gpAnnotate are platform independent. While originally coded using MATLAB, compiled packages are also provided to enable DrawGlycan-SNFG implementation in Python and Java. All programs are available from https://virtualglycome.org/drawglycan; https://virtualglycome.org/gpAnnotate. Supplementary Material are available at Bioinformatics online.