1. DrawGlycan-SNFG and gpAnnotate: rendering glycans and annotating glycopeptide mass spectra.
- Author
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Cheng, Kai, Pawlowski, Gabrielle, Yu, Xinheng, Zhou, Yusen, and Neelamegham, Sriram
- Subjects
MASS spectrometry ,INTERNET servers ,PYTHON programming language ,CHEMISTS ,GLYCANS ,INTERNATIONAL agencies ,CHEMICAL adducts - Abstract
Summary This manuscript describes an open-source program, DrawGlycan-SNFG (version 2), that accepts IUPAC (International Union of Pure and 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 (MS) 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. Availability and implementation 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 information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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