Which Glycan Notation Is Used in the BioPharmaView™ Software?


日付: 11/10/2020
カテゴリー: Academia Omics , Pharma CRO , BioPharmaView Software

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For research use only. Not for use in diagnostic procedures.


Answer

The glycan notation used in BioPharmaView™ Software is the Oxford style, which is shown in column two of the table below.

User-added image

The other nomenclature styles for glycans are also listed in the table, and each style is described and differentiated here:

Ludger Product Name (column 1): Most of these names use a nomenclature system that focuses on the number of sialic acid residues present. This nomenclature system is limited and is only able to describe a few simple glycans. For newer Ludger product names, the Oxford notation is preferred and is utilized instead.

Oxford Notation Name (column 2): This nomenclature system is based on building up the N-glycan structures, and has the capacity to name very complex glycans. Some of the nomenclature rules are listed here:

  • All N-glycans have two core N-acetylglucosamine (GlcNAc) molecules.
  • F at the start of the abbreviation indicates a core fucose.
  • Mx is the number (x) of mannose molecules on the core GlcNAcs.
  • Ax is the number of antenna molecules (GlcNAc) on a trimannosyl core.
  • A2 indicates a biantennary compound, where both GlcNAcs are alpha1-2 linked.
  • Gx is the number (x) of linked galactose on  the antenna.
  • G1 indicates that the galactose is on the antenna of the alpha1-3 or alpha1-6 mannose.
  • Sx is the number (x) of sialic acids linked to galactose.

The Oxford notation can be used for bisecting GlcNAc molecules into tri- and tetra-antennary glycans and for denoting further substitutions such as fucose, sulphation, and phosophorylation. Numbers are also used to indicate linkages where known (e.g., F(6)A2G(4)2S(6)2 is a biantennary glycan with a core fucose in an alpha 6 linkage; the two galactoses are beta 1-4 linked; and the sialic acids are alpha 2-6 linked).

Short Name Used with IgG Glycans (column 3):This naming system, typically associated with IgG glycans, is primarily for indicating the presence of core fucose and the number of galactoses that are present on biantennary glycans. Only a limited number of structures can be described by this system, and the naming complexity increases when the structure is no longer a biantennary glycan (i.e., has only one GlcNAc antenna (-GN)).
 
Select a this link to download a pdf of the table above: Gycan Nomenclature - Ludger