Determine N-Glycan Key Properties

These functions check key properties of an N-glycan:

• n_glycan_type(): Determine the N-glycan type.

• has_bisecting(): Check if the glycan has a bisecting GlcNAc.

• n_antennae(): Count the number of antennae.

• n_fuc(): Count the number of fucoses.

• n_core_fuc(): Count the number of core fucoses.

• n_arm_fuc(): Count the number of arm fucoses.

• n_gal(): Count the number of galactoses.

• n_terminal_gal(): Count the number of terminal galactoses.

• n_sia(): Count the number of sialic acids.

• n_man(): Count the number of mannoses.

All functions assume the glycans are N-glycans without validation, thus may return meaningless values for non-N-glycans. Therefore, please make sure to pass in N-glycans only.

All functions put minimum requirement on the glycans, i.e. they work with glycans with generic monosaccharides (e.g. "Hex", "HexNAc") and no linkage information. This type of structures are common in glycoproteomics and glycomics studies.

Usage

n_glycan_type(glycans)

has_bisecting(glycans)

n_antennae(glycans)

n_fuc(glycans)

n_core_fuc(glycans)

n_arm_fuc(glycans)

n_gal(glycans)

n_terminal_gal(glycans)

n_sia(glycans)

n_man(glycans)

Arguments

glycans

A glyrepr::glycan_structure() vector.

Value

• n_glycan_type(): A factor vector indicating the N-glycan type, either "highmannose", "hybrid", "complex", or "paucimannose".

• has_bisecting(): A logical vector indicating if the glycan has a bisecting GlcNAc.

• n_antennae(): An integer vector indicating the number of antennae.

• n_fuc(): An integer vector indicating the number of fucoses.

• n_core_fuc(): An integer vector indicating the number of core fucoses.

• n_arm_fuc(): An integer vector indicating the number of arm fucoses.

• n_gal(): An integer vector indicating the number of galactoses.

• n_terminal_gal(): An integer vector indicating the number of terminal galactoses.

• n_sia(): An integer vector indicating the number of sialic acids.

• n_man(): An integer vector indicating the number of mannoses.

n_glycan_type(): N-Glycan Types

Four types of N-glycans are recognized: high mannose, hybrid, complex, and paucimannose. For more information about N-glycan types, see Essentials of Glycobiology.

has_bisecting(): Bisecting GlcNAc

Bisecting GlcNAc is a GlcNAc residue attached to the core mannose of N-glycans.

     Man
        \
GlcNAc - Man - GlcNAc - GlcNAc -
~~~~~~  /
     Man

n_antennae(): Number of Antennae

The number of antennae is the number of branching GlcNAc to the core mannoses.

n_fuc(): Number of Fucoses

Number of fucoses. This function assumes the fucose is a dHex.

n_core_fuc(): Number of Core Fucoses

Core fucoses are those fucose residues attached to the core GlcNAc of an N-glycan.

Man             Fuc  <- core fucose
   \             |
    Man - GlcNAc - GlcNAc -
   /
Man

n_arm_fuc(): Number of Arm Fucoses

Arm focuses are those focuse residues attached to the branching GlcNAc of an N-glycan.

 Fuc  <- arm fucose
  |
GlcNAc - Man
            \
             Man - GlcNAc - GlcNAc -
            /
GlcNAc - Man

n_gal(): Number of Galactoses

This function seems useless and silly. It is, if you have a well-structured glycan with concrete monosaccharides. However, if you only have "Hex" or "H" at hand, it is tricky to know how many of them are "Gal" and how many are "Man". This function makes a simply assumption that all the rightmost "H" in a "H-H-N-H" unit is a galactose. The two "H" on the left are mannoses of the N-glycan core. The "N" is a GlcNAc attached to one core mannose.

n_terminal_gal(): Number of Terminal Galactoses

Terminal galactoses are those galactose residues on the non-reducing end without sialic acid capping.

         Gal - GlcNAc - Man
         ~~~               \
     terminal Gal           Man - GlcNAc - GlcNAc -
                           /
Neu5Ac - Gal - GlcNAc - Man
         ~~~
   not terminal Gal

n_sia(): Number of Sialic Acids

Number of sialic acids (Neu5Ac). Neu5Gc is not counted.

n_man(): Number of Mannoses

Number of mannoses. This function assumes the Hex of the N-glycan core is mannoses. Also, for high-mannose and paucimannose glycans, all Hex are mannoses. Finally, for hybrid glycans, all the rightmost (the side without branching HexNAc) are mannoses.