Calculate m/z values of glycans

This function calculates m/z values from glycans. Different adducts, mass types, and derivatives are supported. Custom mass dictionaries are also supported.

Usage

calculate_mz(glycans, charge = 1, adduct = "H+", mass_dict = NULL, safe = TRUE)

Arguments

glycans

Glycans to calculate m/z values from. Valid inputs include:

• A glyrepr::glycan_structure() vector.

• A glyrepr::glycan_composition() vector.

• Byonic style composition strings (e.g. Hex(5)HexNAc(2)).

• Simple style composition strings (e.g. H5N4F1S1).

• Any structure strings supported by glyparse::auto_parse().

charge

Charge to use. Can be 0, 1, 2, 3, -1, -2, -3, etc. 0 means neutral. Default is 1.

adduct

Adduct to use. Can be "H+", "K+", "Na+", "NH4+", "H-", "Cl-", "HCO3-". Default is "H+".

• When charge is 0, adduct is ignored.

• When charge is positive, adduct can only be "H+", "K+", "Na+", "NH4+".

• When charge is negative, adduct can only be "H-", "Cl-", "HCO3-".

mass_dict

A named numeric vector of the mass of each monosaccharide residue. Default is glyanno_mass_dict(deriv = "none", mass_type = "mono"). If a custom mass dictionary is provided, please make sure the names of the vector are the same as the names in glyanno_mass_dict().

safe

Whether to raise an error when unsupported monosaccharides or substituents are found.

• If TRUE (default), an error will be raised.

• If FALSE, a warning will be raised and m/z values for invalid glycans will be set to NA.

Value

A numeric vector of m/z values.

See also

glyanno_mass_dict()

Examples

library(glyrepr)

# Different input types
calculate_mz(glycan_composition(c(Gal = 1, GalNAc = 1)), charge = 0)
#> [1] 383.1428
calculate_mz("Gal(1)GalNAc(1)", charge = 0)
#> [1] 383.1428
calculate_mz(as_glycan_structure("Gal(b1-3)GalNAc(a1-"), charge = 0)
#> [1] 383.1428
calculate_mz("Gal(b1-3)GalNAc(a1-", charge = 0)
#> [1] 383.1428

# For common situation in MALDI-TOF MS
calculate_mz("Man(5)GlcNAc(2)", charge = 1,adduct = "Na+")
#> [1] 1257.423

# For common situation in ESI MS
calculate_mz("Man(5)GlcNAc(2)", charge = 1, adduct = "H+")
#> [1] 1235.441

# Calculate permethylated m/z values
calculate_mz("Man(5)GlcNAc(2)", charge = 0, mass_dict = glyanno_mass_dict(deriv = "permethyl"))
#> [1] 1556.793

# Calculate average mass
calculate_mz("Man(5)GlcNAc(2)", charge = 0, mass_dict = glyanno_mass_dict(mass_type = "average"))
#> [1] 1235.117

# Vectorization
calculate_mz(c("Man(5)GlcNAc(2)", "Gal(1)GalNAc(1)"), charge = 1, adduct = "Na+")
#> [1] 1257.4231  406.1325