Convert m/z values to glycan composition

Given m/z values, this function matches them to all possible glycan compositions in the glydb database.

Usage

mz_to_comp(
  mz,
  tol = ppm(10),
  db = lifecycle::deprecated(),
  return_best = FALSE,
  charge = 1,
  adduct = "H+",
  mass_dict = NULL,
  glycan_type = NULL,
  species = NULL,
  mono_type = "concrete",
  mono_range = NULL
)

Arguments

mz

A numeric vector of m/z values.

tol

A numeric scalar of the tolerance for the m/z value in Da or a ppm() object for dynamic tolerance. Default is ppm(10).

db

Glycan compositions to match against. Can be a glyrepr::glycan_composition() vector or glycan composition strings in Byonic style (e.g. Hex(5)HexNAc(2)) or simple style (e.g. H5N4F1S1). Use the filtering arguments instead. This argument cannot be combined with them.

return_best

A logical scalar. If TRUE, only the match with the highest confidence score is returned for each m/z value. A custom db must have a confidence attribute. Default is FALSE.

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().

glycan_type

Glycan type to select from glydb::glydb_compositions().

species

Species to select, matched without regard to letter case.

mono_type

Monosaccharide resolution, "concrete" (default) or "generic".

mono_range

Named list of monosaccharide count ranges; see glydb::glydb_compositions().

Value

If return_best=TRUE: An unnamed glyrepr::glycan_composition() vector with the same length as mz. Unmatched m/z values are returned as NA. If return_best=FALSE: A tibble with the following columns:

mz: The molecule m/z values, same as the input mz.
composition: The possible glycan compositions, as glyrepr::glycan_composition() vector.
confidence: The database confidence score for each composition, or NA when no score is available. Note that one m/z value can have multiple rows in the result, corresponding to different possible glycan compositions.

Filter the built-in database

Use glycan_type, species, mono_type, and mono_range to select compositions from glydb::glydb_compositions(). For example,

mz_to_comp(mz, species = "Homo sapiens", glycan_type = "N")

Examples

mz_to_comp(933.3175, charge = 1, adduct = "Na+")
#> # A tibble: 10 × 3
#>       mz composition                    confidence
#>    <dbl> <glydb_cm>                          <dbl>
#>  1  933. Man(3)GlcNAc(2)                      5.61
#>  2  933. Glc(1)Gal(2)GlcNAc(1)GalNAc(1)       1.79
#>  3  933. Gal(3)GlcNAc(2)                      1.61
#>  4  933. Glc(1)Gal(2)GlcNAc(2)                1.39
#>  5  933. Man(1)Gal(2)GlcNAc(2)                0   
#>  6  933. Gal(3)GlcNAc(1)GalNAc(1)             1.10
#>  7  933. Glc(1)Gal(2)GalNAc(2)                2.40
#>  8  933. Man(2)Gal(1)GlcNAc(2)                1.39
#>  9  933. Glc(1)GlcNAc(2)Galf(2)              -1   
#> 10  933. Gal(3)GalNAc(2)                     -1

Usage

Arguments

Value

Filter the built-in database

See also

Examples