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Convert m/z values to glycan composition

mz_to_comp.Rd

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 = NULL,
  charge = 1,
  adduct = "H+",
  mass_dict = 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). If not provided, glydb::glydb_compositions(mono_type = "concrete") will be used.

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().

Value

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. Note that one m/z value can have multiple rows in the result, corresponding to different possible glycan compositions.

How to set db

The db parameter is very important for all functions in this package. By default, it uses all available glycans in the glydb package, which is usually larger than what you need. You can use helper functions in glydb to narrow down the database, e.g. glydb::glydb_compositions() or glydb::glydb_structures().

You can use the species and glycan_type parameters to focus on specific species and glycan type. For example, if you are only interested in N-glycan compositions in human, you can use glydb::glydb_compositions(species = "Homo sapiens", glycan_type = "N"). Also, you can decide the level of information in the database by setting mono_type of glydb::glydb_compositions() and structure_level of glydb::glydb_structures().

You can then pass the result to the db parameter of this function. For example,

my_db <- glydb::glydb_compositions(species = "Homo sapiens", glycan_type = "N")
mz_to_comp(mz, db = my_db)

See also

ppm(), glyanno_mass_dict()

Examples

mz_to_comp(933.3175, charge = 1, adduct = "Na+")
#> # A tibble: 9 × 2
#>      mz composition                   
#>   <dbl> <comp>                        
#> 1  933. Glc(1)Gal(2)GlcNAc(1)GalNAc(1)
#> 2  933. Man(3)GlcNAc(2)               
#> 3  933. Gal(3)GlcNAc(2)               
#> 4  933. Gal(3)GlcNAc(1)GalNAc(1)      
#> 5  933. Glc(1)Gal(2)GalNAc(2)         
#> 6  933. Man(1)Gal(2)GlcNAc(2)         
#> 7  933. Glc(1)Gal(2)GlcNAc(2)         
#> 8  933. Man(2)Gal(1)GlcNAc(2)         
#> 9  933. Gal(3)GalNAc(2)