Package 'glyanno'

Description

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

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)
calculate_mz("Gal(1)GalNAc(1)", charge = 0)
calculate_mz(as_glycan_structure("Gal(b1-3)GalNAc(a1-"), charge = 0)
calculate_mz("Gal(b1-3)GalNAc(a1-", charge = 0)

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

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

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

# Calculate average mass
calculate_mz("Man(5)GlcNAc(2)", charge = 0, mass_dict = glyanno_mass_dict(mass_type = "average"))

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

Description

Given glycan compositions, this function matches them to all possible glycan structures in the glydb database.

Usage

comp_to_struc(comps, db = NULL, return_best = FALSE)

Arguments

Value

If return_best=TRUE: A glyrepr::glycan_structure() vector with the same length as comps. Unmatched compositions are returned as NA. If return_best=FALSE: A tibble with the following columns:

• composition: The glycan compositions, as glyrepr::glycan_composition() vector.

• structure: The possible glycan structures, as glyrepr::glycan_structure() vector. Note that one glycan composition can have multiple rows in the result, corresponding to different possible glycan structures.

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

glyparse::auto_parse()

Examples

comp_to_struc("H5N2")

Description

Given a generic glycan composition (e.g. Hex(5)HexNAc(2)), this function gives all possible concrete glycan compositions (e.g. Man(5)GlcNAc(2)).

Usage

enhance_comp(comps, db = NULL, return_best = FALSE)

Arguments

Value

If return_best=TRUE: A glyrepr::glycan_composition() vector with the same length as comps. Unmatched compositions are returned as NA. If return_best=FALSE: A tibble with the following columns:

• raw: The original compositions.

• enhanced: The enhanced compositions. Note that one raw composition can have different enhanced compositions as multiple rows in the result.

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)

Examples

enhance_comp("Hex(5)HexNAc(2)")

Description

Given a glycan structure vector of any resolution level (see glyrepr::get_structure_level() for details), this function gives all possible glycan structures of higher resolution level.

Usage

enhance_struc(strucs, db = NULL, return_best = FALSE)

Arguments

Details

The target resolution level is determined from db. When db is NULL, the default glydb::glydb_structures() at "intact" level is used.

Value

If return_best=TRUE: An unnamed glyrepr::glycan_structure() vector with the same length as strucs. Unmatched structures are returned as NA. If return_best=FALSE: A tibble with the following columns:

• raw: The original glycan structures.

• enhanced: The enhanced glycan structures. Note that one raw glycan structure can have different enhanced glycan structures as multiple rows in the result.

Examples

# From topological level to intact level
db_intact <- c("Gal(b1-3)GalNAc(a1-", "Gal(b1-4)GalNAc(a1-")
enhance_struc("Gal(??-?)GalNAc(??-", db = db_intact)

# From basic level to topological level
db_topo <- "Gal(??-?)GalNAc(??-"
enhance_struc("Hex(??-?)HexNAc(??-", db = db_topo)

# From partial level to intact level
enhance_struc("Gal(b1-?)GalNAc(a1-", db = db_intact)

Description

Add anomer positions to glycan structures with missing anomer information based on biological knowledge. For example, "Gal(??-?)GalNAc(??-" will be converted to "Gal(?1-?)GalNAc(?1-". For anomer positions that are already specified in the input structures, this function will not modify them.

Usage

fill_anomer_pos(strucs)

Arguments

Details

This function is intended to be used by struc_to_glytoucan() to ensure that glycan structures have complete anomer information before attempting to inquire the GlyTouCan database.

For these monosaccharides, the anomer position is "2": "Neu5Ac", "Neu5Gc", "Neu", "Kdn", "Pse", "Leg", "Aci", "4eLeg", "Kdo", "Dha", "Fru", "Tag", "Sor", and "Psi". All other monosaccharides are assumed to have anomer positions on "1".

Value

A glyrepr::glycan_structure() vector with anomer positions added where missing.

Examples

library(glyrepr)
glycans <- as_glycan_structure(c(
  "Gal(??-?)GalNAc(??-",
  "Neu5Ac(??-?)Gal(??-?)GalNAc(??-"
))
fill_anomer_pos(glycans)

Description

A named numeric vector of the mass of each monosaccharide residue. Used by default as the mass_dict argument in calculate_mz().

The names includes:

• Monosaccharides: Hex, HexNAc, dHex, dHexNAc, ddHex, Pen, HexA, HexN, NeuAc, NeuGc, Kdn, Neu

• Ions: H+, H, H2O, K+, Na+, NH4+, H-, Cl-, HCO3-

• Substituents: S, P

• Reducing end: red_end, which is the additional mass of the reducing end of the glycan.

Usage

glyanno_mass_dict(deriv = "none", mass_type = "mono")

Arguments

Value

A named numeric vector.

Examples

glyanno_mass_dict(deriv = "none", mass_type = "mono")
glyanno_mass_dict(deriv = "permethyl", mass_type = "mono")
glyanno_mass_dict(deriv = "none", mass_type = "average")

Description

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,
  return_best = FALSE,
  charge = 1,
  adduct = "H+",
  mass_dict = NULL
)

Arguments

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. 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+")

Description

This helper function should be used in mz_to_comp() as the tol argument. It makes the function using PPM as dynamic tolerance.

Usage

ppm(x)

Arguments

Value

A function that takes a numeric vector of m/z values and returns a numeric vector of tolerances.

Examples

ppm(10)(2368.84)
ppm(10)(c(2368.84, 2368.85))

Description

This function takes a vector of glycan structures and returns the corresponding GlyTouCan accessions. Under the hood, it uses the GlycanFormatConverter API maintained by the Glycosmos project.

Usage

struc_to_glytoucan(strucs)

Arguments

Details

For "topological" structures (e.g., "Gal(??-?)GalNAc(??-"), this function will first call fill_anomer_pos() to fill in the missing anomeric positions before querying the API. This is necessary because all glycan structures in GlyTouCan must have defined anomeric positions.

Value

A character vector of GlyTouCan accessions corresponding to the input glycan structures. If a structure cannot be converted to a GlyTouCan accession, the corresponding entry will be NA.