chem_formula_2_adducts: Get adducts and isotopes for chemical formulas

In szymczak-lab/preprocessHighResMS: Preprocessing of spectra data from high resolution mass spectrometry

Description

Calculates chemical formulas, mz values and theoretical abundances of isotope peaks of adducts of chemical formulas. Based on functions in R package enviPat.

Usage

chem_formula_2_adducts(
  chem.forms,
  isotopes,
  adducts,
  adduct.names = NULL,
  ion.mode = "positive",
  rel_to = 0,
  threshold = 20,
  verbose = TRUE
)

Arguments

chem.forms	Vector of character strings with chemical formulas.
isotopes	dataframe with stable isotopes (see isotopes)
adducts	dataframe with common adducts (see adducts).
adduct.names	Character vector with adducts to be calculated (see adducts for common adducts). If set to NULL, ion.mode needs to be specified.
ion.mode	Character of ionisation mode ("positive", "negative"). If positive adduct.names is set to c("M+H", "M+Na", "M+K"), if negative adduct.names is set to c("M-H", "M+Cl").
rel_to	Integer (0, 1, 2, 3 or 4). Probability definition (see isopattern).
threshold	Numeric (1-100). Probability below which isotope peaks can be omitted (see isopattern).
verbose	Logical. Print out additional information.

Value

data frame with the following information about each feature:

• chemical.form.adduct: chemical formula of adduct

• chemical.form: original chemical formula

• adduct.name: adduct used

• charge: charge of adduct

• chemical.form.isotope: chemical formula of isotope of adduct

• m.z: theoretical mz value of isotope

• abundance: theoretical abundance of isotope peak. Most abundant isotope has value of 100

• id: unique identifier (<chemical.form>.<chemical.form.isotope>)

Examples

library(enviPat)
data("isotopes")
data("adducts")

chem_formula_2_adducts(chem.forms = "C6H12O6",
                       adduct.names = c("M+H", "M+Na", "M+2H"),
                       adducts = adducts,
                       isotopes = isotopes,
                       threshold = 5)

szymczak-lab/preprocessHighResMS documentation built on Oct. 6, 2020, 12:50 a.m.