formula2mz: Calculate mass-to-charge ratio from a formula

In rformassspectrometry/MetaboCoreUtils: Core Utils for Metabolomics Data

Calculate mass-to-charge ratio from a formula

Description

formula2mz calculates the m/z values from a list of molecular formulas and adduct definitions.

Custom adduct definitions can be passed to the adduct parameter in form of a data.frame. This data.frame is expected to have columns "mass_add" and "mass_multi" defining the additive and multiplicative part of the calculation. See adducts() for examples.

Usage

formula2mz(formula, adduct = "[M+H]+", standardize = TRUE)

Arguments

formula	character with one or more valid molecular formulas for which their adduct m/z shall be calculated.
adduct	either a character specifying the name(s) of the adduct(s) for which the m/z should be calculated or a data.frame with the adduct definition. See adductNames() for supported adduct names and the description for more information on the expected format if a data.frame is provided.
standardize	logical whether to standardize the molecular formulas to the Hill notation system before calculating their mass.

Value

Numeric matrix with same number of rows than elements in formula and number of columns being equal to the length of adduct (adduct names are used as column names). Each column thus represents the m/z of formula for each defined adduct.

Author(s)

Roger Gine

Examples

## Calculate m/z values of adducts of a list of formulas
formulas <- c("C6H12O6", "C9H11NO3", "C16H13ClN2O")
ads <- c("[M+H]+", "[M+Na]+", "[2M+H]+", "[M]+")
formula2mz(formulas, ads)
formula2mz(formulas, adductNames()) #All available adducts

## Use custom-defined adducts as input
custom_ads <- data.frame(mass_add = c(1, 2, 3), mass_multi = c(1, 2, 0.5))
formula2mz(formulas, custom_ads)

## Use standardize = FALSE to keep formula unaltered
formula2mz("H12C6O6")
formula2mz("H12C6O6", standardize = FALSE)

rformassspectrometry/MetaboCoreUtils documentation built on Oct. 2, 2024, 5:13 a.m.