R/Utils_adduct_rules.R
In michaelwitting/metabolomicsUtils: Collection of utility functions for metabolomics
Defines functions
adduct_rules
adduct_rules_pos
adduct_rules_neg
get_adduct_names
Documented in
adduct_rules
adduct_rules_neg
adduct_rules_pos
get_adduct_names
#' @title Create list with all adduct calculation rules (all rules)
#'
#' This function returns a list with rules for the calculation of adducts. It is required for the calculation of adduct m/z values from exact masses and the other way round. This list contains all rules for both ionization modes.
#'
#'
#' @author Michael Witting, \email{michael.witting@@helmholtz-muenchen.de}
#'
#' @seealso \code{\link{adduct_rules_pos}}
#' @seealso \code{\link{adduct_rules_neg}}
#' @seealso \code{\link{get_adduct_names}}
#'
#' @export
adduct_rules <- function() {
## create list with all the adduct definitoins
adduct_list <- list(
'[M+3H]3+' = list(mass_multi = 1 / 3,
mass_add = 3 * rcdk::get.formula('H', charge = 1)@mass / 3,
formula_add = 'H3',
formula_sub = 'C0',
charge = 3),
'[M+2H+Na]3+' = list(mass_multi = 1 / 3,
mass_add = (2 * rcdk::get.formula('H', charge = 1)@mass + 1 * rcdk::get.formula('Na', charge = 1)@mass) / 3,
formula_add = 'H2Na',
formula_sub = 'C0',
charge = 3),
'[M+H+Na2]3+' = list(mass_multi = 1 / 3,
mass_add = (1 * rcdk::get.formula('H', charge = 1)@mass + 2 * rcdk::get.formula('Na', charge = 1)@mass) / 3,
formula_add = 'HNa2',
formula_sub = 'C0',
charge = 3),
'[M+Na3]3+' = list(mass_multi = 1 / 3,
mass_add = (3 * rcdk::get.formula('Na', charge = 1)@mass) / 3,
formula_add = 'Na3',
formula_sub = 'C0',
charge = 3),
'[M+2H]2+' = list(mass_multi = 1 / 2,
mass_add = 2 * rcdk::get.formula('H', charge = 1)@mass / 2,
formula_add = 'H2',
formula_sub = 'C0',
charge = 2),
'[M+H+NH4]2+' = list(mass_multi = 1 / 2,
mass_add = (rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('NH4', charge = 1)@mass) / 2,
formula_add = 'NH5',
formula_sub = 'C0',
charge = 2),
'[M+H+K]2+' = list(mass_multi = 1 / 2,
mass_add = (rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('K', charge = 1)@mass) / 2,
formula_add = 'HK',
formula_sub = 'C0',
charge = 2),
'[M+H+Na]2+' = list(mass_multi = 1 / 2,
mass_add = (rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('Na', charge = 1)@mass) / 2,
formula_add = 'HNa',
formula_sub = 'C0',
charge = 2),
'[M+ACN+2H]2+' = list(mass_multi = 1 / 2,
mass_add = (2 * rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass) / 2,
formula_add = 'C2H5N',
formula_sub = 'C0',
charge = 2),
'[M+2Na]2+' = list(mass_multi = 1 / 2,
mass_add = 2 * rcdk::get.formula('Na', charge = 1)@mass / 2,
formula_add = 'Na2',
formula_sub = 'C0',
charge = 2),
'[M+2ACN+2H]2+' = list(mass_multi = 1 / 2,
mass_add = (2 * rcdk::get.formula('H', charge = 1)@mass + 2 * rcdk::get.formula('C2H3N', charge = 0)@mass) / 2,
formula_add = 'C4H8N2',
formula_sub = 'C0',
charge = 2),
'[M+3ACN+2H]2+' = list(mass_multi = 1 / 2,
mass_add = (2 * rcdk::get.formula('H', charge = 1)@mass + 3 * rcdk::get.formula('C2H3N', charge = 0)@mass) / 2,
formula_add = 'C6H11N3',
formula_sub = 'C0',
charge = 2),
'[M+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'H',
formula_sub = 'C0',
charge = 1),
'[M+NH4]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('NH4', charge = 1)@mass,
formula_add = 'NH4',
formula_sub = 'C0',
charge = 1),
'[M+Na]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('Na', charge = 1)@mass,
formula_add = 'Na',
formula_sub = 'C0',
charge = 1),
'[M+CH3OH+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('CH4O', charge = 0)@mass,
formula_add = 'Na',
formula_sub = 'C0',
charge = 1),
'[M+K]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('K', charge = 1)@mass,
formula_add = 'K',
formula_sub = 'C0',
charge = 1),
'[M+ACN+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H4N',
formula_sub = 'C0',
charge = 1),
'[M+2Na-H]+' = list(masS_multi = 1,
mass_add = 2 * rcdk::get.formula('Na', charge = 1)@mass - rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'Na2',
formula_sub = 'H',
charge = 1),
'[M+iPrOH+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C3H8O', charge = 0)@mass,
formula_add = 'C3H9O',
formula_sub = 'C0',
charge = 1),
'[M+ACN+Na]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('Na', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H3NNa',
formula_sub = 'C0',
charge = 1),
'[M+2K-H]+' = list(mass_multi = 1,
mass_add = 2 * rcdk::get.formula('K', charge = 1)@mass - rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'K2',
formula_sub = 'H',
charge = 1),
'[M+DMSO+H]+' = list(mass_multi = 1,
masS_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C2H6OS', charge = 0)@mass,
formula_add = 'C2H7OS',
formula_sub = 'C0',
charge = 1),
'[M+2ACN+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass + 2 * rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H4N',
formula_sub = 'C0',
charge = 1),
'[2M+H]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'H',
formula_sub = 'C0',
charge = 1),
'[2M+NH4]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('NH4', charge = 1)@mass,
formula_add = 'NH4',
formula_sub = 'C0',
charge = 1),
'[2M+Na]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('Na', charge = 1)@mass,
formula_add = 'Na',
formula_sub = 'C0',
charge = 1),
'[2M+K]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('K', charge = 1)@mass,
formula_add = 'K',
formula_sub = 'C0',
charge = 1),
'[2M+ACN+H]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H4N',
formula_sub = 'C0',
charge = 1),
'[2M+ACN+Na]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('Na', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H3NNa',
formula_sub = 'C0',
charge = 1),
'[M-3H]3-' = list(mass_multi = 1 / 3,
mass_add = - 3 * rcdk::get.formula('H', charge = 1)@mass / 3,
formula_add = 'C0',
formula_sub = 'H3',
charge = -3),
'[M-2H]2-' = list(mass_multi = 1 / 2,
mass_add = - 2 * rcdk::get.formula('H', charge = 1)@mass / 2,
formula_add = 'C0',
formula_sub = 'H2',
charge = -2),
'[M-H]-' = list(mass_multi = 1 ,
mass_add = - rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'C0',
formula_sub = 'H',
charge = -1),
'[M+Na-2H]-' = list(mass_multi = 1,
mass_add = - 2 * rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('Na', charge = 1)@mass,
formula_add = 'Na',
formula_sub = 'H2',
charge = -1),
'[M+Cl]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('Cl', charge = -1)@mass,
formula_add = 'Cl',
formula_sub = 'C0',
charge = -1),
'[M+K-2H]-' = list(mass_multi = 1,
mass_add = - 2 * rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('K', charge = 1)@mass,
formula_add = 'K',
formula_sub = 'H2',
charge = -1),
'[M+FA-H]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('CHO2', charge = -1)@mass,
formula_add = 'CHO2',
formula_sub = 'C0',
charge = -1),
'[M+HAc-H]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('C2H3O2', charge = -1)@mass,
formula_add = 'C2H3O2',
formula_sub = 'C0',
charge = -1),
'[M+Br]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('Br', charge = -1)@mass,
formula_add = 'Br',
formula_sub = 'C0',
charge = -1),
'[M+TFA-H]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('C2F3O2', charge = -1)@mass,
formula_add = 'C2F3O2',
formula_sub = 'C0',
charge = -1),
'[2M+FA-H]-' = list(mass_multi = 2,
mass_add = rcdk::get.formula('CHO2', charge = -1)@mass,
formula_add = 'CHO2',
formula_sub = 'C0',
charge = -1),
'[2M+HAc-H]-' = list(mass_multi = 2,
mass_add = rcdk::get.formula('C2H3O2', charge = -1)@mass,
formula_add = 'C2H3O2',
formula_sub = 'C0',
charge = -1),
'3[M-H]-' = list(mass_multi = 3 ,
mass_add = - rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'C0',
formula_sub = 'H',
charge = -1))
## return values
return(adduct_list)
}
#' @title Create list with all adduct calculation rules (positive ionisation)
#'
#' This function returns a list with rules for the calculation of adducts. It is required for the calculation of adduct m/z values from exact masses and the other way round. This list contains all rules for the positive ionization mode.
#'
#'
#' @author Michael Witting, \email{michael.witting@@helmholtz-muenchen.de}
#'
#' @seealso \code{\link{adduct_rules}}
#' @seealso \code{\link{adduct_rules_neg}}
#' @seealso \code{\link{get_adduct_names}}
#'
#' @export
adduct_rules_pos <- function() {
## create list with all the adduct definitoins
adduct_list <- list(
'[M+3H]3+' = list(mass_multi = 1 / 3,
mass_add = 3 * rcdk::get.formula('H', charge = 1)@mass / 3,
formula_add = 'H3',
formula_sub = 'C0',
charge = 3),
'[M+2H+Na]3+' = list(mass_multi = 1 / 3,
mass_add = (2 * rcdk::get.formula('H', charge = 1)@mass + 1 * rcdk::get.formula('Na', charge = 1)@mass) / 3,
formula_add = 'H2Na',
formula_sub = 'C0',
charge = 3),
'[M+H+Na2]3+' = list(mass_multi = 1 / 3,
mass_add = (1 * rcdk::get.formula('H', charge = 1)@mass + 2 * rcdk::get.formula('Na', charge = 1)@mass) / 3,
formula_add = 'HNa2',
formula_sub = 'C0',
charge = 3),
'[M+Na3]3+' = list(mass_multi = 1 / 3,
mass_add = (3 * rcdk::get.formula('Na', charge = 1)@mass) / 3,
formula_add = 'Na3',
formula_sub = 'C0',
charge = 3),
'[M+2H]2+' = list(mass_multi = 1 / 2,
mass_add = 2 * rcdk::get.formula('H', charge = 1)@mass / 2,
formula_add = 'H2',
formula_sub = 'C0',
charge = 2),
'[M+H+NH4]2+' = list(mass_multi = 1 / 2,
mass_add = (rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('NH4', charge = 1)@mass) / 2,
formula_add = 'NH5',
formula_sub = 'C0',
charge = 2),
'[M+H+K]2+' = list(mass_multi = 1 / 2,
mass_add = (rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('K', charge = 1)@mass) / 2,
formula_add = 'HK',
formula_sub = 'C0',
charge = 2),
'[M+H+Na]2+' = list(mass_multi = 1 / 2,
mass_add = (rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('Na', charge = 1)@mass) / 2,
formula_add = 'HNa',
formula_sub = 'C0',
charge = 2),
'[M+ACN+2H]2+' = list(mass_multi = 1 / 2,
mass_add = (2 * rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass) / 2,
formula_add = 'C2H5N',
formula_sub = 'C0',
charge = 2),
'[M+2Na]2+' = list(mass_multi = 1 / 2,
mass_add = 2 * rcdk::get.formula('Na', charge = 1)@mass / 2,
formula_add = 'Na2',
formula_sub = 'C0',
charge = 2),
'[M+2ACN+2H]2+' = list(mass_multi = 1 / 2,
mass_add = (2 * rcdk::get.formula('H', charge = 1)@mass + 2 * rcdk::get.formula('C2H3N', charge = 0)@mass) / 2,
formula_add = 'C4H8N2',
formula_sub = 'C0',
charge = 2),
'[M+3ACN+2H]2+' = list(mass_multi = 1 / 2,
mass_add = (2 * rcdk::get.formula('H', charge = 1)@mass + 3 * rcdk::get.formula('C2H3N', charge = 0)@mass) / 2,
formula_add = 'C6H11N3',
formula_sub = 'C0',
charge = 2),
'[M+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'H',
formula_sub = 'C0',
charge = 1),
'[M+NH4]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('NH4', charge = 1)@mass,
formula_add = 'NH4',
formula_sub = 'C0',
charge = 1),
'[M+Na]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('Na', charge = 1)@mass,
formula_add = 'Na',
formula_sub = 'C0',
charge = 1),
'[M+CH3OH+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('CH4O', charge = 0)@mass,
formula_add = 'Na',
formula_sub = 'C0',
charge = 1),
'[M+K]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('K', charge = 1)@mass,
formula_add = 'K',
formula_sub = 'C0',
charge = 1),
'[M+ACN+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H4N',
formula_sub = 'C0',
charge = 1),
'[M+2Na-H]+' = list(masS_multi = 1,
mass_add = 2 * rcdk::get.formula('Na', charge = 1)@mass - rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'Na2',
formula_sub = 'H',
charge = 1),
'[M+iPrOH+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C3H8O', charge = 0)@mass,
formula_add = 'C3H9O',
formula_sub = 'C0',
charge = 1),
'[M+ACN+Na]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('Na', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H3NNa',
formula_sub = 'C0',
charge = 1),
'[M+2K-H]+' = list(mass_multi = 1,
mass_add = 2 * rcdk::get.formula('K', charge = 1)@mass - rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'K2',
formula_sub = 'H',
charge = 1),
'[M+DMSO+H]+' = list(mass_multi = 1,
masS_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C2H6OS', charge = 0)@mass,
formula_add = 'C2H7OS',
formula_sub = 'C0',
charge = 1),
'[M+2ACN+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass + 2 * rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H4N',
formula_sub = 'C0',
charge = 1),
'[2M+H]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'H',
formula_sub = 'C0',
charge = 1),
'[2M+NH4]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('NH4', charge = 1)@mass,
formula_add = 'NH4',
formula_sub = 'C0',
charge = 1),
'[2M+Na]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('Na', charge = 1)@mass,
formula_add = 'Na',
formula_sub = 'C0',
charge = 1),
'[2M+K]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('K', charge = 1)@mass,
formula_add = 'K',
formula_sub = 'C0',
charge = 1),
'[2M+ACN+H]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H4N',
formula_sub = 'C0',
charge = 1),
'[2M+ACN+Na]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('Na', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H3NNa',
formula_sub = 'C0',
charge = 1)
)
## return values
return(adduct_list)
}
#' @title Create list with all adduct calculation rules (negative ion model)
#'
#' This function returns a list with rules for the calculation of adducts. It is required for the calculation of adduct m/z values from exact masses and the other way round. This list contains all rules for the negative ionization mode.
#'
#'
#' @author Michael Witting, \email{michael.witting@@helmholtz-muenchen.de}
#'
#' @seealso \code{\link{adduct_rules}}
#' @seealso \code{\link{adduct_rules_pos}}
#' @seealso \code{\link{get_adduct_names}}
#'
#' @export
adduct_rules_neg <- function() {
## create list with all the adduct definitoins
adduct_list <- list(
'[M-3H]3-' = list(mass_multi = 1 / 3,
mass_add = - 3 * rcdk::get.formula('H', charge = 1)@mass / 3,
formula_add = 'C0',
formula_sub = 'H3',
charge = -3),
'[M-2H]2-' = list(mass_multi = 1 / 2,
mass_add = - 2 * rcdk::get.formula('H', charge = 1)@mass / 2,
formula_add = 'C0',
formula_sub = 'H2',
charge = -2),
'[M-H]-' = list(mass_multi = 1 ,
mass_add = - rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'C0',
formula_sub = 'H',
charge = -1),
'[M+Na-2H]-' = list(mass_multi = 1,
mass_add = - 2 * rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('Na', charge = 1)@mass,
formula_add = 'Na',
formula_sub = 'H2',
charge = -1),
'[M+Cl]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('Cl', charge = -1)@mass,
formula_add = 'Cl',
formula_sub = 'C0',
charge = -1),
'[M+K-2H]-' = list(mass_multi = 1,
mass_add = - 2 * rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('K', charge = 1)@mass,
formula_add = 'K',
formula_sub = 'H2',
charge = -1),
'[M+FA-H]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('CHO2', charge = -1)@mass,
formula_add = 'CHO2',
formula_sub = 'C0',
charge = -1),
'[M+HAc-H]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('C2H3O2', charge = -1)@mass,
formula_add = 'C2H3O2',
formula_sub = 'C0',
charge = -1),
'[M+Br]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('Br', charge = -1)@mass,
formula_add = 'Br',
formula_sub = 'C0',
charge = -1),
'[M+TFA-H]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('C2F3O2', charge = -1)@mass,
formula_add = 'C2F3O2',
formula_sub = 'C0',
charge = -1),
'[2M+FA-H]-' = list(mass_multi = 2,
mass_add = rcdk::get.formula('CHO2', charge = -1)@mass,
formula_add = 'CHO2',
formula_sub = 'C0',
charge = -1),
'[2M+HAc-H]-' = list(mass_multi = 2,
mass_add = rcdk::get.formula('C2H3O2', charge = -1)@mass,
formula_add = 'C2H3O2',
formula_sub = 'C0',
charge = -1),
'[3M-H]-' = list(mass_multi = 3 ,
mass_add = - rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'C0',
formula_sub = 'H',
charge = -1))
## return values
return(adduct_list)
}
#' @title Return current adduct naming
#'
#' This function returns either all or only positive or negative ionization mode adduct names used in this package.
#'
#' @param mode Ionization mode for which the adduct names shall be returned, either \code{all}, \code{positive} or \code{negative}
#'
#'
#' @author Michael Witting, \email{michael.witting@@helmholtz-muenchen.de}
#'
#' @seealso \code{\link{adduct_rules}}
#' @seealso \code{\link{adduct_rules_pos}}
#' @seealso \code{\link{adduct_rules_neg}}
#'
#' @export
get_adduct_names <- function(mode = c("all", "positive", "negative")) {
# get adduct lists
adduct_list_neg <- adduct_rules_neg()
adduct_list_pos <- adduct_rules_pos()
if(mode == "all") {
return(c(names(adduct_list_neg), names(adduct_list_pos)))
} else if(mode == "positive") {
return(names(adduct_list_pos))
} else if(mode == "negative") {
return(names(adduct_list_neg))
}
}
michaelwitting/metabolomicsUtils documentation built on Nov. 9, 2019, 10:44 a.m.
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Defines functions adduct_rules adduct_rules_pos adduct_rules_neg get_adduct_names
Documented in adduct_rules adduct_rules_neg adduct_rules_pos get_adduct_names
#' @title Create list with all adduct calculation rules (all rules)
#'
#' This function returns a list with rules for the calculation of adducts. It is required for the calculation of adduct m/z values from exact masses and the other way round. This list contains all rules for both ionization modes.
#'
#'
#' @author Michael Witting, \email{michael.witting@@helmholtz-muenchen.de}
#'
#' @seealso \code{\link{adduct_rules_pos}}
#' @seealso \code{\link{adduct_rules_neg}}
#' @seealso \code{\link{get_adduct_names}}
#'
#' @export
adduct_rules <- function() {
## create list with all the adduct definitoins
adduct_list <- list(
'[M+3H]3+' = list(mass_multi = 1 / 3,
mass_add = 3 * rcdk::get.formula('H', charge = 1)@mass / 3,
formula_add = 'H3',
formula_sub = 'C0',
charge = 3),
'[M+2H+Na]3+' = list(mass_multi = 1 / 3,
mass_add = (2 * rcdk::get.formula('H', charge = 1)@mass + 1 * rcdk::get.formula('Na', charge = 1)@mass) / 3,
formula_add = 'H2Na',
formula_sub = 'C0',
charge = 3),
'[M+H+Na2]3+' = list(mass_multi = 1 / 3,
mass_add = (1 * rcdk::get.formula('H', charge = 1)@mass + 2 * rcdk::get.formula('Na', charge = 1)@mass) / 3,
formula_add = 'HNa2',
formula_sub = 'C0',
charge = 3),
'[M+Na3]3+' = list(mass_multi = 1 / 3,
mass_add = (3 * rcdk::get.formula('Na', charge = 1)@mass) / 3,
formula_add = 'Na3',
formula_sub = 'C0',
charge = 3),
'[M+2H]2+' = list(mass_multi = 1 / 2,
mass_add = 2 * rcdk::get.formula('H', charge = 1)@mass / 2,
formula_add = 'H2',
formula_sub = 'C0',
charge = 2),
'[M+H+NH4]2+' = list(mass_multi = 1 / 2,
mass_add = (rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('NH4', charge = 1)@mass) / 2,
formula_add = 'NH5',
formula_sub = 'C0',
charge = 2),
'[M+H+K]2+' = list(mass_multi = 1 / 2,
mass_add = (rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('K', charge = 1)@mass) / 2,
formula_add = 'HK',
formula_sub = 'C0',
charge = 2),
'[M+H+Na]2+' = list(mass_multi = 1 / 2,
mass_add = (rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('Na', charge = 1)@mass) / 2,
formula_add = 'HNa',
formula_sub = 'C0',
charge = 2),
'[M+ACN+2H]2+' = list(mass_multi = 1 / 2,
mass_add = (2 * rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass) / 2,
formula_add = 'C2H5N',
formula_sub = 'C0',
charge = 2),
'[M+2Na]2+' = list(mass_multi = 1 / 2,
mass_add = 2 * rcdk::get.formula('Na', charge = 1)@mass / 2,
formula_add = 'Na2',
formula_sub = 'C0',
charge = 2),
'[M+2ACN+2H]2+' = list(mass_multi = 1 / 2,
mass_add = (2 * rcdk::get.formula('H', charge = 1)@mass + 2 * rcdk::get.formula('C2H3N', charge = 0)@mass) / 2,
formula_add = 'C4H8N2',
formula_sub = 'C0',
charge = 2),
'[M+3ACN+2H]2+' = list(mass_multi = 1 / 2,
mass_add = (2 * rcdk::get.formula('H', charge = 1)@mass + 3 * rcdk::get.formula('C2H3N', charge = 0)@mass) / 2,
formula_add = 'C6H11N3',
formula_sub = 'C0',
charge = 2),
'[M+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'H',
formula_sub = 'C0',
charge = 1),
'[M+NH4]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('NH4', charge = 1)@mass,
formula_add = 'NH4',
formula_sub = 'C0',
charge = 1),
'[M+Na]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('Na', charge = 1)@mass,
formula_add = 'Na',
formula_sub = 'C0',
charge = 1),
'[M+CH3OH+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('CH4O', charge = 0)@mass,
formula_add = 'Na',
formula_sub = 'C0',
charge = 1),
'[M+K]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('K', charge = 1)@mass,
formula_add = 'K',
formula_sub = 'C0',
charge = 1),
'[M+ACN+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H4N',
formula_sub = 'C0',
charge = 1),
'[M+2Na-H]+' = list(masS_multi = 1,
mass_add = 2 * rcdk::get.formula('Na', charge = 1)@mass - rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'Na2',
formula_sub = 'H',
charge = 1),
'[M+iPrOH+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C3H8O', charge = 0)@mass,
formula_add = 'C3H9O',
formula_sub = 'C0',
charge = 1),
'[M+ACN+Na]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('Na', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H3NNa',
formula_sub = 'C0',
charge = 1),
'[M+2K-H]+' = list(mass_multi = 1,
mass_add = 2 * rcdk::get.formula('K', charge = 1)@mass - rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'K2',
formula_sub = 'H',
charge = 1),
'[M+DMSO+H]+' = list(mass_multi = 1,
masS_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C2H6OS', charge = 0)@mass,
formula_add = 'C2H7OS',
formula_sub = 'C0',
charge = 1),
'[M+2ACN+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass + 2 * rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H4N',
formula_sub = 'C0',
charge = 1),
'[2M+H]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'H',
formula_sub = 'C0',
charge = 1),
'[2M+NH4]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('NH4', charge = 1)@mass,
formula_add = 'NH4',
formula_sub = 'C0',
charge = 1),
'[2M+Na]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('Na', charge = 1)@mass,
formula_add = 'Na',
formula_sub = 'C0',
charge = 1),
'[2M+K]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('K', charge = 1)@mass,
formula_add = 'K',
formula_sub = 'C0',
charge = 1),
'[2M+ACN+H]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H4N',
formula_sub = 'C0',
charge = 1),
'[2M+ACN+Na]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('Na', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H3NNa',
formula_sub = 'C0',
charge = 1),
'[M-3H]3-' = list(mass_multi = 1 / 3,
mass_add = - 3 * rcdk::get.formula('H', charge = 1)@mass / 3,
formula_add = 'C0',
formula_sub = 'H3',
charge = -3),
'[M-2H]2-' = list(mass_multi = 1 / 2,
mass_add = - 2 * rcdk::get.formula('H', charge = 1)@mass / 2,
formula_add = 'C0',
formula_sub = 'H2',
charge = -2),
'[M-H]-' = list(mass_multi = 1 ,
mass_add = - rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'C0',
formula_sub = 'H',
charge = -1),
'[M+Na-2H]-' = list(mass_multi = 1,
mass_add = - 2 * rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('Na', charge = 1)@mass,
formula_add = 'Na',
formula_sub = 'H2',
charge = -1),
'[M+Cl]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('Cl', charge = -1)@mass,
formula_add = 'Cl',
formula_sub = 'C0',
charge = -1),
'[M+K-2H]-' = list(mass_multi = 1,
mass_add = - 2 * rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('K', charge = 1)@mass,
formula_add = 'K',
formula_sub = 'H2',
charge = -1),
'[M+FA-H]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('CHO2', charge = -1)@mass,
formula_add = 'CHO2',
formula_sub = 'C0',
charge = -1),
'[M+HAc-H]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('C2H3O2', charge = -1)@mass,
formula_add = 'C2H3O2',
formula_sub = 'C0',
charge = -1),
'[M+Br]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('Br', charge = -1)@mass,
formula_add = 'Br',
formula_sub = 'C0',
charge = -1),
'[M+TFA-H]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('C2F3O2', charge = -1)@mass,
formula_add = 'C2F3O2',
formula_sub = 'C0',
charge = -1),
'[2M+FA-H]-' = list(mass_multi = 2,
mass_add = rcdk::get.formula('CHO2', charge = -1)@mass,
formula_add = 'CHO2',
formula_sub = 'C0',
charge = -1),
'[2M+HAc-H]-' = list(mass_multi = 2,
mass_add = rcdk::get.formula('C2H3O2', charge = -1)@mass,
formula_add = 'C2H3O2',
formula_sub = 'C0',
charge = -1),
'3[M-H]-' = list(mass_multi = 3 ,
mass_add = - rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'C0',
formula_sub = 'H',
charge = -1))
## return values
return(adduct_list)
}
#' @title Create list with all adduct calculation rules (positive ionisation)
#'
#' This function returns a list with rules for the calculation of adducts. It is required for the calculation of adduct m/z values from exact masses and the other way round. This list contains all rules for the positive ionization mode.
#'
#'
#' @author Michael Witting, \email{michael.witting@@helmholtz-muenchen.de}
#'
#' @seealso \code{\link{adduct_rules}}
#' @seealso \code{\link{adduct_rules_neg}}
#' @seealso \code{\link{get_adduct_names}}
#'
#' @export
adduct_rules_pos <- function() {
## create list with all the adduct definitoins
adduct_list <- list(
'[M+3H]3+' = list(mass_multi = 1 / 3,
mass_add = 3 * rcdk::get.formula('H', charge = 1)@mass / 3,
formula_add = 'H3',
formula_sub = 'C0',
charge = 3),
'[M+2H+Na]3+' = list(mass_multi = 1 / 3,
mass_add = (2 * rcdk::get.formula('H', charge = 1)@mass + 1 * rcdk::get.formula('Na', charge = 1)@mass) / 3,
formula_add = 'H2Na',
formula_sub = 'C0',
charge = 3),
'[M+H+Na2]3+' = list(mass_multi = 1 / 3,
mass_add = (1 * rcdk::get.formula('H', charge = 1)@mass + 2 * rcdk::get.formula('Na', charge = 1)@mass) / 3,
formula_add = 'HNa2',
formula_sub = 'C0',
charge = 3),
'[M+Na3]3+' = list(mass_multi = 1 / 3,
mass_add = (3 * rcdk::get.formula('Na', charge = 1)@mass) / 3,
formula_add = 'Na3',
formula_sub = 'C0',
charge = 3),
'[M+2H]2+' = list(mass_multi = 1 / 2,
mass_add = 2 * rcdk::get.formula('H', charge = 1)@mass / 2,
formula_add = 'H2',
formula_sub = 'C0',
charge = 2),
'[M+H+NH4]2+' = list(mass_multi = 1 / 2,
mass_add = (rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('NH4', charge = 1)@mass) / 2,
formula_add = 'NH5',
formula_sub = 'C0',
charge = 2),
'[M+H+K]2+' = list(mass_multi = 1 / 2,
mass_add = (rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('K', charge = 1)@mass) / 2,
formula_add = 'HK',
formula_sub = 'C0',
charge = 2),
'[M+H+Na]2+' = list(mass_multi = 1 / 2,
mass_add = (rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('Na', charge = 1)@mass) / 2,
formula_add = 'HNa',
formula_sub = 'C0',
charge = 2),
'[M+ACN+2H]2+' = list(mass_multi = 1 / 2,
mass_add = (2 * rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass) / 2,
formula_add = 'C2H5N',
formula_sub = 'C0',
charge = 2),
'[M+2Na]2+' = list(mass_multi = 1 / 2,
mass_add = 2 * rcdk::get.formula('Na', charge = 1)@mass / 2,
formula_add = 'Na2',
formula_sub = 'C0',
charge = 2),
'[M+2ACN+2H]2+' = list(mass_multi = 1 / 2,
mass_add = (2 * rcdk::get.formula('H', charge = 1)@mass + 2 * rcdk::get.formula('C2H3N', charge = 0)@mass) / 2,
formula_add = 'C4H8N2',
formula_sub = 'C0',
charge = 2),
'[M+3ACN+2H]2+' = list(mass_multi = 1 / 2,
mass_add = (2 * rcdk::get.formula('H', charge = 1)@mass + 3 * rcdk::get.formula('C2H3N', charge = 0)@mass) / 2,
formula_add = 'C6H11N3',
formula_sub = 'C0',
charge = 2),
'[M+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'H',
formula_sub = 'C0',
charge = 1),
'[M+NH4]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('NH4', charge = 1)@mass,
formula_add = 'NH4',
formula_sub = 'C0',
charge = 1),
'[M+Na]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('Na', charge = 1)@mass,
formula_add = 'Na',
formula_sub = 'C0',
charge = 1),
'[M+CH3OH+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('CH4O', charge = 0)@mass,
formula_add = 'Na',
formula_sub = 'C0',
charge = 1),
'[M+K]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('K', charge = 1)@mass,
formula_add = 'K',
formula_sub = 'C0',
charge = 1),
'[M+ACN+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H4N',
formula_sub = 'C0',
charge = 1),
'[M+2Na-H]+' = list(masS_multi = 1,
mass_add = 2 * rcdk::get.formula('Na', charge = 1)@mass - rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'Na2',
formula_sub = 'H',
charge = 1),
'[M+iPrOH+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C3H8O', charge = 0)@mass,
formula_add = 'C3H9O',
formula_sub = 'C0',
charge = 1),
'[M+ACN+Na]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('Na', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H3NNa',
formula_sub = 'C0',
charge = 1),
'[M+2K-H]+' = list(mass_multi = 1,
mass_add = 2 * rcdk::get.formula('K', charge = 1)@mass - rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'K2',
formula_sub = 'H',
charge = 1),
'[M+DMSO+H]+' = list(mass_multi = 1,
masS_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C2H6OS', charge = 0)@mass,
formula_add = 'C2H7OS',
formula_sub = 'C0',
charge = 1),
'[M+2ACN+H]+' = list(mass_multi = 1,
mass_add = rcdk::get.formula('H', charge = 1)@mass + 2 * rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H4N',
formula_sub = 'C0',
charge = 1),
'[2M+H]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'H',
formula_sub = 'C0',
charge = 1),
'[2M+NH4]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('NH4', charge = 1)@mass,
formula_add = 'NH4',
formula_sub = 'C0',
charge = 1),
'[2M+Na]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('Na', charge = 1)@mass,
formula_add = 'Na',
formula_sub = 'C0',
charge = 1),
'[2M+K]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('K', charge = 1)@mass,
formula_add = 'K',
formula_sub = 'C0',
charge = 1),
'[2M+ACN+H]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H4N',
formula_sub = 'C0',
charge = 1),
'[2M+ACN+Na]+' = list(mass_multi = 2,
mass_add = rcdk::get.formula('Na', charge = 1)@mass + rcdk::get.formula('C2H3N', charge = 0)@mass,
formula_add = 'C2H3NNa',
formula_sub = 'C0',
charge = 1)
)
## return values
return(adduct_list)
}
#' @title Create list with all adduct calculation rules (negative ion model)
#'
#' This function returns a list with rules for the calculation of adducts. It is required for the calculation of adduct m/z values from exact masses and the other way round. This list contains all rules for the negative ionization mode.
#'
#'
#' @author Michael Witting, \email{michael.witting@@helmholtz-muenchen.de}
#'
#' @seealso \code{\link{adduct_rules}}
#' @seealso \code{\link{adduct_rules_pos}}
#' @seealso \code{\link{get_adduct_names}}
#'
#' @export
adduct_rules_neg <- function() {
## create list with all the adduct definitoins
adduct_list <- list(
'[M-3H]3-' = list(mass_multi = 1 / 3,
mass_add = - 3 * rcdk::get.formula('H', charge = 1)@mass / 3,
formula_add = 'C0',
formula_sub = 'H3',
charge = -3),
'[M-2H]2-' = list(mass_multi = 1 / 2,
mass_add = - 2 * rcdk::get.formula('H', charge = 1)@mass / 2,
formula_add = 'C0',
formula_sub = 'H2',
charge = -2),
'[M-H]-' = list(mass_multi = 1 ,
mass_add = - rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'C0',
formula_sub = 'H',
charge = -1),
'[M+Na-2H]-' = list(mass_multi = 1,
mass_add = - 2 * rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('Na', charge = 1)@mass,
formula_add = 'Na',
formula_sub = 'H2',
charge = -1),
'[M+Cl]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('Cl', charge = -1)@mass,
formula_add = 'Cl',
formula_sub = 'C0',
charge = -1),
'[M+K-2H]-' = list(mass_multi = 1,
mass_add = - 2 * rcdk::get.formula('H', charge = 1)@mass + rcdk::get.formula('K', charge = 1)@mass,
formula_add = 'K',
formula_sub = 'H2',
charge = -1),
'[M+FA-H]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('CHO2', charge = -1)@mass,
formula_add = 'CHO2',
formula_sub = 'C0',
charge = -1),
'[M+HAc-H]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('C2H3O2', charge = -1)@mass,
formula_add = 'C2H3O2',
formula_sub = 'C0',
charge = -1),
'[M+Br]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('Br', charge = -1)@mass,
formula_add = 'Br',
formula_sub = 'C0',
charge = -1),
'[M+TFA-H]-' = list(mass_multi = 1,
mass_add = rcdk::get.formula('C2F3O2', charge = -1)@mass,
formula_add = 'C2F3O2',
formula_sub = 'C0',
charge = -1),
'[2M+FA-H]-' = list(mass_multi = 2,
mass_add = rcdk::get.formula('CHO2', charge = -1)@mass,
formula_add = 'CHO2',
formula_sub = 'C0',
charge = -1),
'[2M+HAc-H]-' = list(mass_multi = 2,
mass_add = rcdk::get.formula('C2H3O2', charge = -1)@mass,
formula_add = 'C2H3O2',
formula_sub = 'C0',
charge = -1),
'[3M-H]-' = list(mass_multi = 3 ,
mass_add = - rcdk::get.formula('H', charge = 1)@mass,
formula_add = 'C0',
formula_sub = 'H',
charge = -1))
## return values
return(adduct_list)
}
#' @title Return current adduct naming
#'
#' This function returns either all or only positive or negative ionization mode adduct names used in this package.
#'
#' @param mode Ionization mode for which the adduct names shall be returned, either \code{all}, \code{positive} or \code{negative}
#'
#'
#' @author Michael Witting, \email{michael.witting@@helmholtz-muenchen.de}
#'
#' @seealso \code{\link{adduct_rules}}
#' @seealso \code{\link{adduct_rules_pos}}
#' @seealso \code{\link{adduct_rules_neg}}
#'
#' @export
get_adduct_names <- function(mode = c("all", "positive", "negative")) {
# get adduct lists
adduct_list_neg <- adduct_rules_neg()
adduct_list_pos <- adduct_rules_pos()
if(mode == "all") {
return(c(names(adduct_list_neg), names(adduct_list_pos)))
} else if(mode == "positive") {
return(names(adduct_list_pos))
} else if(mode == "negative") {
return(names(adduct_list_neg))
}
}
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