R/mz_iso_resolve.R

In wmoldham/mzrtools.dev: Make Molecular Formulas Useful for Mass Spectrometry Applications

#' Identify isotopes unresolved from targets
#'
#' \code{mz_iso_resolve} will return the molecular isotopes of interest
#'     (\emph{e.g.}, M0 or label-containing) and those isotopes that cannot be
#'     resolved from these targets by the mass spectrometer.
#'
#' @inheritParams mz_iso_target
#' @param ... Passes the arguments nominal_resolution (default 70,000) and
#'     nominal_mz (default 200) used to determine the delta m/\emph{z} below
#'     which peaks are considered unresolved.
#'
#' @return A list containing a tibble of unresolved isotopes and the output
#'     of `mz_iso_target`.
#'
#' @export
#'
#' @examples
#' mz_iso_resolve("C5H8O5")
#' mz_iso_resolve("C5H8O5", tracer = c("C", "H"))
#'
mz_iso_resolve <- function(molecule, tracer = "C", polarity = "negative", ...) {

  l <- mz_iso_target(molecule = molecule, tracer = tracer, polarity = polarity)
  iso_list <- l$iso_list
  targets <- l$targets

  resolved <-
    targets %>%
    dplyr::select(.data$shift, .data$mass) %>%
    dplyr::left_join(iso_list, by = "shift", suffix = c(".tar", ".iso")) %>%
    dplyr::mutate(diff = abs(.data$mass.tar - .data$mass.iso),
                  delta = delta_mz(.data$mass.tar, ...)) %>%
    dplyr::filter(.data$diff <= .data$delta) %>%
    dplyr::select(.data$shift,
                  .data$mass.tar,
                  .data$mass.iso,
                  .data$diff,
                  .data$delta,
                  dplyr::everything())

  l[["resolved"]] <- resolved

  l

}


# based on Orbitrap detector
delta_mz <-
  function(mz,
           nominal_mz = 200,
           nominal_resolution = 70000) {
    1.67 * mz * sqrt(mz / nominal_mz) / nominal_resolution
  }