metamorphr (version 0.2.0)

calc_nominal_km: Calculate the nominal Kendrick mass

Description

The nominal Kendrick mass is the Kendrick mass (calc_km), rounded up to the nearest whole number. The nominal Kendrick mass and the Kendrick mass are both required to calculate the Kendrick mass defect (KMD). The nominal Kendrick mass is not to be confused with the Kendrick mass defect (calc_kmd) and the Kendrick mass (calc_km).

Usage

calc_nominal_km(mass, repeating_unit = "CH2")

Value

The nominal Kendrick mass.

Arguments

mass

A molecular mass (or m/z).

repeating_unit

The formula of the repeating unit, given as a string.

References

• Kendrick mass on Wikipedia

• Edward Kendrick, Anal. Chem. 1963, 35, 2146–2154.

• C. A. Hughey, C. L. Hendrickson, R. P. Rodgers, A. G. Marshall, K. Qian, Anal. Chem. 2001, 73, 4676–4681.

Examples

# Calculate the nominal Kendrick masses for two measured masses with
# CH2 as the repeating unit.
# See Hughey et al. in the References section above

calc_nominal_km(c(351.3269, 365.3425))

# Construct a KMD plot from m/z values.
# RT is mapped to color and the feature-wise maximum intensity to size.

toy_metaboscape %>%
  dplyr::group_by(UID, `m/z`, RT) %>%
  dplyr::summarise(max_int = max(Intensity, na.rm = TRUE)) %>%
  dplyr::ungroup() %>%
  dplyr::mutate(KMD = calc_kmd(`m/z`),
                `nominal KM` = calc_nominal_km(`m/z`)) %>%
  ggplot2::ggplot(ggplot2::aes(x = `nominal KM`,
                               y = KMD,
                               size = max_int,
                               color = RT)) +
    ggplot2::geom_point()