calc_kmd: Calculate the Kendrick mass defect (KMD)

In metamorphr: Tidy and Streamlined Metabolomics Data Workflows

Calculate the Kendrick mass defect (KMD)

Description

The Kendrick mass defect (KMD) is calculated by subtracting the Kendrick mass (calc_km) from the nominal Kendrick mass (calc_nominal_km). See the References section for more information.

Usage

calc_kmd(mass, repeating_unit = "CH2")

Arguments

mass	A molecular mass (or m/z).
repeating_unit	The formula of the repeating unit, given as a string.

Value

The Kendrick mass defect (KMD)

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

calc_kmd(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()

metamorphr documentation built on June 10, 2026, 5:07 p.m.