metamorphr (version 0.2.0)

calc_km: Calculate the Kendrick mass

Description

Calculate the Kendrick mass for a given mass (or m/z) and repeating unit. The Kendrick mass is a rescaled mass, that usually sets CH2 = 14 but other repeating units can also be used. It is usefull for the visual identification of potential homologues. See the References section for more information. The Kendrick mass is not to be confused with the Kendrick mass defect (KMD, calc_kmd) and the nominal Kendrick mass (calc_nominal_km).

Usage

calc_km(mass, repeating_unit = "CH2")

Value

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

calc_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.
# Note that in the publication by Hughey et al., the nominal Kendrick mass
# is used on the x-axis instead of the exact Kendrick mass.
# See ?calc_nominal_km.

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`),
                KM = calc_km(`m/z`)) %>%
  ggplot2::ggplot(ggplot2::aes(x = KM,
                               y = KMD,
                               size = max_int,
                               color = RT)) +
    ggplot2::geom_point()