Calculate mass-to-charge ratios for proteoform ions.

Source: R/ions.R

For each value \(z\) in charge_states, the function calculates

  • the corresponding mass-to-charge ratio \(m / z + m_c\) (\(m_c\): charge agent mass);

  • upper and lower tolerances for this ratio, so that these values form a window of width \(mz \times ppm / 10^6\) centered at \(mz\).

ionize(p, charge_states, ppm = 400, charge_agent_mass = NULL)

Arguments

p

A data frame describing proteoform masses (see details).
charge_states

Vector of charge states for which m/z values should be calculated.
ppm

Width of the m/z window in parts per million.
charge_agent_mass

Mass of the charge carrier. If NULL, use the average IUPAC mass of the proton.

Value

A data frame containing all columns of the input data frame plus four additional columns: z (charge state), mz (exact mass-to-charge ratio), mz_min, and mz_max. The latter two columns represent lower and upper tolerances for the mass-to-charge ratio and are used as integration boundaries by quantify_ions(). If the supplied data frame has \(r\) rows and \(c\) charge states were specified, the resulting data frame has \(r * c\) rows.

Details

The data frame passed to the first argument must contain at least one column named mass; each of its value represents the mass of a single proteoform. The data frame may contain any number of additional columns, which will be returned unchanged.

Examples

masses <- data.frame(name = c("p1", "p2"), mass = c(140000, 145000))
ionize(masses, 36L:40L)

#> # A tibble: 10 x 6
#>    name    mass     z    mz mz_min mz_max
#>    <chr>  <dbl> <int> <dbl>  <dbl>  <dbl>
#>  1 p1    140000    36 3890.  3889.  3891.
#>  2 p1    140000    37 3785.  3784.  3786.
#>  3 p1    140000    38 3685.  3684.  3686.
#>  4 p1    140000    39 3591.  3590.  3591.
#>  5 p1    140000    40 3501.  3500.  3502.
#>  6 p2    145000    36 4029.  4028.  4030.
#>  7 p2    145000    37 3920.  3919.  3921.
#>  8 p2    145000    38 3817.  3816.  3818.
#>  9 p2    145000    39 3719.  3718.  3720.
#> 10 p2    145000    40 3626.  3625.  3627.