Look up an observed m/z difference against the theoretical differences table

The interpretation workhorse behind "what could this delta be": given a mass difference measured between two peaks in the same spectrum (an in-source fragment, a homologous-series step, a suspected adduct...), returns every entry of mz_diff_table within tolerance.

Usage

mz_diff_lookup(
  delta,
  tol = 100,
  unit = c("ppm", "Da"),
  ref_mz = NULL,
  mode = c("both", "pos", "neg"),
  table = mz_diff_table(match.arg(mode))
)

Arguments

delta: the observed difference, in Da.
tol: the tolerance. In ppm by default (the usual way an instrument's mass accuracy is quoted); switch to unit = "Da" for a flat window instead. When ref_mz is supplied the ppm tolerance is applied relative to ref_mz (i.e. the window is ref_mz * tol / 1e6), matching the scale of the returned error_ppm column. When ref_mz is NULL the tolerance is instead ppm of the DIFFERENCE, not of either peak's own m/z – for a small delta that is an unrealistically tight window (10 ppm of a 1 Da delta is 0.00001 Da), since the true uncertainty of a difference comes from BOTH peaks' own mass accuracy, not from the size of the gap between them. Widen tol accordingly, supply ref_mz, or pass an absolute unit = "Da" tolerance if you already know the window you want.
unit: "ppm" (default) or "Da".
ref_mz: reference m/z the ppm figures are relative to, typically the parent ion's own m/z. Instrument mass accuracy is quoted as ppm of a measured m/z, so a difference between two peaks should be judged against the m/z those peaks were measured at, not against the size of the gap: a 0.002 Da error on a 1 Da difference is 2000 ppm of the difference but only 6.7 ppm of a 300 Da parent ion, and the latter is the realistic number. Supplying ref_mz makes both the unit = "ppm" tolerance and the returned error_ppm column relative to it. The default NULL keeps the legacy behaviour of dividing by abs(delta), which is not recommended for small deltas.
mode: passed to mz_diff_table if table is not supplied.
table: a table from mz_diff_table; computed automatically from mode if omitted. Pass your own to avoid recomputing it when calling this repeatedly (e.g. over every peak pair in a spectrum).

Value

table, filtered to rows within tolerance of delta, with added error_Da and error_ppm columns, sorted by abs(error_Da). error_ppm is relative to ref_mz when supplied, otherwise to abs(delta).

Author

Jan Stanstrup, stanstrup@gmail.com

Examples

# 20 ppm of a 300 Da parent ion, reported as ppm of that parent ion
mz_diff_lookup(18.0106, tol = 20, unit = "ppm", ref_mz = 300)  # water
#> # A tibble: 3 × 7
#>   mz_diff category        mode  origin              reference error_Da error_ppm
#>     <dbl> <chr>           <chr> <chr>               <chr>        <dbl>     <dbl>
#> 1    18.0 adduct/fragment both  ± H2O, water addit… F         -3.00e-5   -0.1000
#> 2    18.0 repeating unit  pos   H2O, water clusters F         -3.00e-5   -0.1000
#> 3    18.0 repeating unit  neg   H2O, water clusters F         -3.00e-5   -0.1000
mz_diff_lookup(18.0106, tol = 0.002, unit = "Da")  # same, as a flat window
#> # A tibble: 3 × 7
#>   mz_diff category        mode  origin              reference error_Da error_ppm
#>     <dbl> <chr>           <chr> <chr>               <chr>        <dbl>     <dbl>
#> 1    18.0 adduct/fragment both  ± H2O, water addit… F         -3.00e-5     -1.67
#> 2    18.0 repeating unit  pos   H2O, water clusters F         -3.00e-5     -1.67
#> 3    18.0 repeating unit  neg   H2O, water clusters F         -3.00e-5     -1.67