Fine isotopologue pattern for a molecular formula

Wraps enviPat::isopattern() to compute the exact fine isotopic structure of a neutral molecular formula: every isotopologue combination above threshold, its exact mass and its abundance relative to the monoisotopic (base) peak. Unlike a nominal-mass isotope pattern (M, M+1, M+2, ...), this resolves the individual contributors within a nominal level – e.g. the M+2 satellite of a sulfur-containing compound is really a 34S isotopologue and a (13C, 13C) isotopologue sitting at two different exact masses, and this function tells them apart.

Usage

isotope_fine_pattern(formula, threshold = 0.01, charge = 0)

Arguments

formula

a molecular formula string, e.g. "C5H11NO2S".

threshold

minimum abundance to keep, in percent of the base peak.

charge

charge state passed to enviPat::isopattern(). This only applies the electron-mass correction for an intrinsically charged species (e.g. a metal ion); it does NOT add a proton or any other adduct. To simulate an ion such as [M+H]+, leave charge = 0 (the default, i.e. the neutral formula's own pattern) and add the adduct's mass difference to mz afterwards, e.g. pattern$mz + 1.007276 for protonation – the same massdiff convention used by MZ_CAMERA.

Value

A tibble with columns mz, abundance (percent of the base peak, 100 = tallest) and label, a human-readable isotope label built from the isotope composition of that isotopologue (e.g. "34S", "13C, 13C"; "" for the monoisotopic peak).

Author

Jan Stanstrup, stanstrup@gmail.com

Examples

# \donttest{
pat <- isotope_fine_pattern("C5H11NO2S")
pat[order(-pat$abundance), ]
#> # A tibble: 16 × 3
#>       mz abundance label     
#>    <dbl>     <dbl> <chr>     
#>  1  149.  100      ""        
#>  2  150.    5.41   "13C"     
#>  3  151.    4.47   "34S"     
#>  4  150.    0.790  "33S"     
#>  5  151.    0.411  "18O"     
#>  6  150.    0.365  "15N"     
#>  7  152.    0.242  "13C, 34S"
#>  8  150.    0.127  "2H"      
#>  9  151.    0.117  "13C, 13C"
#> 10  150.    0.0762 "17O"     
#> 11  151.    0.0427 "13C, 33S"
#> 12  152.    0.0222 "13C, 18O"
#> 13  151.    0.0198 "13C, 15N"
#> 14  153.    0.0184 "18O, 34S"
#> 15  152.    0.0163 "15N, 34S"
#> 16  153.    0.0105 "36S"     
# }