formula2mz calculates the m/z values from a list of molecular formulas and
adduct definitions.
Custom adduct definitions can be passed to the adduct parameter in form of
a data.frame. This data.frame is expected to have columns "mass_add"
and "mass_multi" defining the additive and multiplicative part of the
calculation. See adducts() for examples.
Arguments
- formula
characterwith one or more valid molecular formulas for which their adduct m/z shall be calculated.- adduct
either a
characterspecifying the name(s) of the adduct(s) for which the m/z should be calculated or adata.framewith the adduct definition. SeeadductNames()for supported adduct names and the description for more information on the expected format if adata.frameis provided.- standardize
logicalwhether to standardize the molecular formulas to the Hill notation system before calculating their mass.
Value
Numeric matrix with same number of rows than elements in formula
and number of columns being equal to the length of adduct (adduct names
are used as column names). Each column thus represents the m/z of formula
for each defined adduct.
Examples
## Calculate m/z values of adducts of a list of formulas
formulas <- c("C6H12O6", "C9H11NO3", "C16H13ClN2O")
ads <- c("[M+H]+", "[M+Na]+", "[2M+H]+", "[M]+")
formula2mz(formulas, ads)
#> [M+H]+ [M+Na]+ [2M+H]+ [M]+
#> C6H12O6 181.0707 203.0526 361.1341 180.0634
#> C9H11NO3 182.0812 204.0631 363.1551 181.0739
#> C16H13N2OCl 285.0789 307.0609 569.1506 284.0716
formula2mz(formulas, adductNames()) #All available adducts
#> [M+3H]3+ [M+2H+Na]3+ [M+H+Na2]3+ [M+Na3]3+ [M+2H]2+ [M+H+NH4]2+
#> C6H12O6 61.02841 68.35572 75.68303 83.01035 91.03897 99.55225
#> C9H11NO3 61.36524 68.69256 76.01987 83.34718 91.54422 100.05750
#> C16H13N2OCl 95.69782 103.02514 110.35245 117.67977 143.04310 151.55637
#> [M+H+K]2+ [M+H+Na]2+ [M+C2H3N+2H]2+ [M+2Na]2+ [M+C4H6N2+2H]2+
#> C6H12O6 110.0169 102.0299 111.5522 113.0209 132.0655
#> C9H11NO3 110.5222 102.5352 112.0575 113.5262 132.5708
#> C16H13N2OCl 162.0210 154.0341 163.5564 165.0250 184.0696
#> [M+C6H9N3+2H]2+ [M+H]+ [M+Li]+ [M+2Li-H]+ [M+NH4]+ [M+H2O+H]+
#> C6H12O6 152.5788 181.0707 187.0788 193.0870 198.0972 199.0812
#> C9H11NO3 153.0840 182.0812 188.0893 194.0975 199.1077 200.0917
#> C16H13N2OCl 204.5829 285.0789 291.0871 297.0953 302.1055 303.0895
#> [M+Na]+ [M+CH4O+H]+ [M+K]+ [M+C2H3N+H]+ [M+2Na-H]+ [M+C3H8O+H]+
#> C6H12O6 203.0526 213.0969 219.0265 222.0972 225.0346 241.1282
#> C9H11NO3 204.0631 214.1074 220.0371 223.1077 226.0451 242.1387
#> C16H13N2OCl 307.0609 317.1051 323.0348 326.1055 329.0428 345.1364
#> [M+C2H3N+Na]+ [M+2K-H]+ [M+C2H6OS+H]+ [M+C4H6N2+H]+ [2M+H]+
#> C6H12O6 244.0792 256.9824 259.0846 263.1238 361.1341
#> C9H11NO3 245.0897 257.9929 260.0951 264.1343 363.1551
#> C16H13N2OCl 348.0874 360.9907 363.0929 367.1320 569.1506
#> [2M+NH4]+ [2M+Na]+ [2M+K]+ [2M+C2H3N+H]+ [2M+C2H3N+Na]+ [3M+H]+
#> C6H12O6 378.1606 383.1160 399.0899 402.1606 424.1425 541.1974
#> C9H11NO3 380.1816 385.1370 401.1109 404.1816 426.1636 544.2290
#> C16H13N2OCl 586.1771 591.1325 607.1064 610.1771 632.1591 853.2222
#> [M+H-NH3]+ [M+H-H2O]+ [M+H-Hexose-H2O]+ [M+H-H4O2]+ [M+H-CH2O2]+
#> C6H12O6 164.0441 163.0601 19.01783 145.0495 135.0652
#> C9H11NO3 165.0546 164.0706 20.02834 146.0600 136.0757
#> C16H13N2OCl 268.0524 267.0684 123.02609 249.0578 239.0734
#> [M]+
#> C6H12O6 180.0634
#> C9H11NO3 181.0739
#> C16H13N2OCl 284.0716
## Use custom-defined adducts as input
custom_ads <- data.frame(mass_add = c(1, 2, 3), mass_multi = c(1, 2, 0.5))
formula2mz(formulas, custom_ads)
#> 1 2 3
#> C6H12O6 181.0634 362.1268 93.03169
#> C9H11NO3 182.0739 364.1478 93.53695
#> C16H13N2OCl 285.0716 570.1433 145.03582
## Use standardize = FALSE to keep formula unaltered
formula2mz("H12C6O6")
#> [M+H]+
#> C6H12O6 181.0707
formula2mz("H12C6O6", standardize = FALSE)
#> [M+H]+
#> H12C6O6 181.0707