adducts {enviPat} | R Documentation |
Adduct list
Description
List of common adducts observed for ESI-MS measurements in soft positive and negative ionization modes.
Usage
data(adducts)
Format
A data frame with 47 observations on the following 6 variables.
Name
Adduct name
calc
Equation for calculating adduct m/z from uncharged non-adduct molecular mass M (m/z = M/z + X)
Charge
z
Mult
1/z
Mass
X
Ion_mode
Ionization mode (positive or negative)
Formula_add
Adduct chemical formula to be added
Formula_ded
Adduct chemical formula to be subtracted
Multi
Factor to multiply chemical formula with
Details
The correct way to calculate the isotopic pattern of a specific adduct is the following.
First, multiply the chemical formula of the molecule by the times it appears in the final adduct; multiform
.
Second, add the chemical formula of any adduct to that of the molecule; mergeform
.
Third, subtract the chemical formula of any deduct from that of the molecule; check_ded
& subform
.
Finally, calculate the isotopic fine structure using the correct charge
argument in isopattern
.
Note
Chemical formulas must conform to what is described in check_chemform
.
Source
https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator/
References
Huang N., Siegel M.M., Kruppa G.H., Laukien F.H., J. Am. Soc. Mass. Spectrom. 1999, 10. Automation of a Fourier transform ion cyclotron resonance mass spectrometer for acquisition, analysis, and e-mailing of high-resolution exact-mass electrospray ionization mass spectral data
See Also
multiform
mergeform
check_ded
subform
Examples
# example of M+H adduct batch calculation
data(adducts)
data(isotopes)
data(chemforms)
# (1) check formulas for consistency - recommended
checked_chemforms <- check_chemform(isotopes, chemforms)
# (2) multiply, see column 4 of adducts
chemforms <-multiform(checked_chemforms[,2],1)
# (3) add adduct - see column 7 of adducts
chemforms<-mergeform(chemforms,"H1")
# (4) calculate fine structure
patterns <- isopattern(isotopes, chemforms)