adducts: Adduct list
In enviPat: Isotope Pattern, Profile and Centroid Calculation for Mass Spectrometry

adducts

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

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)

enviPat documentation built on Oct. 21, 2022, 5:06 p.m.