R: Adduct list

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)

[Package enviPat version 2.4 Index]