calc_dbe: Calculate DBE and DBE-O Values
In EMSL-Computing/fticRanalysis: Analysis and visualization tools for FT-MS data

calc_dbe

R Documentation

Calculate DBE and DBE-O Values

Description

Calculate double bond equivalent (DBE) and double bond equivalent minus Oxygen (DBE-O) values for peaks where empirical formula is available

Usage

calc_dbe(ftmsObj, valences = NULL)

Arguments

`ftmsObj`	an object of class 'peakData' or 'compoundData', typically a result of `as.peakData` or `mapPeaksToCompounds`.
`valences`	a dataframe with columns giving the valence for each element. Names must be any of 'C', 'H', 'N', 'O', 'S', 'P'. Values must be integers corresponding to the valence for each element. Defaults to NULL, in which case the valences that result in the formula given in the details section are used.

Details

	If no valences are provided, DBE `= 1 + C - O - S - 0.5*(N + P + H)`
	If valences are provided DBE, `= 1 + \frac{\sum_{i}N_i(V_i-2)}{2}` where `N_i` and `V_i` are the number of atoms and corresponding valences.
	DBE-0 `= 1 + C - O - S - 0.5(N + P + H) - O`

Value

an object of the same class as ftmsObj with a column in e\_meta giving DBE, DBE-O, and DBE_AI values

Author(s)

Lisa Bramer, Allison Thompson

References

Koch, B. P., & Dittmar, T. (2006). From mass to structure: an aromaticity index for high‐resolution mass data of natural organic matter. Rapid communications in mass spectrometry, 20(5), 926-932.

Errata: Koch, B. P., & Dittmar, T. (2016). From mass to structure: an aromaticity index for high-resolution mass data of natural organic matter. Rapid communications in mass spectrometery, 30(1), 250. DOI: 10.1002/rcm.7433

EMSL-Computing/fticRanalysis documentation built on Dec. 18, 2024, 9:51 p.m.