R/compound_calcs.R
compound_calcs.RdCalculate a variety of typical values for FT-MS data associated with each peak/compound where empirical formula is available
compound_calcs(
ftmsObj,
calc_fns = c("calc_aroma", "calc_dbe", "calc_gibbs", "calc_kendrick", "calc_nosc",
"calc_element_ratios"),
calc_args = NULL
)an object of class 'peakData' or 'compoundData', typically a result of as.peakData or mapPeaksToCompounds.
a character string specifying which calculations to perform. Available options are: calc_aroma, calc_dbe, calc_gibbs, calc_kendrick, calc_nosc, and calc_vankrev.
a list with names corresponding to the available calc_fns. Each element is a named sub-list of extra arguments for the specified function. See examples for how to pass extra arguments.
an object of the same class as ftmsData with columns in e_meta giving the newly calculated values
The calculations are as follows for each of the `calc_fns`:
| calc_aroma | calculates aromaticity index (AI) and modified aromaticity index (AI_Mod) |
| AI \(= \frac{1 + C - O - S - 0.5(N + P + H)}{C - O - S - N - P}\) | |
| AI_Mod \(= \frac{1 + C - 0.5O - S - 0.5(N + P + H)}{C - 0.5*O - S - N - P}\) | |
| calc_dbe | calculates double bond equivalent (DBE) and double bond equivalent minux Oxygent (DBE_O) |
| DBE \(= 1 + C - O - S - 0.5*(N + P + H)\) | |
| DBE_0 \(= 1 + C - O - S - 0.5(N + P + H) - O\) | |
| calc_gibbs | calculates Cox Gibbs Free Energy (GFE) |
| GFE = \(= 60.3 - 28.5NOSC\) | |
| calc_kendrick | calculates Kendrick Mass and Kendrick Defect |
| Kendrick-mass = \((Observed-Mass)*(Nominal-Mass(base)/Exact-Mass(base))\) | |
| Kendrick-defect = ceiling(Kendrick-mass) - Kendrick-mass | |
| calc_nosc | calculates nominal oxidation state of Carbon (NOSC) |
| NOSC \(= -(\frac{4C + H - 3N - 2O + 5P - 2S}{C}) + 4\) | |
| calc_element_ratios | calculates O:C, H:C, P:C, N:C, and N:P ratios |
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
LaRowe and Van Cappellen, 2011, "Degradation of natural organic matter: A thermodynamic analysis". Geochimica et Cosmochimica Acta. 75.
Hughey, C. A., Hendrickson, C. L., Rodgers, R. P., Marshall, A. G., & Qian, K. (2001). Kendrick mass defect spectrum: a compact visual analysis for ultrahigh-resolution broadband mass spectra. Analytical Chemistry, 73(19), 4676-4681.
library(ftmsRanalysis)
# default arguments
peakdata_processed = compound_calcs(examplePeakData)
# only calculate aromaticity and kendrick mass/defect
peakdata_processed = compound_calcs(examplePeakData, calc_fns = c("calc_aroma", "calc_kendrick"))
# Specify extra arguments for calc_kendrick and calc_dbe.
calc_args = list('calc_kendrick' = list('base_compounds' = c('CH2', 'CO2', 'H2')),
'calc_dbe' = list('valences' = data.frame('C'=5, 'H' = 4, 'S' = 5)))
peakdata_processed <- compound_calcs(examplePeakData, calc_args = calc_args)