isotopic_profile_molecular_formula_feeder {IDSL.SUFA}

Isotopic Profile Molecular Formula Feeder

Description

A function to calculate isotopic profiles from a molecular formulas

Usage

isotopic_profile_molecular_formula_feeder(molecular_formula, peak_spacing = 0,
intensity_cutoff = 1, IonPathway = "[M]", UFA_IP_memeory_variables = c(1e30, 1e-12, 100),
plotProfile = TRUE, allowedVerbose = TRUE)

Arguments

molecular_formula

A molecular formulas

peak_spacing

A maximum space between isotopologues in Da to merge neighboring isotopologues.

intensity_cutoff

A minimum intensity threshold for isotopic profiles in percentage.

IonPathway

An ionization pathway. Pathways should be like [Coeff*M+ADD1-DED1+...] where "Coeff" should be an integer between 1-9 and ADD1 and DED1 may be ionization pathways. ex: 'IonPathway <- c("[M]+", "[M+H]+", "[2M-Cl]-", "[3M+CO2-H2O+Na-KO2+HCl-NH4]-")'

UFA_IP_memeory_variables

A vector of three variables. Default values are c(1e30, 1e-12, 100) to manage memory usage. UFA_IP_memeory_variables[1] is used to control the overall size of isotopic combinations. UFA_IP_memeory_variables[2] indicates the minimum relative abundance (RA calculated by eq(1) in the reference [1]) of an isotopologue to include in the isotopic profile calculations. UFA_IP_memeory_variables[3] is the maximum elapsed time to calculate the isotopic profile on the 'setTimeLimit' function of base R.

plotProfile

c(TRUE, FALSE). A 'TRUE' plotProfile generates a spectra plot.

allowedVerbose

c(TRUE, FALSE). A 'TRUE' allowedVerbose provides messages about the flow of the function.

Value

A list of isotopic profiles

References

[1] Fakouri Baygi, S., Crimmins, B.S., Hopke, P.K. Holsen, T.M. (2016). Comprehensive emerging chemical discovery: novel polyfluorinated compounds in Lake Michigan trout. Environmental Science and Technology, 50(17), 9460-9468, doi:10.1021/acs.est.6b01349.

See Also

https://ipc.idsl.me/

Examples

molecular_formula <- "C12Cl10"
peak_spacing <- 0.005 # in Da for QToF instruments
# Use this piece of code for intensity cutoff to preserve significant isotopologues
intensity_cutoff <- 1
IonPathway <- "[M+H]+"
isotopic_profile <- isotopic_profile_molecular_formula_feeder(molecular_formula,
peak_spacing, intensity_cutoff, IonPathway)